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Viruses
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Bats and Coronaviruses
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Bats and Coronaviruses

A special issue of Viruses (ISSN 1999-4915). This special issue belongs to the section "SARS-CoV-2 and COVID-19".

Deadline for manuscript submissions: closed (31 December 2021) | Viewed by 26357

Special Issue Editors

Prof. Dr. Peng Zhou

E-Mail Website
Guest Editor
1. Guangzhou Laboratory, Guangzhou, China
2. Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
Interests: bat virus infection and immunity; virus host interaction; SARS-CoV
Dr. Danielle E. Anderson

E-Mail Website
Co-Guest Editor
Department of Microbiology and Immunology, The University of Melbourne, Melbourne, Australia
Interests: virus host interaction; paramyxoviruses; coronaviruses, zoonosis, infectious disease

Special Issue Information

Dear Colleagues,

During the past two decades, three high pathogenic coronaviruses have been identified as the causal agents of large-scale disease outbreaks—SARS-CoV-1, MERS-CoV and SARS-CoV-2—that have claimed tens of thousands of human lives. One of the shared characters between these three viruses is that they all probably originated in bats, which firmly establishes that bats are an important source of highly lethal zoonotic viruses. Thus, it is highly likely that future SARS-like coronavirus outbreaks will originate from bats. While it is almost impossible to predict or prevent the next coronavirus outbreak, we believe that active surveillance is the best we can do at the present time to provide early warnings and, in turn, minimize the impact of such future outbreaks. As a successful example, the identification of bat HKU2-related coronavirus led us to quickly set up diagnosis and control measures against swine disease outbreak caused by SARS-CoV, which shared 95% genome identity to HKU2-CoV. In addition, it is increasingly important to understand why bats can maintain coronaviruses long-term without showing clinical symptoms of diseases. In this regard, global efforts on the discovery and active surveillance of bat coronaviruses, and on understanding of the relationship between bats and coronaviruses are urgently needed. This is also within the scope of this Special Issue “Bats and Coronaviruses”.

Prof. Dr. Peng Zhou
Guest Editor
Dr. Danielle E. Anderson
Co-Guest Editor

Manuscript Submission Information

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Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Viruses is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2600 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • SARS-CoV-1
  • MERS-CoV
  • SARS-CoV-2
  • bat coronaviruses

Published Papers (7 papers)

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Research

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17 pages, 5803 KiB  
Article
SARS-like Coronaviruses in Horseshoe Bats (Rhinolophus spp.) in Russia, 2020
by Sergey Alkhovsky, Sergey Lenshin, Alexey Romashin, Tatyana Vishnevskaya, Oleg Vyshemirsky, Yulia Bulycheva, Dmitry Lvov and Asya Gitelman
Viruses 2022, 14(1), 113; https://0-doi-org.brum.beds.ac.uk/10.3390/v14010113 - 09 Jan 2022
Cited by 28 | Viewed by 4552
Abstract
We found and genetically described two novel SARS-like coronaviruses in feces and oral swabs of the greater (R. ferrumequinum) and the lesser (R. hipposideros) horseshoe bats in southern regions of Russia. The viruses, named Khosta-1 and Khosta-2, together with [...] Read more.
We found and genetically described two novel SARS-like coronaviruses in feces and oral swabs of the greater (R. ferrumequinum) and the lesser (R. hipposideros) horseshoe bats in southern regions of Russia. The viruses, named Khosta-1 and Khosta-2, together with related viruses from Bulgaria and Kenya, form a separate phylogenetic lineage. We found evidence of recombination events in the evolutionary history of Khosta-1, which involved the acquisition of the structural proteins S, E, and M, as well as the nonstructural genes ORF3, ORF6, ORF7a, and ORF7b, from a virus that is related to the Kenyan isolate BtKY72. The examination of bats by RT-PCR revealed that 62.5% of the greater horseshoe bats in one of the caves were positive for Khosta-1 virus, while its overall prevalence was 14%. The prevalence of Khosta-2 was 1.75%. Our results show that SARS-like coronaviruses circulate in horseshoe bats in the region, and we provide new data on their genetic diversity. Full article
(This article belongs to the Special Issue Bats and Coronaviruses)
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14 pages, 2805 KiB  
Article
Genomic Characterization of a Novel Alphacoronavirus Isolated from Bats, Korea, 2020
by Hai-Quynh Do, Van-Giap Nguyen, Chul-Un Chung, Yong-Shin Jeon, Sook Shin, Kuem-Chan Jang, Le Bich Hang Pham, Aeri Kong, Cheong-Ung Kim, Yong-Ho Park, Bong-Kyun Park and Hee-Chun Chung
Viruses 2021, 13(10), 2041; https://0-doi-org.brum.beds.ac.uk/10.3390/v13102041 - 11 Oct 2021
Cited by 5 | Viewed by 3372
Abstract
Coronavirus, an important zoonotic disease, raises concerns of future pandemics. The bat is considered a source of noticeable viruses resulting in human and livestock infections, especially the coronavirus. Therefore, surveillance and genetic analysis of coronaviruses in bats are essential in order to prevent [...] Read more.
Coronavirus, an important zoonotic disease, raises concerns of future pandemics. The bat is considered a source of noticeable viruses resulting in human and livestock infections, especially the coronavirus. Therefore, surveillance and genetic analysis of coronaviruses in bats are essential in order to prevent the risk of future diseases. In this study, the genome of HCQD-2020, a novel alphacoronavirus detected in a bat (Eptesicus serotinus), was assembled and described using next-generation sequencing and bioinformatics analysis. The comparison of the whole-genome sequence and the conserved amino acid sequence of replicated proteins revealed that the new strain was distantly related with other known species in the Alphacoronavirus genus. Phylogenetic construction indicated that this strain formed a separated branch with other species, suggesting a new species of Alphacoronavirus. Additionally, in silico prediction also revealed the risk of cross-species infection of this strain, especially in the order Artiodactyla. In summary, this study provided the genetic characteristics of a possible new species belonging to Alphacoronavirus. Full article
(This article belongs to the Special Issue Bats and Coronaviruses)
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20 pages, 6349 KiB  
Article
Genomic Characterization of Diverse Bat Coronavirus HKU10 in Hipposideros Bats
by Ning Wang, Chu-Ming Luo, Xing-Lou Yang, Hai-Zhou Liu, Li-Biao Zhang, Wei Zhang, Bei Li, Yan Zhu, Cheng Peng, Zheng-Li Shi and Ben Hu
Viruses 2021, 13(10), 1962; https://0-doi-org.brum.beds.ac.uk/10.3390/v13101962 - 29 Sep 2021
Cited by 2 | Viewed by 3487
Abstract
Bats have been identified as natural reservoirs of a variety of coronaviruses. They harbor at least 19 of the 33 defined species of alpha- and betacoronaviruses. Previously, the bat coronavirus HKU10 was found in two bat species of different suborders, Rousettus leschenaultia and [...] Read more.
Bats have been identified as natural reservoirs of a variety of coronaviruses. They harbor at least 19 of the 33 defined species of alpha- and betacoronaviruses. Previously, the bat coronavirus HKU10 was found in two bat species of different suborders, Rousettus leschenaultia and Hipposideros pomona, in south China. However, its geographic distribution and evolution history are not fully investigated. Here, we screened this viral species by a nested reverse transcriptase PCR in our archived samples collected over 10 years from 25 provinces of China and one province of Laos. From 8004 bat fecal samples, 26 were found to be positive for bat coronavirus HKU10 (BtCoV HKU10). New habitats of BtCoV HKU10 were found in the Yunnan, Guangxi, and Hainan Provinces of China, and Louang Namtha Province in Laos. In addition to H. pomona, BtCoV HKU10 variants were found circulating in Aselliscus stoliczkanus and Hipposideros larvatus. We sequenced full-length genomes of 17 newly discovered BtCoV HKU10 strains and compared them with previously published sequences. Our results revealed a much higher genetic diversity of BtCoV HKU10, particularly in spike genes and accessory genes. Besides the two previously reported lineages, we found six novel lineages in their new habitats, three of which were located in Yunnan province. The genotypes of these viruses are closely related to sampling locations based on polyproteins, and correlated to bat species based on spike genes. Combining phylogenetic analysis, selective pressure, and molecular-clock calculation, we demonstrated that Yunnan bats harbor a gene pool of BtCoV HKU10, with H. pomona as a natural reservoir. The cell tropism test using spike-pseudotyped lentivirus system showed that BtCoV HKU10 could enter cells from human and bat, suggesting a potential interspecies spillover. Continuous studies on these bat coronaviruses will expand our understanding of the evolution and genetic diversity of coronaviruses, and provide a prewarning of potential zoonotic diseases from bats. Full article
(This article belongs to the Special Issue Bats and Coronaviruses)
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19 pages, 5444 KiB  
Article
Evolutionary Signatures Governing the Codon Usage Bias in Coronaviruses and Their Implications for Viruses Infecting Various Bat Species
by Naveen Kumar, Rahul Kaushik, Chandana Tennakoon, Vladimir N. Uversky, Anamika Mishra, Richa Sood, Pratiksha Srivastava, Meghna Tripathi, Kam Y. J. Zhang and Sandeep Bhatia
Viruses 2021, 13(9), 1847; https://0-doi-org.brum.beds.ac.uk/10.3390/v13091847 - 16 Sep 2021
Cited by 14 | Viewed by 3257
Abstract
Many viruses that cause serious diseases in humans and animals, including the betacoronaviruses (beta-CoVs), such as SARS-CoV, MERS-CoV, and the recently identified SARS-CoV-2, have natural reservoirs in bats. Because these viruses rely entirely on the host cellular machinery for survival, their evolution is [...] Read more.
Many viruses that cause serious diseases in humans and animals, including the betacoronaviruses (beta-CoVs), such as SARS-CoV, MERS-CoV, and the recently identified SARS-CoV-2, have natural reservoirs in bats. Because these viruses rely entirely on the host cellular machinery for survival, their evolution is likely to be guided by the link between the codon usage of the virus and that of its host. As a result, specific cellular microenvironments of the diverse hosts and/or host tissues imprint peculiar molecular signatures in virus genomes. Our study is aimed at deciphering some of these signatures. Using a variety of genetic methods we demonstrated that trends in codon usage across chiroptera-hosted CoVs are collaboratively driven by geographically different host-species and temporal-spatial distribution. We not only found that chiroptera-hosted CoVs are the ancestors of SARS-CoV-2, but we also revealed that SARS-CoV-2 has the codon usage characteristics similar to those seen in CoVs infecting the Rhinolophus sp. Surprisingly, the envelope gene of beta-CoVs infecting Rhinolophus sp., including SARS-CoV-2, had extremely high CpG levels, which appears to be an evolutionarily conserved trait. The dissection of the furin cleavage site of various CoVs infecting hosts revealed host-specific preferences for arginine codons; however, arginine is encoded by a wider variety of synonymous codons in the murine CoV (MHV-A59) furin cleavage site. Our findings also highlight the latent diversity of CoVs in mammals that has yet to be fully explored. Full article
(This article belongs to the Special Issue Bats and Coronaviruses)
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14 pages, 3085 KiB  
Article
Egyptian Fruit Bats (Rousettus aegyptiacus) Were Resistant to Experimental Inoculation with Avian-Origin Influenza A Virus of Subtype H9N2, But Are Susceptible to Experimental Infection with Bat-Borne H9N2 Virus
by Nico Joel Halwe, Marco Gorka, Bernd Hoffmann, Melanie Rissmann, Angele Breithaupt, Martin Schwemmle, Martin Beer, Ahmed Kandeil, Mohamed A. Ali, Ghazi Kayali, Donata Hoffmann and Anne Balkema-Buschmann
Viruses 2021, 13(4), 672; https://0-doi-org.brum.beds.ac.uk/10.3390/v13040672 - 14 Apr 2021
Cited by 7 | Viewed by 3177
Abstract
Influenza A viruses (IAV) of subtype H9N2, endemic in world-wide poultry holdings, are reported to cause spill-over infections to pigs and humans and have also contributed substantially to recent reassortment-derived pre-pandemic zoonotic viruses of concern, such as the Asian H7N9 viruses. Recently, a [...] Read more.
Influenza A viruses (IAV) of subtype H9N2, endemic in world-wide poultry holdings, are reported to cause spill-over infections to pigs and humans and have also contributed substantially to recent reassortment-derived pre-pandemic zoonotic viruses of concern, such as the Asian H7N9 viruses. Recently, a H9N2 bat influenza A virus was found in Egyptian fruit bats (Rousettus aegyptiacus), raising the question of whether this bat species is a suitable host for IAV. Here, we studied the susceptibility, pathogenesis and transmission of avian and bat-related H9N2 viruses in this new host. In a first experiment, we oronasally inoculated six Egyptian fruit bats with an avian-related H9N2 virus (A/layer chicken/Bangladesh/VP02-plaque/2016 (H9N2)). In a second experiment, six Egyptian fruit bats were inoculated with the newly discovered bat-related H9N2 virus (A/bat/Egypt/381OP/2017 (H9N2)). While R. aegyptiacus turned out to be refractory to an infection with H9N2 avian-type, inoculation with the bat H9N2 subtype established a productive infection in all inoculated animals with a detectable seroconversion at day 21 post-infection. In conclusion, Egyptian fruit bats are most likely not susceptible to the avian H9N2 subtype, but can be infected with fruit bat-derived H9N2. H9-specific sero-reactivities in fruit bats in the field are therefore more likely the result of contact with a bat-adapted H9N2 strain. Full article
(This article belongs to the Special Issue Bats and Coronaviruses)
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Review

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21 pages, 4779 KiB  
Review
Interspecies Jumping of Bat Coronaviruses
by Antonio C. P. Wong, Susanna K. P. Lau and Patrick C. Y. Woo
Viruses 2021, 13(11), 2188; https://0-doi-org.brum.beds.ac.uk/10.3390/v13112188 - 29 Oct 2021
Cited by 15 | Viewed by 3509
Abstract
In the last two decades, several coronavirus (CoV) interspecies jumping events have occurred between bats and other animals/humans, leading to major epidemics/pandemics and high fatalities. The SARS epidemic in 2002/2003 had a ~10% fatality. The discovery of SARS-related CoVs in horseshoe bats and [...] Read more.
In the last two decades, several coronavirus (CoV) interspecies jumping events have occurred between bats and other animals/humans, leading to major epidemics/pandemics and high fatalities. The SARS epidemic in 2002/2003 had a ~10% fatality. The discovery of SARS-related CoVs in horseshoe bats and civets and genomic studies have confirmed bat-to-civet-to-human transmission. The MERS epidemic that emerged in 2012 had a ~35% mortality, with dromedaries as the reservoir. Although CoVs with the same genome organization (e.g., Tylonycteris BatCoV HKU4 and Pipistrellus BatCoV HKU5) were also detected in bats, there is still a phylogenetic gap between these bat CoVs and MERS-CoV. In 2016, 10 years after the discovery of Rhinolophus BatCoV HKU2 in Chinese horseshoe bats, fatal swine disease outbreaks caused by this virus were reported in southern China. In late 2019, an outbreak of pneumonia emerged in Wuhan, China, and rapidly spread globally, leading to >4,000,000 fatalities so far. Although the genome of SARS-CoV-2 is highly similar to that of SARS-CoV, patient zero and the original source of the pandemic are still unknown. To protect humans from future public health threats, measures should be taken to monitor and reduce the chance of interspecies jumping events, either occurring naturally or through recombineering experiments. Full article
(This article belongs to the Special Issue Bats and Coronaviruses)
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Other

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12 pages, 7622 KiB  
Brief Report
Presence of Recombinant Bat Coronavirus GCCDC1 in Cambodian Bats
by Feng Zhu, Veasna Duong, Xiao Fang Lim, Vibol Hul, Tanu Chawla, Lucy Keatts, Tracey Goldstein, Alexandre Hassanin, Vuong Tan Tu, Philippe Buchy, October M. Sessions, Lin-Fa Wang, Philippe Dussart and Danielle E. Anderson
Viruses 2022, 14(2), 176; https://0-doi-org.brum.beds.ac.uk/10.3390/v14020176 - 18 Jan 2022
Cited by 2 | Viewed by 3234
Abstract
Bats have been recognized as an exceptional viral reservoir, especially for coronaviruses. At least three bat zoonotic coronaviruses (SARS-CoV, MERS-CoV and SARS-CoV-2) have been shown to cause severe diseases in humans and it is expected more will emerge. One of the major features [...] Read more.
Bats have been recognized as an exceptional viral reservoir, especially for coronaviruses. At least three bat zoonotic coronaviruses (SARS-CoV, MERS-CoV and SARS-CoV-2) have been shown to cause severe diseases in humans and it is expected more will emerge. One of the major features of CoVs is that they are all highly prone to recombination. An extreme example is the insertion of the P10 gene from reoviruses in the bat CoV GCCDC1, first discovered in Rousettus leschenaultii bats in China. Here, we report the detection of GCCDC1 in four different bat species (Eonycteris spelaea, Cynopterus sphinx, Rhinolophus shameli and Rousettus sp.) in Cambodia. This finding demonstrates a much broader geographic and bat species range for this virus and indicates common cross-species transmission. Interestingly, one of the bat samples showed a co-infection with an Alpha CoV most closely related to RsYN14, a virus recently discovered in the same genus (Rhinolophus) of bat in Yunnan, China, 2020. Taken together, our latest findings highlight the need to conduct active surveillance in bats to assess the risk of emerging CoVs, especially in Southeast Asia. Full article
(This article belongs to the Special Issue Bats and Coronaviruses)
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