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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 (30 April 2023) | Viewed by 28113

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Prof. Dr. Xinglou Yang

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Guest Editor

Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650023, China
Interests: bat and rodent virus discovery; virus isolation; virus–host interaction; viral pathogenesis; viral ecology; emerging infectious diseases; attenuated and inactivated vaccines
Special Issues, Collections and Topics in MDPI journals

Dr. Ben Hu

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Guest Editor

CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
Interests: bat and rodent virus discovery; evolution

Special Issue Information

Dear Colleagues,

Bats, uniquely capable of self-powered flight, are the second most diverse mammalian order, with more than 1,400 species on Earth. More than 64 million years of adaptive evolution have endowed bats with specific characteristics including longevity, social roosting, and immune system, which also shape an ideal reservoir for viruses. During the past few decades, research mainly focused on bat-borne virus discovery which was reactive because of human and/or animal disease outbreak investigation. The fields of bat virus pathology, ecology, and molecular biology are still nascent, with many questions largely unexplored, hence hindering our ability to prepare for the future viral outbreaks. In this Special Issue, we welcome researchers to share their results about bat-borne virome, virus pathology, ecology, and molecular biology study for collaboration in fighting future bat virus outbreaks.

Prof. Dr. Xinglou Yang
Dr. Ben Hu
Guest Editors

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Keywords

bat virome
virus discovery
virus ecology
coronavirus
filovirus
paramyxovirus

Published Papers (12 papers)

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17 pages, 5727 KiB

Open AccessArticle

Genomic Surveillance of Rabies Virus in Georgian Canines

by Celeste Huaman, Adrian C. Paskey, Caitlyn Clouse, Austin Feasley, Madeline Rader, Gregory K. Rice, Andrea E. Luquette, Maren C. Fitzpatrick, Hannah M. Drumm, Lianying Yan, Regina Z. Cer, Marina Donduashvili, Tamar Buchukuri, Anna Nanava, Christine E. Hulseberg, Michael A. Washington, Eric D. Laing, Francisco Malagon, Christopher C. Broder, Kimberly A. Bishop-Lilly and Brian C. Schaefer Show full author list Hide full author list

Viruses 2023, 15(9), 1797; https://doi.org/10.3390/v15091797 - 24 Aug 2023

Viewed by 1365

Abstract

Rabies is a fatal zoonosis that is considered a re-emerging infectious disease. Although rabies remains endemic in canines throughout much of the world, vaccination programs have essentially eliminated dog rabies in the Americas and much of Europe. However, despite the goal of eliminating dog rabies in the European Union by 2020, sporadic cases of dog rabies still occur in Eastern Europe, including Georgia. To assess the genetic diversity of the strains recently circulating in Georgia, we sequenced seventy-eight RABV-positive samples from the brain tissues of rabid dogs and jackals using Illumina short-read sequencing of total RNA shotgun libraries. Seventy-seven RABV genomes were successfully assembled and annotated, with seventy-four of them reaching the coding-complete status. Phylogenetic analyses of the nucleoprotein (N) and attachment glycoprotein (G) genes placed all the assembled genomes into the Cosmopolitan clade, consistent with the Georgian origin of the samples. An amino acid alignment of the G glycoprotein ectodomain identified twelve different sequences for this domain among the samples. Only one of the ectodomain groups contained a residue change in an antigenic site, an R264H change in the G5 antigenic site. Three isolates were cultured, and these were found to be efficiently neutralized by the human monoclonal antibody A6. Overall, our data show that recently circulating RABV isolates from Georgian canines are predominantly closely related phylogroup I viruses of the Cosmopolitan clade. Current human rabies vaccines should offer protection against infection by Georgian canine RABVs. The genomes have been deposited in GenBank (accessions: OQ603609-OQ603685). Full article

(This article belongs to the Special Issue Bat-Borne Viruses Research)

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13 pages, 2918 KiB

Open AccessEditor’s ChoiceArticle

Development of a Pan-Filoviridae SYBR Green qPCR Assay for Biosurveillance Studies in Bats

by Jessica Coertse, Marinda Mortlock, Antoinette Grobbelaar, Naazneen Moolla, Wanda Markotter and Jacqueline Weyer

Viruses 2023, 15(4), 987; https://doi.org/10.3390/v15040987 - 17 Apr 2023

Viewed by 1667

Abstract

Recent studies have indicated that bats are hosts to diverse filoviruses. Currently, no pan-filovirus molecular assays are available that have been evaluated for the detection of all mammalian filoviruses. In this study, a two-step pan-filovirus SYBR Green real-time PCR assay targeting the nucleoprotein gene was developed for filovirus surveillance in bats. Synthetic constructs were designed as representatives of nine filovirus species and used to evaluate the assay. This assay detected all synthetic constructs included with an analytical sensitivity of 3–31.7 copies/reaction and was evaluated against the field collected samples. The assay’s performance was similar to a previously published probe based assay for detecting Ebola- and Marburgvirus. The developed pan-filovirus SYBR Green assay will allow for more affordable and sensitive detection of mammalian filoviruses in bat samples. Full article

(This article belongs to the Special Issue Bat-Borne Viruses Research)

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10 pages, 1386 KiB

Open AccessArticle

Genomic Characterization of a Relative of Mumps Virus in Lesser Dawn Bats of Southeast Asia

by Adrian C. Paskey, Xiao Fang Lim, Justin H. J. Ng, Gregory K. Rice, Wan Ni Chia, Casandra W. Philipson, Randy Foo, Regina Z. Cer, Kyle A. Long, Matthew R. Lueder, Lindsay Glang, Kenneth G. Frey, Theron Hamilton, Ian H. Mendenhall, Gavin J. Smith, Danielle E. Anderson, Lin-Fa Wang and Kimberly A. Bishop-Lilly

Viruses 2023, 15(3), 659; https://doi.org/10.3390/v15030659 - 28 Feb 2023

Viewed by 1745

Abstract

The importance of genomic surveillance on emerging diseases continues to be highlighted with the ongoing SARS-CoV-2 pandemic. Here, we present an analysis of a new bat-borne mumps virus (MuV) in a captive colony of lesser dawn bats (Eonycteris spelaea). This report describes an investigation of MuV-specific data originally collected as part of a longitudinal virome study of apparently healthy, captive lesser dawn bats in Southeast Asia (BioProject ID PRJNA561193) which was the first report of a MuV-like virus, named dawn bat paramyxovirus (DbPV), in bats outside of Africa. More in-depth analysis of these original RNA sequences in the current report reveals that the new DbPV genome shares only 86% amino acid identity with the RNA-dependent RNA polymerase of its closest relative, the African bat-borne mumps virus (AbMuV). While there is no obvious immediate cause for concern, it is important to continue investigating and monitoring bat-borne MuVs to determine the risk of human infection. Full article

(This article belongs to the Special Issue Bat-Borne Viruses Research)

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15 pages, 2032 KiB

Open AccessCommunication

Taiwan Bat Lyssavirus: In Vitro and In Vivo Assessment of the Ability of Rabies Vaccine-Derived Antibodies to Neutralise a Novel Lyssavirus

by Rebecca Shipley, Edward Wright, Samuel P. Smith, David Selden, Anthony R. Fooks and Ashley C. Banyard

Viruses 2022, 14(12), 2750; https://doi.org/10.3390/v14122750 - 9 Dec 2022

Cited by 2 | Viewed by 1841

Abstract

Rabies is a neglected tropical disease. The prototype virus, the rabies virus, still causes tens of thousands of human fatalities annually. Rabies is one member of the genus Lyssavirus. The burden of other lyssaviruses is unclear. The continued emergence of novel lyssaviruses means that assessment of vaccine efficacy against these viruses is critical, as standard rabies vaccines are not efficacious against all lyssaviruses. Taiwan bat lyssavirus (TWBLV) was first reported in 2018 following isolation from Japanese house bats. Since the initial detection and genetic characterisation, no attempts have been made to antigenically define this virus. Due to the inaccessibility of the wildtype isolate, the successful generation of a live recombinant virus, cSN-TWBLV, is described, where the full-length genome clone of the RABV vaccine strain, SAD-B19, was constructed with the glycoprotein of TWBLV. In vitro and in vivo characterization of cSN-TWBLV was undertaken and demonstrated evidence for cross-neutralisation of cSN-TWBLV with phylogroup I -specific sera and rabies virus standard sera. For neutralisation equivalent to 0.5 IU/mL of WHO and World Organisation of Animal Health (WOAH) sera against CVS, 0.5 IU/mL of WOAH sera and 2.5 IU/mL of WHO sera were required to neutralise cSN-TWBLV. In addition, specific sera for ARAV and EBLV-1 exhibited the highest neutralising antibody titres against cSN-TWBLV, compared to other phylogroup I-specific sera. Full article

(This article belongs to the Special Issue Bat-Borne Viruses Research)

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13 pages, 2433 KiB

Open AccessArticle

The Prevalence of Viral Pathogens among Bats in Kazakhstan

by Adilbay I. Karagulov, Takhmina U. Argimbayeva, Zamira D. Omarova, Ali B. Tulendibayev, Laura Zh. Dushayeva, Marina A. Svotina, Aibarys M. Melisbek, Nurdos A. Aubakir, Sabyrkhan M. Barmak, Kulyaisan T. Sultankulova, Dana A. Alibekova, Tanat T. Yermekbai, Askar M. Nametov, Dmitry A. Lozovoy, Khairulla B. Abeuov and Mukhit B. Orynbayev

Viruses 2022, 14(12), 2743; https://doi.org/10.3390/v14122743 - 9 Dec 2022

Cited by 4 | Viewed by 1926

Abstract

Bats carry thousands of viruses from 28 different families. To determine the presence of various pathogens in bat populations in Kazakhstan, 1149 samples (393 oropharyngeal swabs, 349 brain samples, 407 guano) were collected. The samples were collected from four species of bats (Vespertilio murinus, Nyctalus noctula, Myotis blythii, Eptesicus serotinus) in nine regions. The Coronavirus RNA was found in 38 (4.75%) samples, and the rabies virus in 27 (7.74%) samples from bats. Coronaviruses and the rabies virus were found in bats in six out of nine studied areas. The RNAs of SARS-CoV-2, MERS, TBE, CCHF, WNF, influenza A viruses were not detected in the bat samples. The phylogeny of the RdRp gene of 12 samples made it possible to classify them as alphacoronaviruses and divide them into two groups. The main group (n = 11) was closely related to bat coronaviruses from Ghana, Zimbabwe and Kenya. The second group (n = 1) was closely related to viruses previously isolated in the south of Kazakhstan. The phylogeny of the N gene sequence from a bat from west Kazakhstan revealed its close relationship with isolates from the Cosmopolitan group of rabies viruses (Central Asia). These results highlight the need for a continuous monitoring of volatile populations to improve the surveillance and detection of infectious diseases. Full article

(This article belongs to the Special Issue Bat-Borne Viruses Research)

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22 pages, 3433 KiB

Open AccessArticle

Virus Diversity, Abundance, and Evolution in Three Different Bat Colonies in Switzerland

by Myriam Anja Wiederkehr, Weihong Qi, Katja Schoenbaechler, Cornel Fraefel and Jakub Kubacki

Viruses 2022, 14(9), 1911; https://doi.org/10.3390/v14091911 - 29 Aug 2022

Cited by 8 | Viewed by 2184

Abstract

Bats are increasingly recognized as reservoirs for many different viruses that threaten public health, such as Hendravirus, Ebolavirus, Nipahvirus, and SARS- and MERS-coronavirus. To assess spillover risk, viromes of bats from different parts of the world have been investigated in the past. As opposed to most of these prior studies, which determined the bat virome at a single time point, the current work was performed to monitor changes over time. Specifically, fecal samples of three endemic Swiss bat colonies consisting of three different bat species were collected over three years and analyzed using next-generation sequencing. Furthermore, single nucleotide variants of selected DNA and RNA viruses were analyzed to investigate virus genome evolution. In total, sequences of 22 different virus families were found, of which 13 are known to infect vertebrates. Most interestingly, in a Vespertilio murinus colony, sequences from a MERS-related beta-coronavirus were consistently detected over three consecutive years, which allowed us to investigate viral genome evolution in a natural reservoir host. Full article

(This article belongs to the Special Issue Bat-Borne Viruses Research)

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24 pages, 3512 KiB

Open AccessArticle

Myotis fimbriatus Virome, a Window to Virus Diversity and Evolution in the Genus Myotis

by Alix Armero, Ruiya Li, Kathrina Mae Bienes, Xing Chen, Jihao Li, Shiman Xu, Yanhua Chen, Alice C. Hughes, Nicolas Berthet and Gary Wong

Viruses 2022, 14(9), 1899; https://doi.org/10.3390/v14091899 - 27 Aug 2022

Cited by 5 | Viewed by 2504

Abstract

Significant efforts have been made to characterize viral diversity in bats from China. Many of these studies were prospective and focused mainly on Rhinolophus bats that could be related to zoonotic events. However, other species of bats that are part of ecosystems identified as virus diversity hotspots have not been studied in-depth. We analyzed the virome of a group of Myotis fimbriatus bats collected from the Yunnan Province during 2020. The virome of M. fimbriatus revealed the presence of families of pathogenic viruses such as Coronavirus, Astrovirus, Mastadenovirus, and Picornavirus, among others. The viral sequences identified in M. fimbriatus were characterized by significant divergence from other known viral sequences of bat origin. Complex phylogenetic landscapes implying a tendency of co-specificity and relationships with viruses from other mammals characterize these groups. The most prevalent and abundant virus in M. fimbriatus individuals was an alphacoronavirus. The genome of this virus shows evidence of recombination and is likely the product of ancestral host-switch. The close phylogenetic and ecological relationship of some species of the Myotis genus in China may have played an important role in the emergence of this alphacoronavirus. Full article

(This article belongs to the Special Issue Bat-Borne Viruses Research)

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13 pages, 4434 KiB

Open AccessArticle

Detection and Characterization of a Reassortant Mammalian Orthoreovirus Isolated from Bats in Xinjiang, China

by Xiaomin Yan, Jinliang Sheng, Chang Zhang, Nan Li, Le Yi, Zihan Zhao, Ye Feng, Changchun Tu and Biao He

Viruses 2022, 14(9), 1897; https://doi.org/10.3390/v14091897 - 27 Aug 2022

Cited by 6 | Viewed by 1480

Abstract

Mammalian orthoreoviruses (MRVs) are increasingly reported to cause various diseases in humans and other animals, with many possibly originating from bats, highlighting the urgent need to investigate the diversity of bat-borne MRVs (BtMRVs). Here, we report the detection and characterization of a reassortant MRV that was isolated from a bat colony in Xinjiang, China. The BtMRV showed a wide host and organ tropism and can efficiently propagate the cell lines of different animals. It caused mild damage in the lungs of the experimentally inoculated suckling mice and was able to replicate in multiple organs for up to three weeks post-inoculation. Complete genome analyses showed that the virus was closely related to MRVs in a wide range of animals. An intricate reassortment network was revealed between the BtMRV and MRVs of human, deer, cattle, civet and other bat species. Specifically, we found a bat-specific clade of segment M1 that provides a gene source for the reassortment of human MRVs. These data provide important insights to understand the diversity of MRVs and their natural circulation between bats, humans, and other animals. Further investigation and surveillance of MRV in bats and other animals are needed to control and prevent potential MRV-related diseases. Full article

(This article belongs to the Special Issue Bat-Borne Viruses Research)

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16 pages, 2820 KiB

Open AccessArticle

Characterization of Pipistrellus pygmaeus Bat Virome from Sweden

by Harindranath Cholleti, Johnny de Jong, Anne-Lie Blomström and Mikael Berg

Viruses 2022, 14(8), 1654; https://doi.org/10.3390/v14081654 - 28 Jul 2022

Cited by 2 | Viewed by 3398

Abstract

Increasing amounts of data indicate that bats harbor a higher viral diversity relative to other mammalian orders, and they have been recognized as potential reservoirs for pathogenic viruses, such as the Hendra, Nipah, Marburg, and SARS-CoV viruses. Here, we present the first viral metagenomic analysis of Pipistrellus pygmaeus from Uppsala, Sweden. Total RNA was extracted from the saliva and feces of individual bats and analyzed using Illumina sequencing. The results identified sequences related to 51 different viral families, including vertebrate, invertebrate, and plant viruses. These viral families include Coronaviridae, Picornaviridae, Dicistroviridae, Astroviridae, Hepeviridae, Reoviridae, Botourmiaviridae, Lispviridae, Totiviridae, Botoumiaviridae, Parvoviridae, Retroviridae, Adenoviridae, and Partitiviridae, as well as different unclassified viruses. We further characterized three near full-length genome sequences of bat coronaviruses. A phylogenetic analysis showed that these belonged to alphacoronaviruses with the closest similarity (78–99% at the protein level) to Danish and Finnish bat coronaviruses detected in Pipistrellus and Myotis bats. In addition, the full-length and the near full-length genomes of picornavirus were characterized. These showed the closest similarity (88–94% at the protein level) to bat picornaviruses identified in Chinese bats. Altogether, the results of this study show that Swedish Pipistrellus bats harbor a great diversity of viruses, some of which are closely related to mammalian viruses. This study expands our knowledge on the bat population virome and improves our understanding of the evolution and transmission of viruses among bats and to other species. Full article

(This article belongs to the Special Issue Bat-Borne Viruses Research)

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13 pages, 2200 KiB

Open AccessArticle

Assessment of Life Cycle Modeling Systems as Prediction Tools for a Possible Attenuation of Recombinant Ebola Viruses

by Bianca S. Bodmer and Thomas Hoenen

Viruses 2022, 14(5), 1044; https://doi.org/10.3390/v14051044 - 13 May 2022

Cited by 4 | Viewed by 1982

Abstract

Ebola virus (EBOV) causes hemorrhagic fever in humans with high case fatality rates. In the past, a number of recombinant EBOVs expressing different reporters from additional transcription units or as fusion proteins have been rescued. These viruses are important tools for the study of EBOV, and their uses include high throughput screening approaches, the analysis of intercellular localization of viral proteins and of tissue distribution of viruses, and the study of pathogenesis in vivo. However, they all show, at least in vivo, attenuation compared to wild type virus, and the basis of this attenuation is only poorly understood. Unfortunately, rescue of these viruses is a lengthy and not always successful process, and working with them is restricted to biosafety level (BSL)-4 laboratories, so that the search for non-attenuated reporter-expressing EBOVs remains challenging. However, several life cycle modeling systems have been developed to mimic different aspects of the filovirus life cycle under BSL-1 or -2 conditions, but it remains unclear whether these systems can be used to predict the viability and possible attenuation of recombinant EBOVs. To address this question, we systematically fused N- or C-terminally either a flag-HA tag or a green fluorescent protein (GFP) to different EBOV proteins, and analyzed the impact of these additions with respect to protein function in life cycle modeling systems. Based on these results, selected recombinant EBOVs encoding these tags/proteins were then rescued and characterized for a possible attenuation in vitro, and results compared with data from the life cycle modeling systems. While the results for the small molecular tags showed mostly good concordance, GFP-expressing viruses were more attenuated than expected based on the results from the life cycle modeling system, demonstrating a limitation of these systems and emphasizing the importance of work with infectious virus. Nevertheless, life cycle modeling system remain useful tools to exclude non-viable tagging strategies. Full article

(This article belongs to the Special Issue Bat-Borne Viruses Research)

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12 pages, 2374 KiB

Open AccessArticle

Discovery and Evolutionary Analysis of a Novel Bat-Borne Paramyxovirus

by Wentao Zhu, Yuyuan Huang, Xiaojie Yu, Haiyun Chen, Dandan Li, Libo Zhou, Qianni Huang, Liyun Liu, Jing Yang and Shan Lu

Viruses 2022, 14(2), 288; https://doi.org/10.3390/v14020288 - 29 Jan 2022

Cited by 9 | Viewed by 2811

Abstract

Paramyxoviruses are a group of RNA viruses, such as mumps virus, measles virus, Nipah virus, Hendra virus, Newcastle disease virus, and parainfluenza virus, usually transmitted by airborne droplets that are predominantly responsible for acute respiratory diseases. In this paper, we identified a novel paramyxovirus belonging to genus Jeilongvirus infecting 4/112 (3.6%) bats from two trapping sites of Hainan Province of China. In these animals, the viral RNA was detected exclusively in kidney tissues. This is the first full-length Jeilongvirus genome (18,095 nucleotides) from bats of genus Hipposideros, which exhibits a canonical genome organization and encodes SH and TM proteins. Results, based on phylogenic analysis and genetic distances, indicate that the novel paramyxovirus formed an independent lineage belonging to genus Jeilongvirus, representing, thus, a novel species. In addition, the virus-host macro-evolutionary analysis revealed that host-switching was not only a common co-phylogenetic event, but also a potential mechanism by which rats are infected by bat-origin Jeilongvirus through cross-species virus transmission, indicating a bat origin of the genus Jeilongvirus. Overall, our study broadens the viral diversity, geographical distribution, host range, and evolution of genus Jeilongvirus. Full article

(This article belongs to the Special Issue Bat-Borne Viruses Research)

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Review

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20 pages, 3687 KiB

Open AccessReview

Chirohepevirus from Bats: Insights into Hepatitis E Virus Diversity and Evolution

by Bo Wang and Xing-Lou Yang

Viruses 2022, 14(5), 905; https://doi.org/10.3390/v14050905 - 27 Apr 2022

Cited by 15 | Viewed by 3113

Abstract

Homologs of the human hepatitis E virus (HEV) have been identified in more than a dozen animal species. Some of them have been evidenced to cross species barriers and infect humans. Zoonotic HEV infections cause chronic liver diseases as well as a broad range of extrahepatic manifestations, which increasingly become significant clinical problems. Bats comprise approximately one-fifth of all named mammal species and are unique in their distinct immune response to viral infection. Most importantly, they are natural reservoirs of several highly pathogenic viruses, which have induced severe human diseases. Since the first discovery of HEV-related viruses in bats in 2012, multiple genetically divergent HEV variants have been reported in a total of 12 bat species over the last decade, which markedly expanded the host range of the HEV family and shed light on the evolutionary origin of human HEV. Meanwhile, bat-borne HEV also raised critical public health concerns about its zoonotic potential. Bat HEV strains resemble genomic features but exhibit considerable heterogeneity. Due to the close evolutionary relationships, bat HEV altogether has been recently assigned to an independent genus, Chirohepevirus. This review focuses on the current state of bat HEV and provides novel insights into HEV genetic diversity and molecular evolution. Full article

(This article belongs to the Special Issue Bat-Borne Viruses Research)

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