Viral Cross-Species Transmission

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

Deadline for manuscript submissions: closed (10 December 2021) | Viewed by 30727

Special Issue Editor

Professor Caswell Eidson Chair in Poultry Medicine, CVI Affiliated Faculty, Georgia Research Alliance Distinguished Investigator College of Veterinary Medicine, Animal Health Research Center, Center for Vaccines and Immunology, Poultry Diagnostic and Research Center, University of Georgia, Athens, GA, USA
Interests: influenza viruses; emerging viruses; interspecies transmission of viral pathogens; virus entry and replication; virus host-range; virus ecology and evolution
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Today, more than ever, we recognize the importance of understanding the molecular mechanisms and environmental factors that lead to species jump of viral pathogens. From a primordial wild animal reservoir to potential intermediary hosts, viral pathogens are constantly emerging with the capacity of threatening agriculture and causing zoonotic outbreaks and pandemics. The recent emergence of zoonotic and pandemic influenza viruses and coronaviruses are constant reminders of the relevance of studying viral pathogens at the animal–human interface. More importantly, the emergence of the SARS-CoV-2 pandemic virus, the causative agent of COVID-19 disease, highlights the significance of better characterizing animal reservoirs of potentially pandemic pathogens that could affect the food supply or threaten human life. There is an urgent need to better understand the virus–host interactions that modulate host receptor recognition, virus entry, replication, virulence, and host immune responses that tilt the balance between survival and death upon infection. Equally important is the development of both rapid and metagenomics tests and platforms to more efficiently identify viral pathogens with inherent zoonotic or pandemic potential. Overall, such understanding and novel methods will contribute to better prevention, control, and intervention and management strategies of emerging diseases in both animals and humans.

This Special Issue seeks all types of manuscripts (e.g., reviews, research articles, and short communications) on virus–host interactions at the animal–animal and animal–human interface that lead to species jump and the emergence of zoonotic or pandemic viruses. Both basic and applied research work are welcomed that aim to improve understanding of interspecies transmission of viral pathogens, pathogenesis, short- and long-term effects of host-responses to novel pathogens, improved diagnostic methods, and intervention strategies for the prevention and management of zoonotic and pandemic pathogens.

Dr. Daniel R Perez
Guest Editor

Manuscript Submission Information

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Keywords

  • zoonotic viruses
  • animal reservoirs
  • virus–host interactions
  • interspecies transmission

Published Papers (10 papers)

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Research

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12 pages, 1370 KiB  
Article
The Myotis chiloensis Guano Virome: Viral Nucleic Acid Enrichments for High-Resolution Virome Elucidation and Full Alphacoronavirus Genome Assembly
by Sebastian Aguilar Pierlé, Gabriel Zamora, Gonzalo Ossa, Aldo Gaggero and Gonzalo P. Barriga
Viruses 2022, 14(2), 202; https://0-doi-org.brum.beds.ac.uk/10.3390/v14020202 - 20 Jan 2022
Cited by 4 | Viewed by 2867
Abstract
Bats are widespread mammals of the order Chiroptera. They are key for ecosystem functioning, participating in crucial processes. Their unique ability amongst mammals to fly long distances, their frequently large population sizes, and their longevity favor infectious agent persistence and spread. This includes [...] Read more.
Bats are widespread mammals of the order Chiroptera. They are key for ecosystem functioning, participating in crucial processes. Their unique ability amongst mammals to fly long distances, their frequently large population sizes, and their longevity favor infectious agent persistence and spread. This includes a large variety of viruses, encompassing many important zoonotic ones that cause severe diseases in humans and domestic animals. Despite this, the understanding of the viral ecological diversity residing in bat populations remains unclear, which complicates the determination of the origins of zoonotic viruses. To gain knowledge on the viral community of a widely distributed insectivorous bat species, we characterized the guano virome of a native Chilean bat species (Myotis chiloensis (Waterhouse, 1840)). By applying a novel enrichment strategy, we were able to secure a consequent percentage of viral reads, providing unprecedented resolution for a bat virome. This in turn enabled us to identify and assemble a new bat alphacoronavirus from Chilean bats closely related to PEDV, an important viral pathogen with high mortality rates in suckling piglets. This study highlights the importance of applying and improving high-resolution virome studies in this vital order to ultimately enhance epidemiological surveillance for potentially zoonotic pathogens. Full article
(This article belongs to the Special Issue Viral Cross-Species Transmission)
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21 pages, 3342 KiB  
Article
A Novel Terrestrial Rabies Virus Lineage Occurring in South America: Origin, Diversification, and Evidence of Contact between Wild and Domestic Cycles
by Diego A. Caraballo, Cristina Lema, Laura Novaro, Federico Gury-Dohmen, Susana Russo, Fernando J. Beltrán, Gustavo Palacios and Daniel M. Cisterna
Viruses 2021, 13(12), 2484; https://0-doi-org.brum.beds.ac.uk/10.3390/v13122484 - 11 Dec 2021
Cited by 6 | Viewed by 3187
Abstract
The rabies virus (RABV) is characterized by a history dominated by host shifts within and among bats and carnivores. One of the main outcomes of long-term RABV maintenance in dogs was the establishment of variants in a wide variety of mesocarnivores. In this [...] Read more.
The rabies virus (RABV) is characterized by a history dominated by host shifts within and among bats and carnivores. One of the main outcomes of long-term RABV maintenance in dogs was the establishment of variants in a wide variety of mesocarnivores. In this study, we present the most comprehensive phylogenetic and phylogeographic analysis, contributing to a better understanding of the origins, diversification, and the role of different host species in the evolution and diffusion of a dog-related variant endemic of South America. A total of 237 complete Nucleoprotein gene sequences were studied, corresponding to wild and domestic species, performing selection analyses, ancestral states reconstructions, and recombination analyses. This variant originated in Brazil and disseminated through Argentina and Paraguay, where a previously unknown lineage was found. A single host shift was identified in the phylogeny, from dog to the crab-eating fox (Cerdocyon thous) in the Northeast of Brazil. Although this process occurred in a background of purifying selection, there is evidence of adaptive evolution -or selection of sub-consensus sequences- in internal branches after the host shift. The interaction of domestic and wild cycles persisted after host switching, as revealed by spillover and putative recombination events. Full article
(This article belongs to the Special Issue Viral Cross-Species Transmission)
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15 pages, 1922 KiB  
Article
Severe SARS-CoV-2 Infection in a Cat with Hypertrophic Cardiomyopathy
by Francisco R. Carvallo, Mathias Martins, Lok R. Joshi, Leonardo C. Caserta, Patrick K. Mitchell, Thomas Cecere, Sandy Hancock, Erin L. Goodrich, Julia Murphy and Diego G. Diel
Viruses 2021, 13(8), 1510; https://0-doi-org.brum.beds.ac.uk/10.3390/v13081510 - 31 Jul 2021
Cited by 25 | Viewed by 2766
Abstract
Coronavirus disease 19 (COVID-19), has claimed millions of human lives worldwide since the emergence of the zoonotic severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in China in December 2019. Notably, most severe and fatal SARS-CoV-2 infections in humans have been associated with underlying [...] Read more.
Coronavirus disease 19 (COVID-19), has claimed millions of human lives worldwide since the emergence of the zoonotic severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in China in December 2019. Notably, most severe and fatal SARS-CoV-2 infections in humans have been associated with underlying clinical conditions, including diabetes, hypertension and heart diseases. Here, we describe a case of severe SARS-CoV-2 infection in a domestic cat (Felis catus) that presented with hypertrophic cardiomyopathy (HCM), a chronic heart condition that has been described as a comorbidity of COVID-19 in humans and that is prevalent in domestic cats. The lung and heart of the affected cat presented clear evidence of SARS-CoV-2 replication, with histological lesions similar to those observed in humans with COVID-19 with high infectious viral loads being recovered from these organs. The study highlights the potential impact of comorbidities on the outcome of SARS-CoV-2 infection in animals and provides important information that may contribute to the development of a feline model with the potential to recapitulate the clinical outcomes of severe COVID-19 in humans. Full article
(This article belongs to the Special Issue Viral Cross-Species Transmission)
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11 pages, 1126 KiB  
Article
Intravenous, Intratracheal, and Intranasal Inoculation of Swine with SARS-CoV-2
by Alexandra Buckley, Shollie Falkenberg, Mathias Martins, Melissa Laverack, Mitchell V. Palmer, Kelly Lager and Diego G. Diel
Viruses 2021, 13(8), 1506; https://0-doi-org.brum.beds.ac.uk/10.3390/v13081506 - 30 Jul 2021
Cited by 10 | Viewed by 2359
Abstract
Since the emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the susceptibility of animals and their potential to act as reservoirs or intermediate hosts for the virus has been of significant interest. Pigs are susceptible to multiple coronaviruses and have been used [...] Read more.
Since the emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the susceptibility of animals and their potential to act as reservoirs or intermediate hosts for the virus has been of significant interest. Pigs are susceptible to multiple coronaviruses and have been used as an animal model for other human infectious diseases. Research groups have experimentally challenged swine with human SARS-CoV-2 isolates with results suggesting limited to no viral replication. For this study, a SARS-CoV-2 isolate obtained from a tiger which is identical to human SARS-CoV-2 isolates detected in New York City and contains the D614G S mutation was utilized for inoculation. Pigs were challenged via intravenous, intratracheal, or intranasal routes of inoculation (n = 4/route). No pigs developed clinical signs, but at least one pig in each group had one or more PCR positive nasal/oral swabs or rectal swabs after inoculation. All pigs in the intravenous group developed a transient neutralizing antibody titer, but only three other challenged pigs developed titers greater than 1:8. No gross or histologic changes were observed in tissue samples collected at necropsy. In addition, no PCR positive samples were positive by virus isolation. Inoculated animals were unable to transmit virus to naïve contact animals. The data from this experiment as well as from other laboratories supports that swine are not likely to play a role in the epidemiology and spread of SARS-CoV-2. Full article
(This article belongs to the Special Issue Viral Cross-Species Transmission)
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17 pages, 2843 KiB  
Article
Avian Influenza A Viruses Reassort and Diversify Differently in Mallards and Mammals
by Ketaki Ganti, Anish Bagga, Juliana DaSilva, Samuel S. Shepard, John R. Barnes, Susan Shriner, Katia Koelle and Anice C. Lowen
Viruses 2021, 13(3), 509; https://0-doi-org.brum.beds.ac.uk/10.3390/v13030509 - 19 Mar 2021
Cited by 12 | Viewed by 4027
Abstract
Reassortment among co-infecting influenza A viruses (IAVs) is an important source of viral diversity and can facilitate expansion into novel host species. Indeed, reassortment played a key role in the evolution of the last three pandemic IAVs. Observed patterns of reassortment within a [...] Read more.
Reassortment among co-infecting influenza A viruses (IAVs) is an important source of viral diversity and can facilitate expansion into novel host species. Indeed, reassortment played a key role in the evolution of the last three pandemic IAVs. Observed patterns of reassortment within a coinfected host are likely to be shaped by several factors, including viral load, the extent of viral mixing within the host and the stringency of selection. These factors in turn are expected to vary among the diverse host species that IAV infects. To investigate host differences in IAV reassortment, here we examined reassortment of two distinct avian IAVs within their natural host (mallards) and a mammalian model system (guinea pigs). Animals were co-inoculated with A/wildbird/California/187718-36/2008 (H3N8) and A/mallard/Colorado/P66F1-5/2008 (H4N6) viruses. Longitudinal samples were collected from the cloaca of mallards or the nasal tract of guinea pigs and viral genetic exchange was monitored by genotyping clonal isolates from these samples. Relative to those in guinea pigs, viral populations in mallards showed higher frequencies of reassortant genotypes and were characterized by higher genotype richness and diversity. In line with these observations, analysis of pairwise segment combinations revealed lower linkage disequilibrium in mallards as compared to guinea pigs. No clear longitudinal patterns in richness, diversity or linkage disequilibrium were present in either host. Our results reveal mallards to be a highly permissive host for IAV reassortment and suggest that reduced viral mixing limits avian IAV reassortment in a mammalian host. Full article
(This article belongs to the Special Issue Viral Cross-Species Transmission)
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15 pages, 1888 KiB  
Article
Experimental Inoculation of Young Calves with SARS-CoV-2
by Shollie Falkenberg, Alexandra Buckley, Melissa Laverack, Mathias Martins, Mitchell V. Palmer, Kelly Lager and Diego G. Diel
Viruses 2021, 13(3), 441; https://0-doi-org.brum.beds.ac.uk/10.3390/v13030441 - 09 Mar 2021
Cited by 29 | Viewed by 2817
Abstract
The host range of SARS-CoV-2 and the susceptibility of animal species to the virus are topics of great interest to the international scientific community. The angiotensin I converting enzyme 2 (ACE2) protein is the major receptor for the virus, and sequence and structural [...] Read more.
The host range of SARS-CoV-2 and the susceptibility of animal species to the virus are topics of great interest to the international scientific community. The angiotensin I converting enzyme 2 (ACE2) protein is the major receptor for the virus, and sequence and structural analysis of the protein has been performed to determine its cross-species conservation. Based on these analyses, cattle have been implicated as a potential susceptible species to SARS-CoV-2 and have been reported to have increased ACE2 receptor distribution in the liver and kidney, and lower levels in the lungs. The goal of the current study was to determine the susceptibility of cattle to SARS-CoV-2 utilizing inoculation routes that facilitated exposure to tissues with increased ACE2 receptor distribution. For this, colostrum-deprived calves approximately 6 weeks of age were inoculated via the intratracheal or intravenous routes. Nasal and rectal swab samples, as well as blood and urine samples, were collected over the course of the study to evaluate viral shedding, viremia, and seroconversion. Pyrexia was used as the primary criteria for euthanasia and tissue samples were collected during necropsy. Importantly, SARS-CoV-2 RNA was detected in only two nasal swab samples collected on days 3 and 10 post-inoculation (pi) in two calves; one calf in the intratracheal group and the other calf in the intravenous group, respectively. Additionally, the calf in the intratracheal group that was positive on the nasal swab on day 3 pi also had a positive tracheobronchial lymph node on day 9 pi. Viral nucleic acid load on these samples, based on PCR cycle threshold values, were low and infectious virus was not recovered from the samples. These results suggest that there was no productive replication of SARS-CoV-2 in calves following intratracheal and intravenous inoculation. Full article
(This article belongs to the Special Issue Viral Cross-Species Transmission)
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12 pages, 1971 KiB  
Article
Gaps in Serologic Immunity against Contemporary Swine-Origin Influenza A Viruses among Healthy Individuals in the United States
by Joshua N. Lorbach, Theresa Fitzgerald, Carolyn Nolan, Jacqueline M. Nolting, John J. Treanor, David J. Topham and Andrew S. Bowman
Viruses 2021, 13(1), 127; https://0-doi-org.brum.beds.ac.uk/10.3390/v13010127 - 18 Jan 2021
Cited by 4 | Viewed by 2360
Abstract
Influenza A Viruses (IAV) in domestic swine (IAV-S) are associated with sporadic zoonotic transmission at the human–animal interface. Previous pandemic IAVs originated from animals, which emphasizes the importance of characterizing human immunity against the increasingly diverse IAV-S. We analyzed serum samples from healthy [...] Read more.
Influenza A Viruses (IAV) in domestic swine (IAV-S) are associated with sporadic zoonotic transmission at the human–animal interface. Previous pandemic IAVs originated from animals, which emphasizes the importance of characterizing human immunity against the increasingly diverse IAV-S. We analyzed serum samples from healthy human donors (n = 153) using hemagglutination-inhibition (HAI) assay to assess existing serologic protection against a panel of contemporary IAV-S isolated from swine in the United States (n = 11). Age-specific seroprotection rates (SPR), which are the proportion of individuals with HAI ≥ 1:40, corresponded with lower or moderate pandemic risk classifications for the multiple IAV-S examined (one H1-δ1, one H1-δ2, three H3-IVA, one H3-IVB, one H3-IVF). Individuals born between 2004 and 2013 had SPRs of 0% for the five classified H3 subtype IAV-S, indicating youth may be particularly predisposed to infection with these viruses. Expansion of existing immunologic gaps over time could increase likelihood of future IAV-S spillover to humans and facilitate subsequent sustained human-to-human transmission resulting in disease outbreaks with pandemic potential. Full article
(This article belongs to the Special Issue Viral Cross-Species Transmission)
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18 pages, 27734 KiB  
Article
Interface between Bats and Pigs in Heavy Pig Production
by Stefania Leopardi, Pamela Priori, Barbara Zecchin, Gianpiero Zamperin, Adelaide Milani, Francesco Tonon, Mirco Giorgiutti, Maria Serena Beato and Paola De Benedictis
Viruses 2021, 13(1), 4; https://0-doi-org.brum.beds.ac.uk/10.3390/v13010004 - 22 Dec 2020
Cited by 5 | Viewed by 2393
Abstract
Bats are often claimed to be a major source for future viral epidemics, as they are associated with several viruses with zoonotic potential. Here we describe the presence and biodiversity of bats associated with intensive pig farms devoted to the production of heavy [...] Read more.
Bats are often claimed to be a major source for future viral epidemics, as they are associated with several viruses with zoonotic potential. Here we describe the presence and biodiversity of bats associated with intensive pig farms devoted to the production of heavy pigs in northern Italy. Since chiropters or signs of their presence were not found within animal shelters in our study area, we suggest that fecal viruses with high environmental resistance have the highest likelihood for spillover through indirect transmission. In turn, we investigated the circulation of mammalian orthoreoviruses (MRVs), coronaviruses (CoVs) and astroviruses (AstVs) in pigs and bats sharing the same environment. Results of our preliminary study did not show any bat virus in pigs suggesting that spillover from these animals is rare. However, several AstVs, CoVs and MRVs circulated undetected in pigs. Among those, one MRV was a reassortant strain carrying viral genes likely acquired from bats. On the other hand, we found a swine AstV and a MRV strain carrying swine genes in bat guano, indicating that viral exchange at the bat–pig interface might occur more frequently from pigs to bats rather than the other way around. Considering the indoor farming system as the most common system in the European Union (EU), preventive measures should focus on biosecurity rather than displacement of bats, which are protected throughout the EU and provide critical ecosystem services for rural settings. Full article
(This article belongs to the Special Issue Viral Cross-Species Transmission)
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Review

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18 pages, 679 KiB  
Review
Key Factors That Enable the Pandemic Potential of RNA Viruses and Inter-Species Transmission: A Systematic Review
by Santiago Alvarez-Munoz, Nicolas Upegui-Porras, Arlen P. Gomez and Gloria Ramirez-Nieto
Viruses 2021, 13(4), 537; https://0-doi-org.brum.beds.ac.uk/10.3390/v13040537 - 24 Mar 2021
Cited by 14 | Viewed by 2867
Abstract
Viruses play a primary role as etiological agents of pandemics worldwide. Although there has been progress in identifying the molecular features of both viruses and hosts, the extent of the impact these and other factors have that contribute to interspecies transmission and their [...] Read more.
Viruses play a primary role as etiological agents of pandemics worldwide. Although there has been progress in identifying the molecular features of both viruses and hosts, the extent of the impact these and other factors have that contribute to interspecies transmission and their relationship with the emergence of diseases are poorly understood. The objective of this review was to analyze the factors related to the characteristics inherent to RNA viruses accountable for pandemics in the last 20 years which facilitate infection, promote interspecies jump, and assist in the generation of zoonotic infections with pandemic potential. The search resulted in 48 research articles that met the inclusion criteria. Changes adopted by RNA viruses are influenced by environmental and host-related factors, which define their ability to adapt. Population density, host distribution, migration patterns, and the loss of natural habitats, among others, have been associated as factors in the virus–host interaction. This review also included a critical analysis of the Latin American context, considering its diverse and unique social, cultural, and biodiversity characteristics. The scarcity of scientific information is striking, thus, a call to local institutions and governments to invest more resources and efforts to the study of these factors in the region is key. Full article
(This article belongs to the Special Issue Viral Cross-Species Transmission)
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20 pages, 3910 KiB  
Review
Virulence during Newcastle Disease Viruses Cross Species Adaptation
by Claudio L. Afonso
Viruses 2021, 13(1), 110; https://0-doi-org.brum.beds.ac.uk/10.3390/v13010110 - 15 Jan 2021
Cited by 24 | Viewed by 3442
Abstract
The hypothesis that host adaptation in virulent Newcastle disease viruses (NDV) has been accompanied by virulence modulation is reviewed here. Historical records, experimental data, and phylogenetic analyses from available GenBank sequences suggest that currently circulating NDVs emerged in the 1920–1940′s from low virulence [...] Read more.
The hypothesis that host adaptation in virulent Newcastle disease viruses (NDV) has been accompanied by virulence modulation is reviewed here. Historical records, experimental data, and phylogenetic analyses from available GenBank sequences suggest that currently circulating NDVs emerged in the 1920–1940′s from low virulence viruses by mutation at the fusion protein cleavage site. These viruses later gave rise to multiple virulent genotypes by modulating virulence in opposite directions. Phylogenetic and pathotyping studies demonstrate that older virulent NDVs further evolved into chicken-adapted genotypes by increasing virulence (velogenic-viscerotropic pathotypes with intracerebral pathogenicity indexes [ICPIs] of 1.6 to 2), or into cormorant-adapted NDVs by moderating virulence (velogenic–neurotropic pathotypes with ICPIs of 1.4 to 1.6), or into pigeon-adapted viruses by further attenuating virulence (mesogenic pathotypes with ICPIs of 0.9 to 1.4). Pathogenesis and transmission experiments on adult chickens demonstrate that chicken-adapted velogenic-viscerotropic viruses are more capable of causing disease than older velogenic-neurotropic viruses. Currently circulating velogenic–viscerotropic viruses are also more capable of replicating and of being transmitted in naïve chickens than viruses from cormorants and pigeons. These evolutionary virulence changes are consistent with theories that predict that virulence may evolve in many directions in order to achieve maximum fitness, as determined by genetic and ecologic constraints. Full article
(This article belongs to the Special Issue Viral Cross-Species Transmission)
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