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Strategies for Preventing Viral Epidemics and Pandemics

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A special issue of Viruses (ISSN 1999-4915). This special issue belongs to the section "Animal Viruses".

Deadline for manuscript submissions: closed (17 December 2021) | Viewed by 44495

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Special Issue Editors

Prof. Dr. Gregory Tannock

E-Mail Website
Guest Editor

Burnet Institute, Melbourne, VIC, Australia
Interests: influenza viruses; influenza vaccines; respiratory viruses; virus evolution

Dr. Hyunsuh Kim

E-Mail Website
Guest Editor

Department of Infectious Diseases, St. Jude Children’s Reaserch Hospital, Memphis, TN, USA
Interests: influenza viruses; influenza vaccines; vaccine production; B cells; antibodies

Special Issue Information

Dear Colleagues,

The first viral epidemic/pandemic of the 21st century due to the 2002–2004 SARS CoV-1 outbreak was followed by the 2009 H1N1 influenza pandemic and MERS-CoV outbreaks. Smaller, more localized outbreaks of West Nile, Ebola, enterovirus D68, Zika and Chikungunya viruses have occurred since 2005. However, all have been dwarfed—both in terms of their capacity to spread rapidly and to be the cause of life-threatening respiratory illnesses—by the ongoing pandemic of coronavirus disease (COVID-19). Many emerging viruses have zoonotic origins and rapid detection is essential to determine their likely epidemic and pandemic potential; novel surveillance systems have been established and maintained in many countries. The sheer significance of COVID-19 as a respiratory pathogen has led to hitherto unprecedented attempts to develop vaccines for general worldwide use by large numbers of manufacturers and associated research groups. Hopefully, all this activity will bear fruit despite clear evidence that vaccines against most human respiratory viral diseases constitute one of the greatest areas of need in human preventive medicine. The accelerated development of new diagnostic techniques is essential not only for their use in epidemiological studies but also for the development and use of antiviral drugs for the targeted inhibition of viral replication.

This Special Issue will gladly welcome articles pertaining to any of novel viruses and all viruses with epidemic and pandemic potential, such as influenza viruses, coronaviruses, Chikungunya viruses, Dengue viruses, Ebola viruses, Hantaviruses, Hendra viruses, Lassa viruses, Nipah viruses, West Nile viruses, Enteroviruses, Zika viruses and SFTSV, and comprising strategies and techniques to mitigate the epidemic and pandemic potential of viruses.

Prof. Dr. Gregory Tannock
Dr. Hyunsuh Kim
Guest Editors

Manuscript Submission Information

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Keywords

novel viruses
surveillance
discovery
diversity
variation
mutation
reassortment
resistance
geographic differences
epidemic
pandemic
diagnosis
antiviral drug
vaccine
antibody

Published Papers (10 papers)

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Research

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17 pages, 3409 KiB

Open AccessArticle

Epidemiology and Genetic Analysis of SARS-CoV-2 in Myanmar during the Community Outbreaks in 2020

by Wint Wint Phyu, Reiko Saito, Keita Wagatsuma, Takashi Abe, Htay Htay Tin, Eh Htoo Pe, Su Mon Kyaw Win, Nay Chi Win, Lasham Di Ja, Sekizuka Tsuyoshi, Kuroda Makoto, Yadanar Kyaw, Irina Chon, Shinji Watanabe, Hideki Hasegawa and Hisami Watanabe

Viruses 2022, 14(2), 259; https://0-doi-org.brum.beds.ac.uk/10.3390/v14020259 - 27 Jan 2022

Cited by 2 | Viewed by 2679

Abstract

We aimed to analyze the situation of the first two epidemic waves in Myanmar using the publicly available daily situation of COVID-19 and whole-genome sequencing data of SARS-CoV-2. From March 23 to December 31, 2020, there were 33,917 confirmed cases and 741 deaths in Myanmar (case fatality rate of 2.18%). The first wave in Myanmar from March to July was linked to overseas travel, and then a second wave started from Rakhine State, a western border state, leading to the second wave spreading countrywide in Myanmar from August to December 2020. The estimated effective reproductive number (R_t) nationwide reached 6–8 at the beginning of each wave and gradually decreased as the epidemic spread to the community. The whole-genome analysis of 10 Myanmar SARS-CoV-2 strains together with 31 previously registered strains showed that the first wave was caused by GISAID clade O or PANGOLIN lineage B.6 and the second wave was changed to clade GH or lineage B.1.36.16 with a close genetic relationship with other South Asian strains. Constant monitoring of epidemiological situations combined with SARS-CoV-2 genome analysis is important for adjusting public health measures to mitigate the community transmissions of COVID-19. Full article

(This article belongs to the Special Issue Strategies for Preventing Viral Epidemics and Pandemics)

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14 pages, 3339 KiB

Open AccessArticle

Bridging the Local Persistence and Long-Range Dispersal of Highly Pathogenic Avian Influenza Virus (HPAIv): A Case Study of HPAIv-Infected Sedentary and Migratory Wildfowls Inhabiting Infected Premises

by Dae-sung Yoo, Sung-Il Kang, Yu-Na Lee, Eun-Kyoung Lee, Woo-yuel Kim and Youn-Jeong Lee

Viruses 2022, 14(1), 116; https://0-doi-org.brum.beds.ac.uk/10.3390/v14010116 - 10 Jan 2022

Cited by 6 | Viewed by 2085

Abstract

The past two decades have seen the emergence of highly pathogenic avian influenza (HPAI) infections that are characterized as extremely contagious, with a high fatality rate in chickens, and humans; this has sparked considerable concerns for global health. Generally, the new variant of the HPAI virus crossed into various countries through wild bird migration, and persisted in the local environment through the interactions between wild and farmed birds. Nevertheless, no studies have found informative cases associated with connecting local persistence and long-range dispersal. During the 2016–2017 HPAI H5N6 epidemic in South Korea, we observed several waterfowls with avian influenza infection under telemetric monitoring. Based on the telemetry records and surveillance data, we conducted a case study to test hypotheses related to the transmission pathway between wild birds and poultry. One sedentary wildfowl naturally infected with HPAI H5N6, which overlapped with the home range of one migratory bird with H5-specific antibody-positive, showed itself to be phylogenetically close to the isolates from a chicken farm located within its habitat. Our study is the first observational study that provides scientific evidence supporting the hypothesis that the HPAI spillover into poultry farms is caused by local persistence in sedentary birds, in addition to its long-range dispersal by sympatric migratory birds. Full article

(This article belongs to the Special Issue Strategies for Preventing Viral Epidemics and Pandemics)

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11 pages, 4836 KiB

Open AccessArticle

Detection of a Novel Reassortant H9N9 Avian Influenza Virus in Free-Range Ducks in Bangladesh

by Rabeh El-Shesheny, Jasmine C. M. Turner, David Walker, John Franks, Patrick Seiler, Subrata Barman, Mohammed M. Feeroz, Md Kamrul Hasan, Sharmin Akhtar, Nabanita Mukherjee, Lisa Kercher, Pamela McKenzie, Robert G. Webster and Richard J. Webby

Viruses 2021, 13(12), 2357; https://0-doi-org.brum.beds.ac.uk/10.3390/v13122357 - 24 Nov 2021

Cited by 1 | Viewed by 1853

Abstract

Wild aquatic birds are the primary natural reservoir for influenza A viruses (IAVs). In this study, an A(H9N9) influenza A virus (A/duck/Bangladesh/44493/2020) was identified via routine surveillance in free-range domestic ducks in Bangladesh. Phylogenetic analysis of hemagglutinin showed that the H9N9 virus belonged to the Y439-like lineage. The HA gene had the highest nucleotide identity to A/Bean Goose (Anser fabalis)/South Korea/KNU 2019-16/2019 (H9N2). The other seven gene segments clustered within the Eurasian lineage. Full article

(This article belongs to the Special Issue Strategies for Preventing Viral Epidemics and Pandemics)

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17 pages, 2457 KiB

Open AccessArticle

Virucidal Efficacy of Blue LED and Far-UVC Light Disinfection against Feline Infectious Peritonitis Virus as a Model for SARS-CoV-2

by Amanda Gardner, Sayani Ghosh, Magdalena Dunowska and Gale Brightwell

Viruses 2021, 13(8), 1436; https://0-doi-org.brum.beds.ac.uk/10.3390/v13081436 - 23 Jul 2021

Cited by 9 | Viewed by 4284

Abstract

Transmission of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) occurs through respiratory droplets passed directly from person to person or indirectly through fomites, such as common use surfaces or objects. The aim of this study was to determine the virucidal efficacy of blue LED (405 nm) and far-UVC (222 nm) light in comparison to standard UVC (254 nm) irradiation for the inactivation of feline infectious peritonitis virus (FIPV) on different matrices as a model for SARS-CoV-2. Wet or dried FIPV on stainless steel, plastic, or paper discs, in the presence or absence of artificial saliva, were exposed to various wavelengths of light for different time periods (1–90 min). Dual activity of blue LED and far-UVC lights were virucidal for most wet and dried FIPV within 4 to 16 min on all matrices. Individual action of blue LED and far-UVC lights were virucidal for wet FIPV but required longer irradiation times (8–90 min) to reach a 4-log reduction. In comparison, LED (265 nm) and germicidal UVC (254 nm) were virucidal on almost all matrices for both wet and dried FIPV within 1 min exposure. UVC was more effective for the disinfection of surfaces as compared to blue LED and far-UVC individually or together. However, dual action of blue LED and far-UVC was virucidal. This combination of lights could be used as a safer alternative to traditional UVC. Full article

(This article belongs to the Special Issue Strategies for Preventing Viral Epidemics and Pandemics)

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11 pages, 855 KiB

Open AccessArticle

Comparison and Sensitivity Evaluation of Three Different Commercial Real-Time Quantitative PCR Kits for SARS-CoV-2 Detection

by Ana Banko, Gordana Petrovic, Danijela Miljanovic, Ana Loncar, Marija Vukcevic, Dragana Despot and Andja Cirkovic

Viruses 2021, 13(7), 1321; https://0-doi-org.brum.beds.ac.uk/10.3390/v13071321 - 08 Jul 2021

Cited by 30 | Viewed by 4686

Abstract

Real-time reverse transcription polymerase chain reaction (RT-qPCR) is the most sensitive and specific assay and, therefore, is the “gold standard” diagnostic method for the diagnosis of SARS-CoV-2 infection. The aim of this study was to compare and analyze the detection performance of three different commercially available SARS-CoV-2 nucleic acid detection kits: Sansure Biotech, GeneFinder^TM, and TaqPath^TM on 354 randomly selected samples from hospitalized COVID-19 patients. All PCR reactions were performed using the same RNA isolates and one real-time PCR machine. The final result of the three evaluated kits was not statistically different (p = 0.107), and also had a strong positive association and high Cohen’s κ coefficient. In contrast, the average Ct values that refer to the ORF1ab and N gene amplification were significantly different (p < 0.001 and p < 0.001, respectively), with the lowest obtained by the TaqPath^TM for the ORF1ab and by the Sansure Biotech for the N gene. The results show a high similarity in the analytical sensitivities for SARS-CoV-2 detection, which indicates that the diagnostic accuracy of the three assays is comparable. However, the SanSure Biotech kit showed a bit better diagnostic performance. Our findings suggest that the imperative for improvement should address the determination of cut-off Ct values and rapid modification of the primer sets along with the appearance of new variants. Full article

(This article belongs to the Special Issue Strategies for Preventing Viral Epidemics and Pandemics)

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11 pages, 1927 KiB

Open AccessArticle

Superiority of MALDI-TOF Mass Spectrometry over Real-Time PCR for SARS-CoV-2 RNA Detection

by Magda Rybicka, Ewa Miłosz and Krzysztof Piotr Bielawski

Viruses 2021, 13(5), 730; https://0-doi-org.brum.beds.ac.uk/10.3390/v13050730 - 22 Apr 2021

Cited by 31 | Viewed by 5221

Abstract

At present, the RT-PCR test remains the gold standard for early diagnosis of SARS-CoV-2. Nevertheless, there is growing evidence demonstrating that this technique may generate false-negative results. Here, we aimed to compare the new mass spectrometry-based assay MassARRAY^® SARS-CoV-2 Panel with the RT-PCR diagnostic test approved for clinical use. The study group consisted of 168 suspected patients with symptoms of a respiratory infection. After simultaneous analysis by RT-PCR and mass spectrometry methods, we obtained discordant results for 17 samples (10.12%). Within fifteen samples officially reported as presumptive positive, 13 were positive according to the MS-based assay. Moreover, four samples reported by the officially approved RT-PCR as negative were positive in at least one MS assay. We have successfully demonstrated superior sensitivity of the MS-based assay in SARS-CoV-2 detection, showing that MALDI-TOF MS seems to be ideal for the detection as well as discrimination of mutations within the viral genome. Full article

(This article belongs to the Special Issue Strategies for Preventing Viral Epidemics and Pandemics)

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Review

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18 pages, 1737 KiB

Open AccessReview

Influenza A and D Viruses in Non-Human Mammalian Hosts in Africa: A Systematic Review and Meta-Analysis

by Annie Kalonda, Marvin Phonera, Ngonda Saasa, Masahiro Kajihara, Catherine G. Sutcliffe, Hirofumi Sawa, Ayato Takada and Edgar Simulundu

Viruses 2021, 13(12), 2411; https://0-doi-org.brum.beds.ac.uk/10.3390/v13122411 - 02 Dec 2021

Cited by 4 | Viewed by 3192

Abstract

We conducted a systematic review and meta-analysis to investigate the prevalence and current knowledge of influenza A virus (IAV) and influenza D virus (IDV) in non-human mammalian hosts in Africa. PubMed, Google Scholar, Wiley Online Library and World Organisation for Animal Health (OIE-WAHIS) were searched for studies on IAV and IDV from 2000 to 2020. Pooled prevalence and seroprevalences were estimated using the quality effects meta-analysis model. The estimated pooled prevalence and seroprevalence of IAV in pigs in Africa was 1.6% (95% CI: 0–5%) and 14.9% (95% CI: 5–28%), respectively. The seroprevalence of IDV was 87.2% (95% CI: 24–100%) in camels, 9.3% (95% CI: 0–24%) in cattle, 2.2% (95% CI: 0–4%) in small ruminants and 0.0% (95% CI: 0–2%) in pigs. In pigs, H1N1 and H1N1pdm09 IAVs were commonly detected. Notably, the highly pathogenic H5N1 virus was also detected in pigs. Other subtypes detected serologically and/or virologically included H3N8 and H7N7 in equids, H1N1, and H3N8 and H5N1 in dogs and cats. Furthermore, various wildlife animals were exposed to different IAV subtypes. For prudent mitigation of influenza epizootics and possible human infections, influenza surveillance efforts in Africa should not neglect non-human mammalian hosts. The impact of IAV and IDV in non-human mammalian hosts in Africa deserves further investigation. Full article

(This article belongs to the Special Issue Strategies for Preventing Viral Epidemics and Pandemics)

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21 pages, 15989 KiB

Open AccessReview

Targeting Antigens for Universal Influenza Vaccine Development

by Quyen-Thi Nguyen and Young-Ki Choi

Viruses 2021, 13(6), 973; https://0-doi-org.brum.beds.ac.uk/10.3390/v13060973 - 24 May 2021

Cited by 14 | Viewed by 4175

Abstract

Traditional influenza vaccines generate strain-specific antibodies which cannot provide protection against divergent influenza virus strains. Further, due to frequent antigenic shifts and drift of influenza viruses, annual reformulation and revaccination are required in order to match circulating strains. Thus, the development of a universal influenza vaccine (UIV) is critical for long-term protection against all seasonal influenza virus strains, as well as to provide protection against a potential pandemic virus. One of the most important strategies in the development of UIVs is the selection of optimal targeting antigens to generate broadly cross-reactive neutralizing antibodies or cross-reactive T cell responses against divergent influenza virus strains. However, each type of target antigen for UIVs has advantages and limitations for the generation of sufficient immune responses against divergent influenza viruses. Herein, we review current strategies and perspectives regarding the use of antigens, including hemagglutinin, neuraminidase, matrix proteins, and internal proteins, for universal influenza vaccine development. Full article

(This article belongs to the Special Issue Strategies for Preventing Viral Epidemics and Pandemics)

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9 pages, 641 KiB

Open AccessReview

Evaluating the Virucidal Activity of Disinfectants According to European Union Standards

by Patryk Tarka and Aneta Nitsch-Osuch

Viruses 2021, 13(4), 534; https://0-doi-org.brum.beds.ac.uk/10.3390/v13040534 - 24 Mar 2021

Cited by 17 | Viewed by 6428

Abstract

The disinfection of surfaces in medical facilities is an important element of infection control, including the control of viral infections such as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Preparations used for surface disinfection are typically characterized via their activity against test organisms (i.e., viruses, bacteria and fungi) in the laboratory. Typically, these methods use a suspension of the test organism to assess the bactericidal, fungicidal or virucidal activity of a given preparation. However, such suspension methods do not fully imitate real-life conditions. To address this issue, carrier methods have been developed, in which microorganisms are applied to the surface of a carrier (e.g., stainless steel, glass and polyvinyl chloride (PVC)) and then dried. Such methods more accurately reflect the applications in real-life clinical practice. This article summarizes the available methods for assessing the virucidal activity of chemical disinfectants for use in medical facilities based on the current European standards, including the activity against coronaviruses. Full article

(This article belongs to the Special Issue Strategies for Preventing Viral Epidemics and Pandemics)

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Other

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18 pages, 621 KiB

Open AccessCommentary

Effective Communication at Different Phases of COVID-19 Prevention: Roles, Enablers and Barriers

by Khayriyyah Mohd Hanafiah, Celine Ng and Abdul Matiin Wan

Viruses 2021, 13(6), 1058; https://0-doi-org.brum.beds.ac.uk/10.3390/v13061058 - 03 Jun 2021

Cited by 10 | Viewed by 8382

Abstract

In an age of globalisation and hyperconnectivity, the COVID-19 pandemic has caused unprecedented and sustained impact worldwide. This article discusses issues related to (science) communication at different phases of the COVID-19 epidemic timeline. We consider the role of communication for prevention from the ecological perspective, taking into consideration that many emerging pathogens, including COVID-19, likely arise in part due to anthropogenic changes to natural environments. Communication forms part of the early response setting the scene for public buy-in of public health interventions at the start of an outbreak, as well as to maintain precautions over time. Finally, communication is a key element in increasing acceptance for new tools that require mass uptake to be effective, as seen with roll-out challenges for the COVID-19 vaccines, which faced heightened concerns of efficacy and safety while mired with rampant misinformation. Ultimately, strategies for prevention of viral epidemics such as COVID-19 must include communication strategies at the forefront to reduce the risk of the emergence of new diseases and enhance efforts to control their spread and burden. Despite key themes emerging, what constitutes effective communication strategies for different people and contexts needs to be investigated further. Full article

(This article belongs to the Special Issue Strategies for Preventing Viral Epidemics and Pandemics)

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