Editorial

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5 pages, 228 KiB

Open AccessEditorial

Special Issue “Emerging Viruses: Surveillance, Prevention, Evolution, and Control”

by Jônatas Santos Abrahão and Luciana Barros de Arruda

Viruses 2020, 12(3), 306; https://0-doi-org.brum.beds.ac.uk/10.3390/v12030306 - 11 Mar 2020

Cited by 4 | Viewed by 2180

Abstract

Emerging viruses represent a major concern for public health offices [...] Full article

(This article belongs to the Special Issue Emerging Viruses: Surveillance, Prevention, Evolution and Control)

Research

Jump to: Editorial, Review, Other

15 pages, 1041 KiB

Open AccessArticle

High Genomic Variability in Equine Infectious Anemia Virus Obtained from Naturally Infected Horses in Pantanal, Brazil: An Endemic Region Case

by Camila Dantas Malossi, Eduardo Gorzoni Fioratti, Jedson Ferreira Cardoso, Angelo Jose Magro, Erna Geessien Kroon, Daniel Moura de Aguiar, Alice Mamede Costa Marque Borges, Marcia Furlan Nogueira, Leila Sabrina Ullmann and João Pessoa Araujo, Jr.

Viruses 2020, 12(2), 207; https://0-doi-org.brum.beds.ac.uk/10.3390/v12020207 - 12 Feb 2020

Cited by 7 | Viewed by 3048

Abstract

Equine infectious anemia virus (EIAV) is a persistent lentivirus that causes equine infectious anemia (EIA). In Brazil, EIAV is endemic in the Pantanal region, and euthanasia is not mandatory in this area. All of the complete genomic sequences from field viruses are from [...] Read more.

Equine infectious anemia virus (EIAV) is a persistent lentivirus that causes equine infectious anemia (EIA). In Brazil, EIAV is endemic in the Pantanal region, and euthanasia is not mandatory in this area. All of the complete genomic sequences from field viruses are from North America, Asia, and Europe, and only proviral genomic sequences are available. Sequences from Brazilian EIAV are currently available only for gag and LTR regions. Thus, the present study aimed for the first time to sequence the entire EIAV genomic RNA in naturally infected horses from an endemic area in Brazil. RNA in plasma from naturally infected horses was used for next-generation sequencing (NGS), and gaps were filled using Sanger sequencing methodology. Complete viral genomes of EIAV from two horses were obtained and annotated (Access Number: MN560970 and MN560971). Putative genes were analyzed and compared with previously described genes, showing conservation in gag and pol genes and high variations in LTR and env sequences. Amino acid changes were identified in the p26 protein, one of the most common targets used for diagnosis, and p26 molecular modelling showed surface amino acid alterations in some epitopes. Brazilian genome sequences presented 88.6% nucleotide identity with one another and 75.8 to 77.3% with main field strains, such as EIAV Liaoning, Wyoming, Ireland, and Italy isolates. Furthermore, phylogenetic analysis suggested that this Brazilian strain comprises a separate monophyletic group. These results may help to better characterize EIAV and to overcome the challenges of diagnosing and controlling EIA in endemic regions. Full article

(This article belongs to the Special Issue Emerging Viruses: Surveillance, Prevention, Evolution and Control)

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11 pages, 951 KiB

Open AccessArticle

Changes in the Transmission Dynamic of Chikungunya Virus in Southeastern Senegal

by Abdourahmane Sow, Birgit Nikolay, Oumar Faye, Simon Cauchemez, Jorge Cano, Mawlouth Diallo, Ousmane Faye, Bakary Sadio, Oumar Ndiaye, Scott C. Weaver, Anta T. Dia, Amadou Alpha Sall and Denis Malvy

Viruses 2020, 12(2), 196; https://0-doi-org.brum.beds.ac.uk/10.3390/v12020196 - 10 Feb 2020

Cited by 6 | Viewed by 2966

Abstract

In Senegal, chikungunya virus (CHIKV) is maintained in a sylvatic cycle and causes sporadic cases or small outbreaks in rural areas. However, little is known about the influence of the environment on its transmission. To address the question, 120 villages were randomly selected [...] Read more.

In Senegal, chikungunya virus (CHIKV) is maintained in a sylvatic cycle and causes sporadic cases or small outbreaks in rural areas. However, little is known about the influence of the environment on its transmission. To address the question, 120 villages were randomly selected in the Kedougou region of southeastern Senegal. In each selected village, 10 persons by randomly selected household were sampled and tested for specific anti-CHIKV IgG antibodies by ELISA. We investigated the association of CHIKV seroprevalence with environmental variables using logistic regression analysis and the spatial correlation of village seroprevalence based on semivariogram analysis. Fifty-four percent (51%–57%) of individuals sampled during the survey tested positive for CHIKV-specific IgG. CHIKV seroprevalence was significantly higher in populations living close to forested areas (Normalized Difference Vegetation Index (NDVI), Odds Ratio (OR) = 1.90 (1.42–2.57)), and was negatively associated with population density (OR = 0.76 (0.69–0.84)). In contrast, in gold mining sites where population density was >400 people per km², seroprevalence peaked significantly among adults (46% (27%–67%)) compared to all other individuals (20% (12%–31%)). However, traditional gold mining activities significantly modify the transmission dynamic of CHIKV, leading to a potential increase of the risk of human exposition in the region. Full article

(This article belongs to the Special Issue Emerging Viruses: Surveillance, Prevention, Evolution and Control)

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8 pages, 242 KiB

Open AccessArticle

Evaluation of the LIAISON XL Zika Capture IgM II for the Diagnosis of Zika Virus Infections

by Mayte Pérez-Olmeda, María Paz Sánchez-Seco, Ana Vázquez, Pilar Balfagón, Jesús de la Fuente, María Ángeles Murillo, Teodora Minguito and Fernando de Ory

Viruses 2020, 12(1), 69; https://0-doi-org.brum.beds.ac.uk/10.3390/v12010069 - 07 Jan 2020

Cited by 4 | Viewed by 2274

Abstract

The aim of this study is to evaluate the performance characteristics of the LIAISON XL Zika Capture IgM II. For this purpose we tested 128 samples obtained from recent infections caused by the Zika (ZIKV; 74 samples), dengue (DENV; 10 samples), chikungunya (CHIK [...] Read more.

The aim of this study is to evaluate the performance characteristics of the LIAISON XL Zika Capture IgM II. For this purpose we tested 128 samples obtained from recent infections caused by the Zika (ZIKV; 74 samples), dengue (DENV; 10 samples), chikungunya (CHIK V; 11 samples), rubella (RUBV; 10 samples) and measles (MeV; 10 samples) viruses, as well as human parvovirus B19 (HPVB19; 13 samples). The results of the assay under evaluation are compared with those obtained from an indirect immunofluorescence (IIF) assay, and the discrepancies are resolved by considering other laboratory results (PCR and a plaque-reduction neutralization test). The LIAISON showed excellent sensitivity (100%). The specificity (91.25%) was hampered by some false-positive results in recent dengue virus, chikungunya virus, measles virus and human parvovirus B19 infections. The method evaluated is adequate, but the low specificity makes it necessary to consider the clinical and epidemiological contexts of patients, as well as other laboratory results. Full article

(This article belongs to the Special Issue Emerging Viruses: Surveillance, Prevention, Evolution and Control)

14 pages, 3721 KiB

Open AccessArticle

Identification, Genetic Analysis, and Pathogenicity of Classical Swine H1N1 and Human-Swine Reassortant H1N1 Influenza Viruses from Pigs in China

by Yafen Song, Yong Zhang, Bing Zhang, Ling Chen, Min Zhang, Jingwen Wang, Ying Jiang, Chenghuai Yang and Taozhen Jiang

Viruses 2020, 12(1), 55; https://0-doi-org.brum.beds.ac.uk/10.3390/v12010055 - 02 Jan 2020

Cited by 5 | Viewed by 3511

Abstract

Swine influenza virus causes a substantial disease burden to swine populations worldwide and poses an imminent threat to the swine industry and humans. Given its importance, we characterized two swine influenza viruses isolated from Shandong, China. The homology and phylogenetic analyses showed that [...] Read more.

Swine influenza virus causes a substantial disease burden to swine populations worldwide and poses an imminent threat to the swine industry and humans. Given its importance, we characterized two swine influenza viruses isolated from Shandong, China. The homology and phylogenetic analyses showed that all eight gene segments of A/swine/Shandong/AV1522/2011(H1N1) were closely related to A/Maryland/12/1991(H1N1) circulating in North America. The HA, NA, M, and NS genes of the isolate were also confirmed to have a high homology to A/swine/Hubei/02/2008(H1N1) which appeared in China in 2008, and the virus was clustered into the classical swine lineage. The gene segments of A/swine/Shandong/AV1523/2011(H1N1) were highly homologous to the early human H1N1 and H2N2 influenza viruses, except for the HA gene, and the virus was a reassortant H1N1 virus containing genes from the classical swine (HA) and human (NA, PB2, PB1, PA, NP, M, and NS) lineages. Both the viruses could cause lethal infection and replicate efficiently in the lungs, brains, spleens, and kidneys of mice. Histopathological examinations showed that AV1522 and AV1523 viruses caused a spectrum of marked pneumonia and meningoencephalitis according to the duration of infection, demonstrating a progression of respiratory disease and neurological disease over the course of infection that ultimately resulted in lethality for the infected mice. The changes in the pathogenicity of swine influenza viruses to mammals, accompanied with the continuous reassortment and evolution of the viruses, highlights the importance of ongoing epidemiological investigation. Full article

(This article belongs to the Special Issue Emerging Viruses: Surveillance, Prevention, Evolution and Control)

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10 pages, 1914 KiB

Open AccessArticle

TREX1 531C>T Polymorphism is Associated with High Proviral Load Levels in HTLV-1-Infected Persons

by Denis de Castro Silva, Ednelza da Silva Graça Amoras, Tuane Carolina Ferreira Moura, Felipe Teixeira Lopes, Samara Tatielle Monteiro Gomes, Carlos A. da Costa, Maísa Silva Sousa, Ricardo Ishak, Antonio Carlos Rosário Vallinoto and Maria Alice Freitas Queiroz

Viruses 2020, 12(1), 7; https://0-doi-org.brum.beds.ac.uk/10.3390/v12010007 - 19 Dec 2019

Cited by 11 | Viewed by 2703

Abstract

Human T-lymphotropic virus type 1 (HTLV-1) deregulates the immune system and cell cycle, resulting in loss of immune tolerance and disease, including HTLV-1-associated myelopathy/tropical spastic paraparesis (HAM/TSP). Three prime repair exonuclease 1 (TREX1) maintains innate immune tolerance of the host and host-cell permissiveness [...] Read more.

Human T-lymphotropic virus type 1 (HTLV-1) deregulates the immune system and cell cycle, resulting in loss of immune tolerance and disease, including HTLV-1-associated myelopathy/tropical spastic paraparesis (HAM/TSP). Three prime repair exonuclease 1 (TREX1) maintains innate immune tolerance of the host and host-cell permissiveness to retroviral infections. TREX1 polymorphisms may influence the course of infection and autoimmune manifestations. The influence of TREX1 531C/T polymorphism was investigated in HTLV-1 infection and development of symptoms among 151 persons infected with HTLV-1 (32 HAM/TSP, 19 rheumatologic manifestations, two dermatitis, five more than one diagnosis, two probable HAM/TSP, and 91 asymptomatic individuals) and 100 uninfected persons in the control group. Polymorphism genotyping and proviral load quantification were performed by real-time polymerase chain reaction (PCR) and antinuclear antibodies (ANAs) were screened by an indirect immunofluorescence assay. No statistically significant difference was found in polymorphism genotype and allele frequencies between the infected and control groups. HAM/TSP patients showed higher frequency of TT genotype than asymptomatic persons (p = 0.0339). Proviral load was significantly higher among individuals with CT/TT genotypes and CC genotype carriers had lower proviral load and higher levels of proinflammatory cytokines. ANAs were present only in the HAM/TSP group. TREX1 531C>T polymorphism seems to be associated with TREX-1 regulation and HTLV-1 infection. Full article

(This article belongs to the Special Issue Emerging Viruses: Surveillance, Prevention, Evolution and Control)

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23 pages, 6393 KiB

Open AccessArticle

Genetic Characteristics and Pathogenicity Analysis in Chickens and Mice of Three H9N2 Avian Influenza Viruses

by Yafen Song, Yong Zhang, Ling Chen, Bing Zhang, Min Zhang, Jingwen Wang, Ying Jiang, Chenghuai Yang and Taozhen Jiang

Viruses 2019, 11(12), 1127; https://0-doi-org.brum.beds.ac.uk/10.3390/v11121127 - 06 Dec 2019

Cited by 13 | Viewed by 3227

Abstract

H9N2 avian influenza is a remarkable disease that has circulated in domestic poultry in large regions of China and posed a serious threat to the poultry industry. The H9N2 virus can not only infect mammals directly, but also provide gene segments to generate [...] Read more.

H9N2 avian influenza is a remarkable disease that has circulated in domestic poultry in large regions of China and posed a serious threat to the poultry industry. The H9N2 virus can not only infect mammals directly, but also provide gene segments to generate novel, but lethal human reassortants. Therefore, it is important to study the evolution, pathogenicity, and transmission of the H9N2 virus. In this study, three H9N2 viruses isolated from chickens in different layer farms were identified. Phylogenetic analysis revealed that these H9N2 viruses were all multiple genotype reassortants, with genes originating from Y280-like, F/98-like, and G1-like viruses. Animal studies indicated that the AV1535 and AV1548 viruses replicated efficiently in the lungs, tracheas, spleens, kidneys, and brains of chickens; the viruses shed for at least 11 days post-inoculation (DPI) and were transmitted efficiently among contact chickens. The AV1534 virus replicated poorly in chickens, shed for 7 DPI, and were not transmitted efficiently among contact chickens. The AV1534 virus replicated well in mice lungs and caused about 2% weight loss. The AV1535 and AV1548 viruses were not able to replicate in the lungs of mice. Our results indicate that we should pay attention to H9N2 avian influenza virus surveillance in poultry and changes in the pathogenicity of them to mammals. Full article

(This article belongs to the Special Issue Emerging Viruses: Surveillance, Prevention, Evolution and Control)

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18 pages, 1533 KiB

Open AccessArticle

Natural Infection of Aedes aegypti by Chikungunya and Dengue type 2 Virus in a Transition Area of North-Northeast Brazil

by Carine Fortes Aragão, Valéria Cristina Soares Pinheiro, Joaquim Pinto Nunes Neto, Eliana Vieira Pinto da Silva, Glennda Juscely Galvão Pereira, Bruna Laís Sena do Nascimento, Karoline da Silva Castro, Ariadne Mendonça Maia, Clistenes Pamplona Catete, Lívia Carício Martins, Wanderli Pedro Tadei, Sandro Patroca da Silva and Ana Cecília Ribeiro Cruz

Viruses 2019, 11(12), 1126; https://0-doi-org.brum.beds.ac.uk/10.3390/v11121126 - 05 Dec 2019

Cited by 11 | Viewed by 4033

Abstract

Dengue fever, chikungunya, and Zika are diseases caused by viruses transmitted by Aedes aegypti and Aedes albopictus. In Brazil, the number of human infections is high, but few studies are performed in mosquito vectors. This study aimed to investigate the presence of [...] Read more.

Dengue fever, chikungunya, and Zika are diseases caused by viruses transmitted by Aedes aegypti and Aedes albopictus. In Brazil, the number of human infections is high, but few studies are performed in mosquito vectors. This study aimed to investigate the presence of Zika, Dengue and Chikungunya viruses in Ae. aegypti and Ae. albopictus from the municipalities of Alto Alegre, Caxias, Codó, and São Mateus do Maranhão, located in the state of Maranhão, Northeast Brazil. The mosquitoes were collected with a mechanical aspirator, identified, triturated, and then submitted to RNA extraction and RT-qPCR. The positive samples were confirmed by virus isolation and genome sequencing. Three hundred and forty-eight Ae. aegypti (176 males and 172 females) and 12 Ae. albopictus (eight males and four females) were collected and tested. Ae. aegypti was the only vector positive in two municipalities—Codó, with detection of Chikungunya virus (CHIKV) belonging to the East-Central-South African genotype, and in Caxias, with detection of Dengue virus (DENV)-2 belonging to the Asian/American genotype. The detection of CHIKV and DENV-2 is evidence that those viruses are maintained in arthropod vectors, and shows the epidemiological risk in the area for chikungunya cases and a possible increase of severe dengue cases, associated with the occurrence of dengue hemorrhagic fever. Full article

(This article belongs to the Special Issue Emerging Viruses: Surveillance, Prevention, Evolution and Control)

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16 pages, 4103 KiB

Open AccessArticle

Identification of B-Cell Epitopes with Potential to Serologicaly Discrimnate Dengue from Zika Infections

by Alice F. Versiani, Raissa Prado Rocha, Tiago A. O. Mendes, Glauco C. Pereira, Jordana Graziella A. Coelho dos Reis, Daniella C. Bartholomeu and Flávio G. da Fonseca

Viruses 2019, 11(11), 1079; https://0-doi-org.brum.beds.ac.uk/10.3390/v11111079 - 19 Nov 2019

Cited by 7 | Viewed by 3531

Abstract

Dengue is currently one of the most important arbovirus infections worldwide. Early diagnosis is important for disease outcome, particularly for those afflicted with the severe forms of infection. The goal of this work was to identify conserved and polymorphic linear B-cell Dengue virus [...] Read more.

Dengue is currently one of the most important arbovirus infections worldwide. Early diagnosis is important for disease outcome, particularly for those afflicted with the severe forms of infection. The goal of this work was to identify conserved and polymorphic linear B-cell Dengue virus (DENV) epitopes that could be used for diagnostic purposes. To this end, we aligned the predicted viral proteome of the four DENV serotype and performed in silico B-cell epitope mapping. We developed a script in Perl integrating alignment and prediction information to identify potential serotype-specific epitopes. We excluded epitopes that were similarly present in the yellow fever and zika viruses’ proteomes. A total of 15 polymorphic and nine conserved peptides among DENV serotypes were selected. Peptides were spotted on cellulose membranes and tested against sera from rabbits that were monoinfected with each DENV serotype. Although serotype-specific peptides failed to recognize any sera, three conserved peptides were recognized by all anti-dengue sera and were included on an ELISA test employing a well-characterized human sera bank. Of the three peptides, one was able to efficiently identify sera from all four DENV serotypes and to discriminate them from Zika virus positive sera. Full article

(This article belongs to the Special Issue Emerging Viruses: Surveillance, Prevention, Evolution and Control)

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20 pages, 3470 KiB

Open AccessArticle

Phylogeny, Pathogenicity, Transmission, and Host Immune Responses of Four H5N6 Avian Influenza Viruses in Chickens and Mice

by Yafen Song, Weiqiang Li, Wenbo Wu, Zhiting Liu, Zhuoliang He, Zuxian Chen, Bingbing Zhao, Siyu Wu, Chenghuai Yang, Xiaoyun Qu, Ming Liao and Peirong Jiao

Viruses 2019, 11(11), 1048; https://0-doi-org.brum.beds.ac.uk/10.3390/v11111048 - 10 Nov 2019

Cited by 7 | Viewed by 3497

Abstract

H5Nx viruses have continuously emerged in the world, causing poultry industry losses and posing a potential public health risk. Here, we studied the phylogeny, pathogenicity, transmission, and immune response of four H5N6 avian influenza viruses in chickens and mice, which were isolated from [...] Read more.

H5Nx viruses have continuously emerged in the world, causing poultry industry losses and posing a potential public health risk. Here, we studied the phylogeny, pathogenicity, transmission, and immune response of four H5N6 avian influenza viruses in chickens and mice, which were isolated from waterfowl between 2013 and 2014. Their HA genes belong to Clade 2.3.4.4, circulated in China since 2008. Their NA genes fall into N6-like/Eurasian sublineage. Their internal genes originated from different H5N1 viruses. The results suggested that the four H5N6 viruses were reassortants of the H5N1 and H6N6 viruses. They cause lethal infection with high transmission capability in chickens. They also cause mild to severe pathogenicity in mice and can spread to the brain through the blood–brain barrier. During the infection, the viruses result in the up-regulation of PRRs and cytokine in brains and lungs of chickens and mice. Our results suggested that the high viral loads of several organs may result in disease severity in chickens and mice; there were varying levels of cytokines induced by the H5N6 viruses with different pathogenicity in chickens and mice. Full article

(This article belongs to the Special Issue Emerging Viruses: Surveillance, Prevention, Evolution and Control)

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9 pages, 517 KiB

Open AccessArticle

Comparative Pathogenicity and Transmissibility of the H7N9 Highly Pathogenic Avian Influenza Virus and the H7N9 Low Pathogenic Avian Influenza Virus in Chickens

by Hao Yu, Kunpeng Zhang, Xumeng Ye, Wenqing Wang, Wenbo Wu, Xia Wang, Yun Guan, Zhuoliang He, Yong Wang and Peirong Jiao

Viruses 2019, 11(11), 1047; https://0-doi-org.brum.beds.ac.uk/10.3390/v11111047 - 10 Nov 2019

Cited by 7 | Viewed by 3478

Abstract

There were five outbreaks of H7N9 influenza virus in humans in China since it emerged in 2013, infecting >1000 people. The H7N9 low pathogenic influenza virus was inserted into four amino acids in the HA protein cleavage site to mutate into the H7N9 [...] Read more.

There were five outbreaks of H7N9 influenza virus in humans in China since it emerged in 2013, infecting >1000 people. The H7N9 low pathogenic influenza virus was inserted into four amino acids in the HA protein cleavage site to mutate into the H7N9 highly pathogenic virus. This emerging virus caused 15 outbreaks in chickens from the end of 2016 to date. Two H7N9 avian influenza virus (AIV) strains, A/chicken/Guangdong/A46/2013 (LPAIV) and A/chicken/Guangdong/Q29/2017 (HPAIV), were selected to compare the pathogenicity and transmissibility between H7N9 LPAIVs and HPAIVs in chickens. We inoculated 3- to 4-week-old specific-pathogen-free (SPF) chickens with 6 log₁₀EID₅₀/0.1 mL viruses via the ocular-nasal route and co-housed four chickens in each group. The inoculated chicken mortality rate in the A46 and Q29 groups was 1/5 and 5/5, respectively. Q29 virus replication was more efficient compared to the A46 virus in inoculated chickens. Infected chickens initiated viral shedding to naïve contact chickens through respiratory and digestive routes. Both viruses transmitted between chickens by naïve contact, but the Q29 virus had a higher pathogenicity in contact chickens than the A46 virus. Compared with early H7N9 LPAIVs, the pathogenicity and transmissibility of the emerging H7N9 HPAIV was stronger in chickens, indicating that H7N9 influenza virus may continue to threaten human and poultry health. Full article

(This article belongs to the Special Issue Emerging Viruses: Surveillance, Prevention, Evolution and Control)

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12 pages, 1332 KiB

Open AccessArticle

Molecular Characterization of a Novel Avian Influenza A (H2N9) Strain Isolated from Wild Duck in Korea in 2018

by Seon-Ju Yeo, Duc-Duong Than, Hong-Seog Park, Haan Woo Sung and Hyun Park

Viruses 2019, 11(11), 1046; https://0-doi-org.brum.beds.ac.uk/10.3390/v11111046 - 10 Nov 2019

Cited by 11 | Viewed by 4443

Abstract

A novel avian influenza virus (A/wild duck/Korea/K102/2018) (H2N9) was isolated from wild birds in South Korea in 2018, and phylogenetic and molecular analyses were conducted on complete gene sequences obtained by next-generation sequencing. Phylogenetic analysis indicated that the hemagglutinin (HA) and neuraminidase (NA) [...] Read more.

A novel avian influenza virus (A/wild duck/Korea/K102/2018) (H2N9) was isolated from wild birds in South Korea in 2018, and phylogenetic and molecular analyses were conducted on complete gene sequences obtained by next-generation sequencing. Phylogenetic analysis indicated that the hemagglutinin (HA) and neuraminidase (NA) genes of the A/wild duck/Korea/K102/2018 (H2N9) virus belonged to the Eurasian countries, whereas other internal genes (polymerase basic protein 1 (PB1), PB2, nucleoprotein (NP), polymerase acidic protein (PA), matrix protein (M), and non-structural protein (NS)) belonged to the East Asian countries. A monobasic amino acid (PQIEPR/GLF) at the HA cleavage site, E627 in the PB2 gene, and no deletion of the stalk region in the NA gene indicated that the A/wild duck/Korea/K102/2018 (H2N9) isolate was a typical low pathogenicity avian influenza (LPAI). Nucleotide sequence similarity analysis of HA revealed that the highest homology (98.34%) is to that of A/duck/Mongolia/482/2015 (H2N3), and amino acid sequence of NA was closely related to that of A/duck/Bangladesh/8987/2010 (H10N9) (96.45%). In contrast, internal genes showed homology higher than 98% compared to those of other isolates derived from duck and wild birds of China or Japan in 2016–2018. The newly isolated A/wild duck/Korea/K102/2018 (H2N9) strain is the first reported avian influenza virus in Korea, and may have evolved from multiple genotypes in wild birds and ducks in Mongolia, China, and Japan. Full article

(This article belongs to the Special Issue Emerging Viruses: Surveillance, Prevention, Evolution and Control)

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24 pages, 9142 KiB

Open AccessArticle

Genetic, Molecular, and Pathogenic Characterization of the H9N2 Avian Influenza Viruses Currently Circulating in South China

by Hailiang Sun, Jiate Lin, Zhiting Liu, Yanan Yu, Meihua Wu, Shuo Li, Yang Liu, Yaling Feng, Yuqian Wu, Mingliang Li, Peirong Jiao, Kaijian Luo and Ming Liao

Viruses 2019, 11(11), 1040; https://0-doi-org.brum.beds.ac.uk/10.3390/v11111040 - 08 Nov 2019

Cited by 9 | Viewed by 4077

Abstract

The prevalence and variation of the H9N2 avian influenza virus (AIV) pose a threat to public health. A total of eight viruses isolated from farmed poultry in South China during 2017–2018 were selected as representative strains for further systematic study. Phylogenetic analyses indicated [...] Read more.

The prevalence and variation of the H9N2 avian influenza virus (AIV) pose a threat to public health. A total of eight viruses isolated from farmed poultry in South China during 2017–2018 were selected as representative strains for further systematic study. Phylogenetic analyses indicated that these prevalent viruses belong to the Y280-like lineage and that the internal genes are highly similar to those of recently circulating human H7N9 viruses. The receptor-binding assay showed that most of the H9N2 isolates preferentially bound to the human-like receptor, increasing the risk of them crossing the species barrier and causing human infection. Our in vitro, multi-step growth curve results indicate these viruses can effectively replicate in mammalian cells. Infection in mice showed that three viruses effectively replicated in the lung of mice. Infection in swine revealed that the viruses readily replicated in the upper respiratory tract of pig and effectively induced viral shedding. Our findings suggested that the H9N2 AIVs circulating in poultry recently acquired an enhanced ability to transmit from avian to mammalians, including humans. Based on our findings, we propose that it is essential to strengthen the efforts to surveil and test the pathogenicity of H9N2 AIVs. Full article

(This article belongs to the Special Issue Emerging Viruses: Surveillance, Prevention, Evolution and Control)

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10 pages, 1910 KiB

Open AccessArticle

Silent Circulation of the Saint Louis Encephalitis Virus among Humans and Equids, Southeast Brazil

by Galileu Barbosa Costa, Paula Eillany Silva Marinho, Ana Paula Pessoa Vilela, Ana Teresa Saraiva-Silva, Ana Paula Correia Crispim, Iara Apolinário Borges, Ana Gabriella Stoffella Dutra, Zélia Inês Portela Lobato, Jenner Karlison Pimenta dos Reis, Danilo Bretas de Oliveira, Betania Paiva Drumond, Erna Geessien Kroon and Giliane de Souza Trindade

Viruses 2019, 11(11), 1029; https://0-doi-org.brum.beds.ac.uk/10.3390/v11111029 - 05 Nov 2019

Cited by 9 | Viewed by 2769

Abstract

Saint Louis encephalitis virus (SLEV) is a mosquito-borne flavivirus that occurs throughout the Americas, and is considered a public health threat. In Brazil, SLEV has been detected from human cases associated with dengue-like disease, but no neurological symptoms were reported. Furthermore, the epidemiology [...] Read more.

Saint Louis encephalitis virus (SLEV) is a mosquito-borne flavivirus that occurs throughout the Americas, and is considered a public health threat. In Brazil, SLEV has been detected from human cases associated with dengue-like disease, but no neurological symptoms were reported. Furthermore, the epidemiology of SLEV in human populations is still poorly explored in the country. We reported serological and molecular detection of SLEV in a healthy population of equids and humans from rural areas in Southeast Brazil. A plaque reduction neutralization test was applied, and neutralizing antibodies were detected in 11 individuals (4.6%) and 60 horses (21.5%). A qPCR targeting the 5′UTR region and reverse transcription-PCR (RT-PCR) targeting the non-structural protein (NS5) gene were performed and three individuals tested positive in both assays. Subsequent phylogenetic analysis confirmed SLEV circulation and its findings suggest the occurrence of an asymptomatic or subclinical presence in human and animal cases, correlating with the risks for outbreaks and consequently burden of SLEV infections to public health. Preventive strategies should include improved surveillance in regions with a high probability of SLEV occurrence, improvement in diagnostic methods, and evaluation of exposure/risk factors that can favor SLEV emergence. Full article

(This article belongs to the Special Issue Emerging Viruses: Surveillance, Prevention, Evolution and Control)

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14 pages, 4186 KiB

Open AccessArticle

Emergence of Rare Bovine–Human Reassortant DS-1-Like Rotavirus A Strains with G8P[8] Genotype in Human Patients in the Czech Republic

by Romana Moutelíková, Pavel Sauer, Monika Dvořáková Heroldová, Veronika Holá and Jana Prodělalová

Viruses 2019, 11(11), 1015; https://0-doi-org.brum.beds.ac.uk/10.3390/v11111015 - 01 Nov 2019

Cited by 17 | Viewed by 3422

Abstract

Group A Rotaviruses (RVA) are the leading cause of acute gastroenteritis in children and a major cause of childhood mortality in low-income countries. RVAs are mostly host-specific, but interspecies transmission and reassortment between human and animal RVAs significantly contribute to their genetic diversity. [...] Read more.

Group A Rotaviruses (RVA) are the leading cause of acute gastroenteritis in children and a major cause of childhood mortality in low-income countries. RVAs are mostly host-specific, but interspecies transmission and reassortment between human and animal RVAs significantly contribute to their genetic diversity. We investigated the VP7 and VP4 genotypes of RVA isolated from 225 stool specimens collected from Czech patients with gastroenteritis during 2016–2019. The most abundant genotypes were G1P[8] (42.7%), G3P[8] (11.1%), G9P[8] (9.8%), G2P[4] (4.4%), G4P[8] (1.3%), G12P[8] (1.3%), and, surprisingly, G8P[8] (9.3%). Sequence analysis of G8P[8] strains revealed the highest nucleotide similarity of all Czech G8 sequences to the G8P[8] rotavirus strains that were isolated in Vietnam in 2014/2015. The whole-genome backbone of the Czech G8 strains was determined with the use of next-generation sequencing as DS-1-like. Phylogenetic analysis of all segments clustered the Czech isolates with RVA strains that were formerly described in Southeast Asia, which had emerged following genetic reassortment between bovine and human RVAs. This is the first time that bovine–human DS-1-like G8P[8] strains were detected at a high rate in human patients in Central Europe. Whether the emergence of this unusual genotype reflects the establishment of a new RVA strain in the population requires the continuous monitoring of rotavirus epidemiology. Full article

(This article belongs to the Special Issue Emerging Viruses: Surveillance, Prevention, Evolution and Control)

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12 pages, 2308 KiB

Open AccessArticle

The First Complete Genome Sequences of Hepatitis C Virus Subtype 2b from Latin America: Molecular Characterization and Phylogeographic Analysis

by Natália Spitz, José J. Barros, Kycia M. do Ó, Carlos E. Brandão-Mello and Natalia M. Araujo

Viruses 2019, 11(11), 1000; https://0-doi-org.brum.beds.ac.uk/10.3390/v11111000 - 31 Oct 2019

Cited by 17 | Viewed by 2618

Abstract

The hepatitis C virus (HCV) has remarkable genetic diversity and exists as eight genotypes (1 to 8) with distinct geographic distributions. No complete genome sequence of HCV subtype 2b (HCV-2b) is available from Latin American countries, and the factors underlying its emergence and [...] Read more.

The hepatitis C virus (HCV) has remarkable genetic diversity and exists as eight genotypes (1 to 8) with distinct geographic distributions. No complete genome sequence of HCV subtype 2b (HCV-2b) is available from Latin American countries, and the factors underlying its emergence and spread within the continent remain unknown. The present study was conducted to determine the first full-length genomic sequences of HCV-2b isolates from Latin America and reconstruct the spatial and temporal diversification of this subtype in Brazil. Nearly complete HCV-2b genomes isolated from two Brazilian patients were obtained by direct sequencing of long PCR fragments and analyzed together with reference sequences using the Bayesian coalescent and phylogeographic framework approaches. The two HCV-2b genomes were 9318 nucleotides (nt) in length (nt 37–9354). Interestingly, the long RT-PCR technique was able to detect co-circulation of viral variants that contained an in-frame deletion of 2022 nt encompassing E1, E2, and p7 proteins. Spatiotemporal reconstruction analyses suggest that HCV-2b had a single introduction in Brazil during the early 1980s, displaying an epidemic history characterized by a low and virtually constant population size until the present time. These results coincide with epidemiological data in Brazil and may explain the low national prevalence of this subtype. Full article

(This article belongs to the Special Issue Emerging Viruses: Surveillance, Prevention, Evolution and Control)

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15 pages, 2426 KiB

Open AccessArticle

Novel Viruses in Mosquitoes from Brazilian Pantanal

by Laura Marina Siqueira Maia, Andressa Zelenski de Lara Pinto, Michellen Santos de Carvalho, Fernando Lucas de Melo, Bergmann Morais Ribeiro and Renata Dezengrini Slhessarenko

Viruses 2019, 11(10), 957; https://0-doi-org.brum.beds.ac.uk/10.3390/v11100957 - 17 Oct 2019

Cited by 12 | Viewed by 4224

Abstract

Viruses are ubiquitous and diverse microorganisms arising as a result of interactions within their vertebrate and invertebrate hosts. Here we report the presence of different viruses in the salivary glands of 1657 mosquitoes classified over 28 culicinae species from the North region of [...] Read more.

Viruses are ubiquitous and diverse microorganisms arising as a result of interactions within their vertebrate and invertebrate hosts. Here we report the presence of different viruses in the salivary glands of 1657 mosquitoes classified over 28 culicinae species from the North region of the Brazilian Pantanal wetland through metagenomics, viral isolation, and RT-PCR. In total, 12 viruses were found, eight putative novel viruses with relatively low similarity with pre-existing species of viruses within their families, named Pirizal iflavirus, Furrundu phlebovirus, Pixé phlebovirus, Guampa vesiculovirus, Chacororé flavivirus, Rasqueado orbivirus, Uru chuvirus, and Bororo circovirus. We also found the already described Lobeira dielmorhabdovirus, Sabethes flavivirus, Araticum partitivirus, and Murici totivirus. Therefore, these findings underscore the vast diversity of culicinae and novel viruses yet to be explored in Pantanal, the largest wetland on the planet. Full article

(This article belongs to the Special Issue Emerging Viruses: Surveillance, Prevention, Evolution and Control)

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26 pages, 4166 KiB

Open AccessArticle

Genetic Analysis of Avian Coronavirus Infectious Bronchitis Virus in Yellow Chickens in Southern China over the Past Decade: Revealing the Changes of Genetic Diversity, Dominant Genotypes, and Selection Pressure

by Wensheng Fan, Ning Tang, Zhihua Dong, Jiming Chen, Wen Zhang, Changrun Zhao, Yining He, Meng Li, Cuilan Wu, Tianchao Wei, Teng Huang, Meilan Mo and Ping Wei

Viruses 2019, 11(10), 898; https://0-doi-org.brum.beds.ac.uk/10.3390/v11100898 - 26 Sep 2019

Cited by 24 | Viewed by 5421

Abstract

The high mutation rates of infectious bronchitis virus (IBV) pose economic threats to the poultry industry. In order to track the genetic evolutionary of IBV isolates circulating in yellow chickens, we continued to conduct the genetic analyses of the structural genes S1, E, [...] Read more.

The high mutation rates of infectious bronchitis virus (IBV) pose economic threats to the poultry industry. In order to track the genetic evolutionary of IBV isolates circulating in yellow chickens, we continued to conduct the genetic analyses of the structural genes S1, E, M, and N from 64 IBV isolates in southern China during 2009–2017. The results showed that the dominant genotypes based on the four genes had changed when compared with those during 1985–2008. Based on the S1 gene phylogenetic tree, LX4-type (GI-19) was the most dominant genotype, which was different from that during 1985–2008. The second most dominant genotype was LDT3-A-type, but this genotype disappeared after 2012. New-type 1 (GVI-1) isolates showed increasing tendency and there were four aa (QKEP) located in the hypervariable region (HVR) III and one aa (S) insertion in all the New-type 1 isolates. Both the analyses of amino acid entropy and molecular evolutionary rate revealed that the variations from large to small were S1, E, M, and N. Purifying selection was detected in the S1, E, M, and N gene proteins, which was different from the positive selection during 1985–2008. Six isolates were confirmed to be recombinants, possibly generated from a vaccine virus of the 4/91-type or LDT3-A-type and a circulating virus. The estimated times for the most recent common ancestors based on the S1, E, M, and N genes were the years of 1744, 1893, 1940, and 1945, respectively. Bayesian skyline analysis revealed a sharp decrease in genetic diversity of all the four structural genes after 2010 and since late 2015, the viral population rapidly rose. In conclusion, the IBVs circulating in southern China over the past decade have experienced a remarkable change in genetic diversity, dominant genotypes, and selection pressure, indicating the importance of permanent monitoring of circulating strains and the urgency for developing new vaccines to counteract the emerging LX4-type and New-type IBVs. Full article

(This article belongs to the Special Issue Emerging Viruses: Surveillance, Prevention, Evolution and Control)

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15 pages, 3064 KiB

Open AccessArticle

Identification of Two Porcine Reproductive and Respiratory Syndrome Virus Variants Sharing High Genomic Homology but with Distinct Virulence

by Nanhua Chen, Mengxue Ye, Yucheng Huang, Shuai Li, Yanzhao Xiao, Xinshuai Li, Shubin Li, Xiangdong Li, Xiuling Yu, Kegong Tian and Jianzhong Zhu

Viruses 2019, 11(9), 875; https://0-doi-org.brum.beds.ac.uk/10.3390/v11090875 - 18 Sep 2019

Cited by 22 | Viewed by 3902

Abstract

Porcine reproductive and respiratory syndrome virus (PRRSV) causes huge economic loss to the global swine industry. Even though several control strategies have been applied, PRRS is still not effectively controlled due to the continuous emergence of new variants and limited cross-protection by current [...] Read more.

Porcine reproductive and respiratory syndrome virus (PRRSV) causes huge economic loss to the global swine industry. Even though several control strategies have been applied, PRRS is still not effectively controlled due to the continuous emergence of new variants and limited cross-protection by current vaccines. During the routine epidemiological investigation in 2017, two PRRSV variants were identified from a severe abortion farm and a clinically healthy farm, respectively. The viruses were isolated and denominated as XJ17-5 and JSTZ1712-12. Genomic sequencing indicated that their genomes are both 14,960 bp in length sharing 99.45% nucleotide identity. Sequence alignments identified a discontinuous 30-amino-acid deletion and a continuous 120-amino-acid deletion in nsp2 of both isolates. Genome-based phylogenetic analysis confirmed that XJ17-5 and JSTZ1712-12 belong to the HP-PRRSV subtype but form a new branch with other isolates containing the same 150-amino-acid deletion in nsp2. Pathogenic analysis showed that XJ17-5 is highly virulent causing 60% mortality, while JSTZ1712-12 is avirulent for piglets. Furthermore, fragment comparisons identified 34-amino-acid differences between XJ17-5 and JSTZ1712-12 that might be associated with the distinct virulence. The identification of highly homologous HP-PRRSV variants with new genetic feature and distinct virulence contributes to further analyze the pathogenesis and evolution of PRRSV in the field. Full article

(This article belongs to the Special Issue Emerging Viruses: Surveillance, Prevention, Evolution and Control)

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11 pages, 1243 KiB

Open AccessArticle

Presence of a Novel Subtype of Bovine Hepacivirus in China and Expanded Classification of Bovine Hepacivirus Strains Worldwide into 7 Subtypes

by Gang Lu, Jiajun Ou, Jiawei Zhao and Shoujun Li

Viruses 2019, 11(9), 843; https://0-doi-org.brum.beds.ac.uk/10.3390/v11090843 - 11 Sep 2019

Cited by 11 | Viewed by 2810

Abstract

The newest member of the Hepacivirus genus, bovine hepacivirus (BovHepV), was first identified in cattle in 2015 and is a novel hepacivirus C virus (HCV)-like virus. This virus has been detected in five countries so far and is classified into four subtypes. Bovine [...] Read more.

The newest member of the Hepacivirus genus, bovine hepacivirus (BovHepV), was first identified in cattle in 2015 and is a novel hepacivirus C virus (HCV)-like virus. This virus has been detected in five countries so far and is classified into four subtypes. Bovine serum is commonly used for cell cultures and is considered the major source of viral contamination of pharmaceutical products. In this study, bovine serum samples were collected from seven countries located in Asia, America, Oceania, and Europe and were tested for BovHepV RNA using nested PCR, in order to: (i) obtain more knowledge on the geographical distribution and subtypes of BovHepV; and (ii) detect the potential contamination of BovHepV in commercial bovine serum samples used for cell culture propagation. The results demonstrated that bovine serum samples from individual donor cattle in China contained BovHepV RNA. After PCR, sequencing, and assembly, the genomes of the Chinese BovHepV strains were obtained. Genetic analysis of the polyprotein gene revealed a protein identity of <77% and a nucleotide identity of <85% between the Chinese BovHepV strains and all other previously reported BovHepV strains. Using cut-off values for determination of HCV genotypes and subtypes, BovHepV strains worldwide were classified into one unique genotype and seven subtypes. The BovHepV strains identified in the present study were classified into a novel subtype, which was provisionally designated subtype G. The genetic relationships among the different BovHepV subtypes were further confirmed through phylogenetic analysis. The present study provides critical insights into BovHepV’s geographical distribution and genetic variability. Full article

(This article belongs to the Special Issue Emerging Viruses: Surveillance, Prevention, Evolution and Control)

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23 pages, 3356 KiB

Open AccessArticle

Faecal Virome Analysis of Wild Animals from Brazil

by Matheus A. Duarte, João M. F. Silva, Clara R. Brito, Danilo S. Teixeira, Fernando L. Melo, Bergmann M. Ribeiro, Tatsuya Nagata and Fabrício S. Campos

Viruses 2019, 11(9), 803; https://0-doi-org.brum.beds.ac.uk/10.3390/v11090803 - 30 Aug 2019

Cited by 44 | Viewed by 9133

Abstract

The Brazilian Cerrado fauna shows very wide diversity and can be a potential viral reservoir. Therefore, the animal’s susceptibility to some virus can serve as early warning signs of potential human virus diseases. Moreover, the wild animal virome of this biome is unknown. [...] Read more.

The Brazilian Cerrado fauna shows very wide diversity and can be a potential viral reservoir. Therefore, the animal’s susceptibility to some virus can serve as early warning signs of potential human virus diseases. Moreover, the wild animal virome of this biome is unknown. Based on this scenario, high-throughput sequencing contributes a robust tool for the identification of known and unknown virus species in this environment. In the present study, faeces samples from cerrado birds (Psittacara leucophthalmus, Amazona aestiva, and Sicalis flaveola) and mammals (Didelphis albiventris, Sapajus libidinosus, and Galictis cuja) were collected at the Veterinary Hospital, University of Brasília. Viral nucleic acid was extracted, submitted to random amplification, and sequenced by Illumina HiSeq platform. The reads were de novo assembled, and the identities of the contigs were evaluated by Blastn and tblastx searches. Most viral contigs analyzed were closely related to bacteriophages. Novel archaeal viruses of the Smacoviridae family were detected. Moreover, sequences of members of Adenoviridae, Anelloviridae, Circoviridae, Caliciviridae, and Parvoviridae families were identified. Complete and nearly complete genomes of known anelloviruses, circoviruses, and parvoviruses were obtained, as well as putative novel species. We demonstrate that the metagenomics approach applied in this work was effective for identification of known and putative new viruses in faeces samples from Brazilian Cerrado fauna. Full article

(This article belongs to the Special Issue Emerging Viruses: Surveillance, Prevention, Evolution and Control)

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16 pages, 4334 KiB

Open AccessArticle

Phylodynamics of Influenza A/H1N1pdm09 in India Reveals Circulation Patterns and Increased Selection for Clade 6b Residues and Other High Mortality Mutants

by Dillon C. Adam, Matthew Scotch and C Raina. MacIntyre

Viruses 2019, 11(9), 791; https://0-doi-org.brum.beds.ac.uk/10.3390/v11090791 - 27 Aug 2019

Cited by 8 | Viewed by 4139

Abstract

The clinical severity and observed case fatality ratio of influenza A/H1N1pdm09 in India, particularly in 2015 and 2017 far exceeds current global estimates. Reasons for these frequent and severe epidemic waves remain unclear. We used Bayesian phylodynamic methods to uncover possible genetic explanations [...] Read more.

The clinical severity and observed case fatality ratio of influenza A/H1N1pdm09 in India, particularly in 2015 and 2017 far exceeds current global estimates. Reasons for these frequent and severe epidemic waves remain unclear. We used Bayesian phylodynamic methods to uncover possible genetic explanations for this, while also identifying the transmission dynamics of A/H1N1pdm09 between 2009 and 2017 to inform future public health interventions. We reveal a disproportionate selection at haemagglutinin residue positions associated with increased morbidity and mortality in India such as position 222 and clade 6B characteristic residues, relative to equivalent isolates circulating globally. We also identify for the first time, increased selection at position 186 as potentially explaining the severity of recent A/H1N1pdm09 epidemics in India. We reveal national routes of A/H1N1pdm09 transmission, identifying Maharashtra as the most important state for the spread throughout India, while quantifying climactic, ecological, and transport factors as drivers of within-country transmission. Together these results have important implications for future A/H1N1pdm09 surveillance and control within India, but also for epidemic and pandemic risk prediction around the world. Full article

(This article belongs to the Special Issue Emerging Viruses: Surveillance, Prevention, Evolution and Control)

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10 pages, 1861 KiB

Open AccessArticle

Evolution and Genetic Diversity of Porcine Circovirus 3 in China

by Ye Chen, Quanming Xu, Hong Chen, Xian Luo, Qi Wu, Chen Tan, Qidong Pan and Ji-Long Chen

Viruses 2019, 11(9), 786; https://0-doi-org.brum.beds.ac.uk/10.3390/v11090786 - 27 Aug 2019

Cited by 18 | Viewed by 4336

Abstract

The identification of a new circovirus (Porcine Circovirus 3, PCV3) has raised concern because its impact on swine health is not fully known. In Fujian Province in eastern China, even its circulating status and genetic characteristics are unclear. Here, we tested 127 tissue [...] Read more.

The identification of a new circovirus (Porcine Circovirus 3, PCV3) has raised concern because its impact on swine health is not fully known. In Fujian Province in eastern China, even its circulating status and genetic characteristics are unclear. Here, we tested 127 tissue samples from swine from Fujian Province that presented respiratory symptoms. All of the PCV3 positive samples were negative for many other pathogens involved in respiratory diseases like PCV2, PRRSV, and CSFV, suggesting that PCV3 is potentially pathogenic. From phylogenetic analysis, PCV3 strains are divided into two main clades and five sub-clades; PCV3a-1, PCV3a-2, PCV3a-3, PCV3b-1, and PCV3b-2. Our identified strains belong to genotypes PCV3a-1, PCV3a-2, PCV3a-3, and PCV3b-2, indicating a high degree of genetic diversity of PCV3 in Fujian province until 2019. Interestingly, we found the time of the most recent common ancestor (tMRCA) of PCV3 was dated to the 1950s, and PCV3 has a similar evolutionary rate as PCV2 (the main epidemic genotypes PCV2b and PCV2d). In addition, positive selection sites N56D/S and S77T/N on the capsid gene are located on the PCV3 antigen epitope, indicating that PCV3 is gradually adaptive in swine. In summary, our results provide important insights into the epidemiology of PCV3. Full article

(This article belongs to the Special Issue Emerging Viruses: Surveillance, Prevention, Evolution and Control)

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15 pages, 4881 KiB

Open AccessArticle

Proteomics Computational Analyses Suggest that the Antennavirus Glycoprotein Complex Includes a Class I Viral Fusion Protein (α-Penetrene) with an Internal Zinc-Binding Domain and a Stable Signal Peptide

by Courtney E. Garry and Robert F. Garry

Viruses 2019, 11(8), 750; https://0-doi-org.brum.beds.ac.uk/10.3390/v11080750 - 14 Aug 2019

Cited by 8 | Viewed by 4672

Abstract

A metatranscriptomic study of RNA viruses in cold-blooded vertebrates identified two related viruses from frogfish (Antennarius striatus) that represent a new genus Antennavirus in the family Arenaviridae (Order: Bunyavirales). Computational analyses were used to identify features common to class I [...] Read more.

A metatranscriptomic study of RNA viruses in cold-blooded vertebrates identified two related viruses from frogfish (Antennarius striatus) that represent a new genus Antennavirus in the family Arenaviridae (Order: Bunyavirales). Computational analyses were used to identify features common to class I viral fusion proteins (VFPs) in antennavirus glycoproteins, including an N-terminal fusion peptide, two extended alpha-helices, an intrahelical loop, and a carboxyl terminal transmembrane domain. Like mammarenavirus and hartmanivirus glycoproteins, the antennavirus glycoproteins have an intracellular zinc-binding domain and a long virion-associated stable signal peptide (SSP). The glycoproteins of reptarenaviruses are also class I VFPs, but do not contain zinc-binding domains nor do they encode SSPs. Divergent evolution from a common progenitor potentially explains similarities of antennavirus, mammarenavirus, and hartmanivirus glycoproteins, with an ancient recombination event resulting in a divergent reptarenavirus glycoprotein. Full article

(This article belongs to the Special Issue Emerging Viruses: Surveillance, Prevention, Evolution and Control)

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11 pages, 1667 KiB

Open AccessArticle

Isolation and Full-Length Sequence Analysis of a Pestivirus from Aborted Lamb Fetuses in Italy

by Enrica Sozzi, Antonio Lavazza, Alessandra Gaffuri, Fabio Carlo Bencetti, Alice Prosperi, Davide Lelli, Chiara Chiapponi and Ana Moreno

Viruses 2019, 11(8), 744; https://0-doi-org.brum.beds.ac.uk/10.3390/v11080744 - 13 Aug 2019

Cited by 20 | Viewed by 3658

Abstract

Pestiviruses are distributed worldwide and are responsible for a variety of economically important diseases. They are not very host-specific, and thus sheep can be infected by well-known pestiviruses like bovine viral diarrhea virus (BVDV) and border disease virus (BDV), as well as by [...] Read more.

Pestiviruses are distributed worldwide and are responsible for a variety of economically important diseases. They are not very host-specific, and thus sheep can be infected by well-known pestiviruses like bovine viral diarrhea virus (BVDV) and border disease virus (BDV), as well as by other recently discovered pestivirus species. The aim of this study is to describe the isolation and characterization of four pestivirus strains detected in aborted lamb fetuses from a single farm in the Brescia province (Northern Italy). A total of twelve aborted fetuses were collected and examined. After necropsy, organs were tested for the presence of infectious agents known as potential causes of abortion (Brucella spp., Listeria spp., Coxiella burnetii, Chlamydophila spp., Mycoplasma spp., Neospora caninum, and Toxoplasma gondii), and submitted to viral identification by isolation on Madin Darby bovine kidney (MDBK) cell culture and by PCR assay for Schmallenberg virus and pan-pestivirus RT-PCR real time assay. Three viral strains (Ovine/IT/1756/2017, Ovine/IT/338710-2/2017, and Ovine/IT/338710-3/2017) were isolated in the absence of cytopathic effects (CPEs) in cell cultures and identified with RT-PCR. Another pestivirus strain (Ovine/IT/16235-2/2018) was detected by PCR, but was not successfully isolated. Complete sequence genomic data of the three isolated viruses showed that they were highly similar, differed genetically from known pestivirus species, and were closely related to classical swine fever virus (CSFV). Beyond the identification of new ovine pestiviruses, this study indicates that a systematic diagnostic approach is important to identify the presence and map the distribution of both known and emerging pestiviruses. Full article

(This article belongs to the Special Issue Emerging Viruses: Surveillance, Prevention, Evolution and Control)

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16 pages, 1255 KiB

Open AccessArticle

Middle East Respiratory Syndrome Coronavirus (MERS-CoV) in Dromedary Camels in Africa and Middle East

by Ahmed Kandeil, Mokhtar Gomaa, Ahmed Nageh, Mahmoud M. Shehata, Ahmed E. Kayed, Jamal S. M. Sabir, Awatef Abiadh, Jamel Jrijer, Zuhair Amr, Mounir Abi Said, Denis K. Byarugaba, Fred Wabwire-Mangen, Titus Tugume, Nadira S. Mohamed, Roba Attar, Sabah M. Hassan, Sabah Abdulaziz Linjawi, Yassmin Moatassim, Omnia Kutkat, Sara Mahmoud, Ola Bagato, Noura M. Abo Shama, Rabeh El-Shesheny, Ahmed Mostafa, Ranawaka A. P. M. Perera, Daniel K. W. Chu, Nagla Hassan, Basma Elsokary, Ahmed Saad, Heba Sobhy, Ihab El Masry, Pamela P. McKenzie, Richard J. Webby, Malik Peiris, Yilma J. Makonnen, Mohamed A. Ali and Ghazi Kayali Show full author list Hide full author list

Viruses 2019, 11(8), 717; https://0-doi-org.brum.beds.ac.uk/10.3390/v11080717 - 05 Aug 2019

Cited by 36 | Viewed by 6979

Abstract

Dromedary camels are the natural reservoirs of the Middle East respiratory syndrome coronavirus (MERS-CoV). Camels are mostly bred in East African countries then exported into Africa and Middle East for consumption. To understand the distribution of MERS-CoV among camels in North Africa and [...] Read more.

Dromedary camels are the natural reservoirs of the Middle East respiratory syndrome coronavirus (MERS-CoV). Camels are mostly bred in East African countries then exported into Africa and Middle East for consumption. To understand the distribution of MERS-CoV among camels in North Africa and the Middle East, we conducted surveillance in Egypt, Senegal, Tunisia, Uganda, Jordan, Saudi Arabia, and Iraq. We also performed longitudinal studies of three camel herds in Egypt and Jordan to elucidate MERS-CoV infection and transmission. Between 2016 and 2018, a total of 4027 nasal swabs and 3267 serum samples were collected from all countries. Real- time PCR revealed that MERS-CoV RNA was detected in nasal swab samples from Egypt, Senegal, Tunisia, and Saudi Arabia. Microneutralization assay showed that antibodies were detected in all countries. Positive PCR samples were partially sequenced, and a phylogenetic tree was built. The tree suggested that all sequences are of clade C and sequences from camels in Egypt formed a separate group from previously published sequences. Longitudinal studies showed high seroprevalence in adult camels. These results indicate the widespread distribution of the virus in camels. A systematic active surveillance and longitudinal studies for MERS-CoV are needed to understand the epidemiology of the disease and dynamics of viral infection. Full article

(This article belongs to the Special Issue Emerging Viruses: Surveillance, Prevention, Evolution and Control)

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16 pages, 4908 KiB

Open AccessArticle

Identification, Pathogenicity of Novel Fowl Adenovirus Serotype 4 SDJN0105 in Shandong, China and Immunoprotective Evaluation of the Newly Developed Inactivated Oil-emulsion FAdV-4 Vaccine

by Kai Meng, Xiaoyuan Yuan, Jiang Yu, Yuxia Zhang, Wu Ai and Youling Wang

Viruses 2019, 11(7), 627; https://0-doi-org.brum.beds.ac.uk/10.3390/v11070627 - 08 Jul 2019

Cited by 32 | Viewed by 5268

Abstract

Since mid-2015, numerous outbreaks of hydropericardium-hepatitis syndrome (HHS), which is caused by a novel fowl adenovirus serotype 4 (FAdV-4), have been reported in chickens in parts of China, thereby causing huge economic losses to the poultry industry. Thus, an effective vaccine to control [...] Read more.

Since mid-2015, numerous outbreaks of hydropericardium-hepatitis syndrome (HHS), which is caused by a novel fowl adenovirus serotype 4 (FAdV-4), have been reported in chickens in parts of China, thereby causing huge economic losses to the poultry industry. Thus, an effective vaccine to control the further spread of infections with this hyper-virulent FAdV-4 is imperative. In this study, we isolated a novel FAdV-4 strain SDJN0105 from a broiler farm with HHS disease in Shandong Province. Pathogenicity was evaluated by the observation of clinical symptoms, necropsy changes, and pathological tissue sections after oral and intramuscular (IM) infection of Specific pathogen free (SPF) chickens. The chickens infected by IM injection all died within three days, and chickens infected via the oculonasal route died within five days post-infection (dpi). Histopathological examination revealed that the pathology was confined to heart, liver, spleen, lung, kidney, and particularly the liver. Irrespective of the inoculation route, the highest viral DNA copy numbers were detected in the livers of infected chickens. The mRNA expression levels of IL-1β, IL-6, IL-8, IFNs, TNF-α, Mx, and OASL were significantly upregulated during the viral infection. In addition, an inactivated oil-emulsion FAdV-4 vaccine was developed. The vaccine could provide full protection for SPF chickens against a lethal dose of the FAdV-4 strain SDJN0105 and a high level of antibodies. These results improve our understanding of the innate immune responses in chickens infected with FAdV-4 and the pathogenesis of FAdV-4 caused by host factors, and the developed FAdV-4 vaccine is promising as a drug candidate for the prevention and reduction of the spread of HHS in poultry in China. Full article

(This article belongs to the Special Issue Emerging Viruses: Surveillance, Prevention, Evolution and Control)

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20 pages, 3512 KiB

Open AccessArticle

Different Pathogenicity and Transmissibility of Goose-Origin H5N6 Avian Influenza Viruses in Chickens

by Kun Mei, Yang Guo, Xuhui Zhu, Nannan Qu, Jianni Huang, Zuxian Chen, You Zhang, Bingbing Zhao, Zhuoliang He, Ming Liao and Peirong Jiao

Viruses 2019, 11(7), 612; https://0-doi-org.brum.beds.ac.uk/10.3390/v11070612 - 04 Jul 2019

Cited by 6 | Viewed by 3122

Abstract

Highly pathogenic avian influenza H5N6 viruses have been circulating in poultry in Asia since 2013 and producing serious diseases in chickens. Here, we analyzed the genetic properties of 10 H5N6 subtypes AIVs from geese in 2015–2016 in Guangdong province. Phylogenic analysis showed that [...] Read more.

Highly pathogenic avian influenza H5N6 viruses have been circulating in poultry in Asia since 2013 and producing serious diseases in chickens. Here, we analyzed the genetic properties of 10 H5N6 subtypes AIVs from geese in 2015–2016 in Guangdong province. Phylogenic analysis showed that all HA genes of the 10 viruses belonged to clade 2.3.4.4, and their genes including HA, PA, PB1, M, NP, and NS all derived from Mix-like 1 (CH, VN, LS). Their PB2 genes come from Mix-like 2 (CH, VN, JP). The NA genes were classified into a Eurasian lineage. Therefore, the 10 viruses likely originate from the same ancestor and were all recombinant viruses between different genotypes. We selected A/Goose/Guangdong/GS144/2015(H5N6) (GS144) and A/Goose/Guangdong/GS148/2016(H5N6) (GS148) viruses to inoculate 5-week-old chickens intranasally with 10⁴ EID₅₀/0.1 mL dose intranasally to assess their pathogenicity and transmissibility. Inoculated chickens showed that the GS144 virus caused systematic infection with a lethality of 100%, but the lethality of GS148 virus was 0%. The two viruses were efficiently transmitted to contact chickens. The lethality of GS144 and GS148 virus in contact with chickens was 87.5% and 0%, respectively, which suggests that the transmissibility of GS144 virus was stronger than GS148 virus in chickens. Thus, different H5N6 viruses from the same waterfowl can show different pathogenicity and transmissibility in chickens. Continued surveillance and characteristic analysis of the H5N6 viruses will help us to keep abreast of evolution and variation in avian influenza viruses in the future. Full article

(This article belongs to the Special Issue Emerging Viruses: Surveillance, Prevention, Evolution and Control)

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12 pages, 2313 KiB

Open AccessArticle

A Nymphalid-Infecting Group I Alphabaculovirus Isolated from the Major Passion Fruit Caterpillar Pest Dione juno juno (Lepidoptera: Nymphalidae)

by Bergmann Morais Ribeiro, Ethiane Rozo dos Santos, Luana Beló Trentin, Leonardo Assis da Silva, Fernando Lucas de Melo, Elliot Watanabe Kitajima and Daniel M. P. Ardisson-Araújo

Viruses 2019, 11(7), 602; https://0-doi-org.brum.beds.ac.uk/10.3390/v11070602 - 03 Jul 2019

Cited by 5 | Viewed by 3548

Abstract

Baculoviruses are capable of infecting a wide diversity of insect pests. In the 1990s, the Dione juno nucleopolyhedrovirus (DijuNPV) was isolated from larvae of the major passionfruit defoliator pest Dione juno juno (Nymphalidae) and described at ultrastructural and pathological levels. In this study, [...] Read more.

Baculoviruses are capable of infecting a wide diversity of insect pests. In the 1990s, the Dione juno nucleopolyhedrovirus (DijuNPV) was isolated from larvae of the major passionfruit defoliator pest Dione juno juno (Nymphalidae) and described at ultrastructural and pathological levels. In this study, the complete genome sequence of DijuNPV was determined and analyzed. The circular genome presents 122,075 bp with a G + C content of 50.9%. DijuNPV is the first alphabaculovirus completely sequenced that was isolated from a nymphalid host and may represent a divergent species. It appeared closely related to Orgyia pseudotsugata multiple nucleopolyhedrovirus (OpMNPV) and other Choristoneura-isolated group I alphabaculoviruses. We annotated 153 open reading frames (ORFs), including a set of 38 core genes, 26 ORFs identified as present in lepidopteran baculoviruses, 17 ORFs unique in baculovirus, and several auxiliary genes (e.g., bro, cathepsin, chitinase, iap-1, iap-2, and thymidylate kinase). The thymidylate kinase (tmk) gene was present fused to a dUTPase (dut) gene in other baculovirus genomes. DijuNPV likely lost the dut portion together with the iap-3 homolog. Overall, the genome sequencing of novel alphabaculoviruses enables a wide understanding of baculovirus evolution. Full article

(This article belongs to the Special Issue Emerging Viruses: Surveillance, Prevention, Evolution and Control)

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14 pages, 2445 KiB

Open AccessArticle

Immunogenicity in Rabbits of Virus-Like Particles from a Contemporary Rabbit Haemorrhagic Disease Virus Type 2 (GI.2/RHDV2/b) Isolated in The Netherlands

by Qiuhong Miao, Ruibing Qi, Luut Veldkamp, Jooske Ijzer, Marja L. Kik, Jie Zhu, Aoxing Tang, Dandan Dong, Yonghong Shi, Monique M. van Oers, Guangqing Liu and Gorben P. Pijlman

Viruses 2019, 11(6), 553; https://0-doi-org.brum.beds.ac.uk/10.3390/v11060553 - 14 Jun 2019

Cited by 14 | Viewed by 4796

Abstract

Rabbit haemorrhagic disease virus (RHDV) type 2 (GI.2/RHDV2/b) is an emerging pathogen in wild rabbits and in domestic rabbits vaccinated against RHDV (GI.1). Here we report the genome sequence of a contemporary RHDV2 isolate from the Netherlands and investigate the immunogenicity of virus-like [...] Read more.

Rabbit haemorrhagic disease virus (RHDV) type 2 (GI.2/RHDV2/b) is an emerging pathogen in wild rabbits and in domestic rabbits vaccinated against RHDV (GI.1). Here we report the genome sequence of a contemporary RHDV2 isolate from the Netherlands and investigate the immunogenicity of virus-like particles (VLPs) produced in insect cells. RHDV2 RNA was isolated from the liver of a naturally infected wild rabbit and the complete viral genome sequence was assembled from sequenced RT-PCR products. Phylogenetic analysis based on the VP60 capsid gene demonstrated that the RHDV2 NL2016 isolate clustered with other contemporary RHDV2 strains. The VP60 gene was cloned in a baculovirus expression vector to produce VLPs in Sf9 insect cells. Density-gradient purified RHDV2 VLPs were visualized by transmission electron microscopy as spherical particles of around 30 nm in diameter with a morphology resembling authentic RHDV. Immunization of rabbits with RHDV2 VLPs resulted in high production of serum antibodies against VP60, and the production of cytokines (IFN-γ and IL-4) was significantly elevated in the immunized rabbits compared to the control group. The results demonstrate that the recombinant RHDV2 VLPs are highly immunogenic and may find applications in serological detection assays and might be further developed as a vaccine candidate to protect domestic rabbits against RHDV2 infection. Full article

(This article belongs to the Special Issue Emerging Viruses: Surveillance, Prevention, Evolution and Control)

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16 pages, 9654 KiB

Open AccessArticle

Genetic Characterization of a Recombinant Myxoma Virus in the Iberian Hare (Lepus granatensis)

by Ana Águeda-Pinto, Ana Lemos de Matos, Mário Abrantes, Simona Kraberger, Maria A. Risalde, Christian Gortázar, Grant McFadden, Arvind Varsani and Pedro J. Esteves

Viruses 2019, 11(6), 530; https://0-doi-org.brum.beds.ac.uk/10.3390/v11060530 - 07 Jun 2019

Cited by 35 | Viewed by 7381

Abstract

Myxomatosis is a lethal disease in wild European and domestic rabbits (Oryctolagus cuniculus), which is caused by a Myxoma virus (MYXV) infection—a leporipoxvirus that is found naturally in some Sylvilagus rabbit species in South America and California. The introduction of MYXV [...] Read more.

Myxomatosis is a lethal disease in wild European and domestic rabbits (Oryctolagus cuniculus), which is caused by a Myxoma virus (MYXV) infection—a leporipoxvirus that is found naturally in some Sylvilagus rabbit species in South America and California. The introduction of MYXV into feral European rabbit populations of Australia and Europe, in the early 1950s, demonstrated the best-documented field example of host–virus coevolution, following a cross-species transmission. Recently, a new cross-species jump of MYXV has been suggested in both Great Britain and Spain, where European brown hares (Lepus europaeus) and Iberian hares (Lepus granatensis) were found dead with lesions consistent with those observed in myxomatosis. To investigate the possibility of a new cross-species transmission event by MYXV, tissue samples collected from a wild Iberian hare found dead in Spain (Toledo region) were analyzed and deep sequenced. Our results reported a new MYXV isolate (MYXV Toledo) in the tissues of this species. The genome of this new virus was found to encode three disruptive genes (M009L, M036L, and M152R) and a novel ~2.8 kb recombinant region, which resulted from an insertion of four novel poxviral genes towards the 3’ end of the negative strand of its genome. From the open reading frames inserted into the MYXV Toledo virus, a new orthologue of a poxvirus host range gene family member was identified, which was related to the MYXV gene M064R. Overall, we confirmed the identity of a new MYXV isolate in Iberian hares, which, we hypothesized, was able to more effectively counteract the host defenses in hares and start an infectious process in this new host. Full article

(This article belongs to the Special Issue Emerging Viruses: Surveillance, Prevention, Evolution and Control)

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9 pages, 3483 KiB

Open AccessCommunication

Prevalence of Fowl Adenovirus Serotype 4 and Co-Infection by Immunosuppressive Viruses in Fowl with Hydropericardium Hepatitis Syndrome in Shandong Province, China

by Guanliu Yu, Yun Lin, Yanguo Dou, Yi Tang and Youxiang Diao

Viruses 2019, 11(6), 517; https://0-doi-org.brum.beds.ac.uk/10.3390/v11060517 - 05 Jun 2019

Cited by 19 | Viewed by 4530

Abstract

Fowl adenovirus serotype 4 (FAdV-4) is the pathogenic agent of hydropericardium hepatitis syndrome (HHS) in chickens and ducks, which has caused huge economic losses for the Chinese poultry industry since 2015. In order to objectively determine the prevalence and co-infection status of the [...] Read more.

Fowl adenovirus serotype 4 (FAdV-4) is the pathogenic agent of hydropericardium hepatitis syndrome (HHS) in chickens and ducks, which has caused huge economic losses for the Chinese poultry industry since 2015. In order to objectively determine the prevalence and co-infection status of the virus in Shandong province in China, we analyzed a total of 679 clinical cases of chickens and ducks from 36 farms in the province. The results showed that the FAdV-4 infection rate was 65.2% (443/679), and the rate in breeder ducks was almost two-fold higher than that in breeder chickens (68.57% vs. 34.30%). Notably, co-infection by H9N2 avian influenza virus, infectious bursal disease virus, and/or chicken infectious anemia virus was very common in the 443 FAdV-4-positive cases. Furthermore, phylogenetic analysis of the hexon genes of four Shandong FAdV-4 isolates revealed that these strains clustered into Indian reference strains, indicating that the Shandong FAdV-4 strains might have originated in India. These findings provide the first data on the prevalence and co-infection status of FAdV-4 in Shandong province, which may serve as a foundation for the prevention of FAdV-4 in the field. Full article

(This article belongs to the Special Issue Emerging Viruses: Surveillance, Prevention, Evolution and Control)

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Review

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17 pages, 8173 KiB

Open AccessReview

Antivirals Against Chikungunya Virus: Is the Solution in Nature?

by Daniel Oliveira Silva Martins, Igor de Andrade Santos, Débora Moraes de Oliveira, Victória Riquena Grosche and Ana Carolina Gomes Jardim

Viruses 2020, 12(3), 272; https://0-doi-org.brum.beds.ac.uk/10.3390/v12030272 - 29 Feb 2020

Cited by 19 | Viewed by 6334

Abstract

The worldwide outbreaks of the chikungunya virus (CHIKV) in the last years demonstrated the need for studies to screen antivirals against CHIKV. The virus was first isolated in Tanzania in 1952 and was responsible for outbreaks in Africa and Southwest Asia in subsequent [...] Read more.

The worldwide outbreaks of the chikungunya virus (CHIKV) in the last years demonstrated the need for studies to screen antivirals against CHIKV. The virus was first isolated in Tanzania in 1952 and was responsible for outbreaks in Africa and Southwest Asia in subsequent years. Between 2007 and 2014, some cases were documented in Europe and America. The infection is associated with low rates of death; however, it can progress to a chronic disease characterized by severe arthralgias in infected patients. This infection is also associated with Guillain–Barré syndrome. There is no specific antivirus against CHIKV. Treatment of infected patients is palliative and based on analgesics and non-steroidal anti-inflammatory drugs to reduce arthralgias. Several natural molecules have been described as antiviruses against viruses such as dengue, yellow fever, hepatitis C, and influenza. This review aims to summarize the natural compounds that have demonstrated antiviral activity against chikungunya virus in vitro. Full article

(This article belongs to the Special Issue Emerging Viruses: Surveillance, Prevention, Evolution and Control)

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17 pages, 2348 KiB

Open AccessReview

Review on Outbreak Dynamics, the Endemic Serotypes, and Diversified Topotypic Profiles of Foot and Mouth Disease Virus Isolates in Ethiopia from 2008 to 2018

by Ashenafi Kiros Wubshet, Junfei Dai, Qian Li and Jie Zhang

Viruses 2019, 11(11), 1076; https://0-doi-org.brum.beds.ac.uk/10.3390/v11111076 - 18 Nov 2019

Cited by 17 | Viewed by 5859

Abstract

Foot and mouth disease (FMD) endemicity in Ethiopia’s livestock remains an ongoing cause for economic concern, with new topotypes still arising even in previously unaffected areas. FMD outbreaks occur every year almost throughout the country. Understanding the outbreak dynamics, endemic serotypes, and lineage [...] Read more.

Foot and mouth disease (FMD) endemicity in Ethiopia’s livestock remains an ongoing cause for economic concern, with new topotypes still arising even in previously unaffected areas. FMD outbreaks occur every year almost throughout the country. Understanding the outbreak dynamics, endemic serotypes, and lineage profiles of FMD in this country is very critical in designing control and prevention programs. For this, detailed information on outbreak dynamics in Ethiopia needs to be understood clearly. In this article, therefore, we review the spatial and temporal patterns and dynamics of FMD outbreaks from 2008 to 2018. The circulating serotypes and the topotypic profiles of the virus are also discussed. FMD outbreak data were obtained from; reports of MoARD (Ministry of Agriculture and Rural Development)/MoLF (Ministry of livestock and Fishery, NVI (National Veterinary Institute), and NAHDIC (National Animal Health Diagnostic and Investigation Center); published articles; MSc works; PhD theses; and documents from international organizations. To effectively control and prevent FMD outbreaks, animal health agencies should focus on building surveillance systems that can quickly identify and control ongoing outbreaks and implement efficient preventive measures. Full article

(This article belongs to the Special Issue Emerging Viruses: Surveillance, Prevention, Evolution and Control)

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12 pages, 490 KiB

Open AccessReview

Nosocomial Transmission of Emerging Viruses via Aerosol-Generating Medical Procedures

by Seth D. Judson and Vincent J. Munster

Viruses 2019, 11(10), 940; https://0-doi-org.brum.beds.ac.uk/10.3390/v11100940 - 12 Oct 2019

Cited by 214 | Viewed by 21534

Abstract

Recent nosocomial transmission events of emerging and re-emerging viruses, including Ebola virus, Middle East respiratory syndrome coronavirus, Nipah virus, and Crimean–Congo hemorrhagic fever orthonairovirus, have highlighted the risk of nosocomial transmission of emerging viruses in health-care settings. In particular, concerns and precautions have [...] Read more.

Recent nosocomial transmission events of emerging and re-emerging viruses, including Ebola virus, Middle East respiratory syndrome coronavirus, Nipah virus, and Crimean–Congo hemorrhagic fever orthonairovirus, have highlighted the risk of nosocomial transmission of emerging viruses in health-care settings. In particular, concerns and precautions have increased regarding the use of aerosol-generating medical procedures when treating patients with such viral infections. In spite of increasing associations between aerosol-generating medical procedures and the nosocomial transmission of viruses, we still have a poor understanding of the risks of specific procedures and viruses. In order to identify which aerosol-generating medical procedures and emerging viruses pose a high risk to health-care workers, we explore the mechanisms of aerosol-generating medical procedures, as well as the transmission pathways and characteristics of highly pathogenic viruses associated with nosocomial transmission. We then propose how research, both in clinical and experimental settings, could advance current infection control guidelines. Full article

(This article belongs to the Special Issue Emerging Viruses: Surveillance, Prevention, Evolution and Control)

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Other

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9 pages, 1800 KiB

Open AccessCase Report

Late-Relapsing Hepatitis after Yellow Fever

by Izabela Maurício Rezende, Leonardo Soares Pereira, Jordana Rodrigues Barbosa Fradico, Marcelo Antônio Pascoal Xavier, Pedro Augusto Alves, Ana Carolina Campi-Azevedo, Elaine Speziali, Lívia Zignago Moreira dos Santos, Natalia Soares Albuquerque, Indiara Penido, Tayrine Araujo Santos, Ana Paula Dinis Ano Bom, Andrea Marques Vieira da Silva, Camilla Bayma Fernandes, Carlos Eduardo Calzavara, Erna Geessien Kroon, Olindo Assis Martins-Filho, Andréa Teixeira-Carvalho and Betânia Paiva Drumond

Viruses 2020, 12(2), 222; https://0-doi-org.brum.beds.ac.uk/10.3390/v12020222 - 17 Feb 2020

Cited by 12 | Viewed by 3977

Abstract

One patient presented hyporexia, asthenia, adynamia, and jaundice two months after acute yellow fever (YF) onset; plus laboratory tests indicating hepatic cytolysis and a rebound of alanine and aspartate transaminases, and total and direct bilirubin levels. Laboratory tests discarded autoimmune hepatitis, inflammatory or [...] Read more.

One patient presented hyporexia, asthenia, adynamia, and jaundice two months after acute yellow fever (YF) onset; plus laboratory tests indicating hepatic cytolysis and a rebound of alanine and aspartate transaminases, and total and direct bilirubin levels. Laboratory tests discarded autoimmune hepatitis, inflammatory or metabolic liver disease, and new infections caused by hepatotropic agents. Anti-YFV IgM, IgG and neutralizing antibodies were detected in different times, but no viremia. A liver biopsy was collected three months after YF onset and tested positive for YFV antigens and wild-type YFV-RNA (364 RNA-copies/gram/liver). Transaminases and bilirubin levels remained elevated for five months, and the arresting of symptoms persisted for six months after the acute YF onset. Several serum chemokines, cytokines, and growth factors were measured. A similar immune response profile was observed in the earlier phases of the disease, followed by more pronounced changes in the later stages, when transaminases levels returned to normal. The results indicated viral persistence in the liver and continual liver cell damage three months after YF onset and reinforced the need for extended follow-ups of YF patients. Further studies to investigate the role of possible viral persistence and the immune response causing relapsing hepatitis following YF are also necessary. Full article

(This article belongs to the Special Issue Emerging Viruses: Surveillance, Prevention, Evolution and Control)

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10 pages, 1946 KiB

Open AccessBrief Report

Identification of a Novel Adélie Penguin Circovirus at Cape Crozier (Ross Island, Antarctica)

by Virginia Morandini, Katie M. Dugger, Grant Ballard, Megan Elrod, Annie Schmidt, Valeria Ruoppolo, Amélie Lescroël, Dennis Jongsomjit, Melanie Massaro, Jean Pennycook, Gerald L. Kooyman, Kara Schmidlin, Simona Kraberger, David G. Ainley and Arvind Varsani

Viruses 2019, 11(12), 1088; https://0-doi-org.brum.beds.ac.uk/10.3390/v11121088 - 22 Nov 2019

Cited by 20 | Viewed by 4898

Abstract

Understanding the causes of disease in Antarctic wildlife is crucial, as many of these species are already threatened by environmental changes brought about by climate change. In recent years, Antarctic penguins have been showing signs of an unknown pathology: a feather disorder characterised [...] Read more.

Understanding the causes of disease in Antarctic wildlife is crucial, as many of these species are already threatened by environmental changes brought about by climate change. In recent years, Antarctic penguins have been showing signs of an unknown pathology: a feather disorder characterised by missing feathers, resulting in exposed skin. During the 2018–2019 austral summer breeding season at Cape Crozier colony on Ross Island, Antarctica, we observed for the first time an Adélie penguin chick missing down over most of its body. A guano sample was collected from the nest of the featherless chick, and using high-throughput sequencing, we identified a novel circovirus. Using abutting primers, we amplified the full genome, which we cloned and Sanger-sequenced to determine the complete genome of the circovirus. The Adélie penguin guano-associated circovirus genome shares <67% genome-wide nucleotide identity with other circoviruses, representing a new species of circovirus; therefore, we named it penguin circovirus (PenCV). Using the same primer pair, we screened 25 previously collected cloacal swabs taken at Cape Crozier from known-age adult Adélie penguins during the 2014–2015 season, displaying no clinical signs of feather-loss disorder. Three of the 25 samples (12%) were positive for a PenCV, whose genome shared >99% pairwise identity with the one identified in 2018–2019. This is the first report of a circovirus associated with a penguin species. This circovirus could be an etiological agent of the feather-loss disorder in Antarctic penguins. Full article

(This article belongs to the Special Issue Emerging Viruses: Surveillance, Prevention, Evolution and Control)

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9 pages, 5773 KiB

Open AccessBrief Report

A Fusion Peptide in the Spike Protein of MERS Coronavirus

by Entedar A. J. Alsaadi, Benjamin W. Neuman and Ian M. Jones

Viruses 2019, 11(9), 825; https://0-doi-org.brum.beds.ac.uk/10.3390/v11090825 - 05 Sep 2019

Cited by 30 | Viewed by 8219

Abstract

Coronaviruses represent current and emerging threats for many species, including humans. Middle East respiratory syndrome-related coronavirus (MERS-CoV) is responsible for sporadic infections in mostly Middle Eastern countries, with occasional transfer elsewhere. A key step in the MERS-CoV replication cycle is the fusion of [...] Read more.

Coronaviruses represent current and emerging threats for many species, including humans. Middle East respiratory syndrome-related coronavirus (MERS-CoV) is responsible for sporadic infections in mostly Middle Eastern countries, with occasional transfer elsewhere. A key step in the MERS-CoV replication cycle is the fusion of the virus and host cell membranes mediated by the virus spike protein, S. The location of the fusion peptide within the MERS S protein has not been precisely mapped. We used isolated peptides and giant unilamellar vesicles (GUV) to demonstrate membrane binding for a peptide located near the N-terminus of the S2 domain. Key residues required for activity were mapped by amino acid replacement and their relevance in vitro tested by their introduction into recombinant MERS S protein expressed in mammalian cells. Mutations preventing membrane binding in vitro also abolished S-mediated syncytium formation consistent with the identified peptide acting as the fusion peptide for the S protein of MERS-CoV. Full article

(This article belongs to the Special Issue Emerging Viruses: Surveillance, Prevention, Evolution and Control)

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8 pages, 1087 KiB

Open AccessBrief Report

The Emergence of Avian Orthoavulavirus 13 in Wild Migratory Waterfowl in China Revealed the Existence of Diversified Trailer Region Sequences and HN Gene Lengths within this Serotype

by Yidong Fei, Xinxin Liu, Jiaqi Mu, Junjiao Li, Xibing Yu, Jin Chang, Yuhai Bi, Tobias Stoeger, Abdul Wajid, Denys Muzyka, Kirill Sharshov, Alexander Shestopalov, Alongkorn Amonsin, Jianjun Chen, Zhuang Ding and Renfu Yin

Viruses 2019, 11(7), 646; https://0-doi-org.brum.beds.ac.uk/10.3390/v11070646 - 13 Jul 2019

Cited by 11 | Viewed by 4452

Abstract

Avian orthoavulavirus 13 (AOAV-13), also named avian paramyxovirus 13 (APMV-13), has been found sporadically in wild birds around the world ever since the discovery of AOAV-13 (AOAV-13/wild goose/Shimane/67/2000) in a wild goose from Japan in 2000. However, there are no reports of AOAV-13 [...] Read more.

Avian orthoavulavirus 13 (AOAV-13), also named avian paramyxovirus 13 (APMV-13), has been found sporadically in wild birds around the world ever since the discovery of AOAV-13 (AOAV-13/wild goose/Shimane/67/2000) in a wild goose from Japan in 2000. However, there are no reports of AOAV-13 in China. In the present study, a novel AOAV-13 virus (AOAV-13/wild goose/China/Hubei/V93-1/2015), isolated from a wild migratory waterfowl in a wetland of Hubei province of China, during active surveillance from 2013 to 2018, was biologically and genetically characterized. Phylogenetic analyses demonstrated a very close genetic relationship among all AOAV-13 strains, as revealed by very few genetic variations. Moreover, pathogenicity tests indicated that the V93-1 strain is a low virulent virus for chickens. However, the genome of the V93-1 virus was found to be 16,158 nucleotides (nt) in length, which is 12 nt or 162 nt longer than the other AOAV-13 strains that have been reported to date. The length difference of 12 nt in strain V93-1 is due to the existence of three repeats of the conserved sequence, “AAAAAT”, in the 5′-end trailer of the genome. Moreover, the HN gene of the V93-1 virus is 2070 nt in size, encoding 610 aa, which is the same size as the AOAV-13 strain from Japan, whereas that of two strains from Ukraine and Kazakhstan are 2080 nt in length, encoding 579 aa. We describe a novel AOAV-13 in migratory waterfowl in China, which suggests that diversified trailer region sequences and HN gene lengths exist within serotype AOAV-13, and highlight the need for its constant surveillance in poultry from live animal markets, and especially migratory birds. Full article

(This article belongs to the Special Issue Emerging Viruses: Surveillance, Prevention, Evolution and Control)

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