#Genomic #Characterization of the 2019 Novel Human-Pathogenic #Coronavirus Isolated From a #Patient With Atypical #Pneumonia After Visiting #Wuhan (Emerg Microbes Infect., abstract)

[Source: US National Library of Medicine, full page: (LINK). Abstract, edited.]

Emerg Microbes Infect, 9 (1), 221-236 Dec 2020

Genomic Characterization of the 2019 Novel Human-Pathogenic Coronavirus Isolated From a Patient With Atypical Pneumonia After Visiting Wuhan

Jasper Fuk-Woo Chan 1 2 3 4, Kin-Hang Kok 1 3 4, Zheng Zhu 3, Hin Chu 1 3 4, Kelvin Kai-Wang To 1 2 3 4, Shuofeng Yuan 1 3 4, Kwok-Yung Yuen 2 3 4

Affiliations: 1 State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China. 2 Department of Clinical Microbiology and Infection Control, The University of Hong Kong-Shenzhen Hospital, Shenzhen, Guangdong, People’s Republic of China. 3 Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China. 4 Carol Yu Centre for Infection, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China.

PMID: 31987001  DOI: 10.1080/22221751.2020.1719902



A mysterious outbreak of atypical pneumonia in late 2019 was traced to a seafood wholesale market in Wuhan of China. Within a few weeks, a novel coronavirus tentatively named as 2019 novel coronavirus (2019-nCoV) was announced by the World Health Organization. We performed bioinformatics analysis on a virus genome from a patient with 2019-nCoV infection and compared it with other related coronavirus genomes. Overall, the genome of 2019-nCoV has 89% nucleotide identity with bat SARS-like-CoVZXC21 and 82% with that of human SARS-CoV. The phylogenetic trees of their orf1a/b, Spike, Envelope, Membrane and Nucleoprotein also clustered closely with those of the bat, civet and human SARS coronaviruses. However, the external subdomain of Spike’s receptor binding domain of 2019-nCoV shares only 40% amino acid identity with other SARS-related coronaviruses. Remarkably, its orf3b encodes a completely novel short protein. Furthermore, its new orf8 likely encodes a secreted protein with an alpha-helix, following with a beta-sheet(s) containing six strands. Learning from the roles of civet in SARS and camel in MERS, hunting for the animal source of 2019-nCoV and its more ancestral virus would be important for understanding the origin and evolution of this novel lineage B betacoronavirus. These findings provide the basis for starting further studies on the pathogenesis, and optimizing the design of diagnostic, antiviral and vaccination strategies for this emerging infection.

Keywords: Coronavirus; SARS; Wuhan; bioinformatics; emerging; genome; respiratory; virus.

Keywords: 2019-nCoV; Human; Bats.


Homologous #Recombination Within the #Spike Glycoprotein of the Newly Identified #Coronavirus May Boost Cross-Species #Transmission From Snake to Human (J Med Virol., abstract)

[Source: US National Library of Medicine, full page: (LINK). Abstract, edited.]

J Med Virol  /  2020 Jan 22 [Online ahead of print]

Homologous Recombination Within the Spike Glycoprotein of the Newly Identified Coronavirus May Boost Cross-Species Transmission From Snake to Human

Wei Ji 1, Wei Wang 2, Xiaofang Zhao 3, Junjie Zai 4, Xingguang Li 5

Affiliations: 1 Department of Microbiology, Peking University Health Science Center School of Basic Medical Sciences, Beijing, China. 2 Department of Spleen and Stomach Diseases, The First affiliated Hospital of Guangxi university of Chinese Medicine, Nanning, 530023, China. 3 Department of Science and Technology, Ruikang Hospital Affiliated to Guangxi University of Chinese Medicine, Nanning, 530011, China. 4 Immunology innovation team, School of Medicine, Ningbo University, Ningbo, 315211, China. 5 Hubei Engineering Research Center of Viral Vector, Wuhan University of Bioengineering, Wuhan, 430415, China.

PMID: 31967321 DOI: 10.1002/jmv.25682



The current outbreak of viral pneumonia in the city of Wuhan, China, was caused by a novel coronavirus designated 2019-nCoV by the World Health Organization, as determined by sequencing the viral RNA genome. Many patients were potentially exposed to wildlife animals at the Huanan seafood wholesale market, where poultry, snake, bats, and other farm animals were also sold. To determine the possible virus reservoir, we have carried out comprehensive sequence analysis and comparison in conjunction with relative synonymous codon usage (RSCU) bias among different animal species based on existing sequences of the newly identified coronavirus 2019-nCoV. Results obtained from our analyses suggest that the 2019-nCoV appears to be a recombinant virus between the bat coronavirus and an origin-unknown coronavirus. The recombination occurred within the viral spike glycoprotein, which recognizes cell surface receptor. Additionally, our findings suggest that snake is the most probable wildlife animal reservoir for the 2019-nCoV based on its RSCU bias resembling snake compared to other animals. Taken together, our results suggest that homologous recombination within the spike glycoprotein may contribute to cross-species transmission from snake to humans.

Keywords: 2019-nCoV; RSCU; cross-species transmission; phylogenetic analysis; recombination.

This article is protected by copyright. All rights reserved.

Keywords: Coronavirus; Bats; 2019-nCoV.


#Seroreactive profiling of #filoviruses in Chinese #bats reveals extensive #infection of diverse viruses (J Virol., abstract)

[Source: Journal of Virology, full page: (LINK). Abstract, edited.]

Seroreactive profiling of filoviruses in Chinese bats reveals extensive infection of diverse viruses

Chang Zhang, Zhongyi Wang, Jianqiu Cai, Xiaomin Yan, Fuqiang Zhang, Jianmin Wu, Lin Xu, Zongzheng Zhao, Tingsong Hu, Changchun Tu, Biao He

DOI: 10.1128/JVI.02042-19



Southern China is a hotspot of emerging infectious diseases, in which dwell diverse species of bats, a large group of flying mammals considered natural reservoirs for zoonotic viruses. Recently, divergent filoviruses (FiVs) have been identified in bats within this region, which pose a potential risk to public health, but their true infection situation in bats remains largely unclear. Here, 689 archived bat serum samples were analyzed by ELISA, western blot and neutralization assay to investigate the seroprevalence and cross-reactivity of four divergent FiVs and two other viruses (Rabies virus and Tuhoko pararubulavirus 1) of different families within the order Mononegavirales. Results showed no cross-antigenicity between FiVs and other mononegaviruses, but different cross-reactivity among the FiVs themselves. The total FiV seroreactive rate was 36.3% (250/689), with infection by the indigenous Chinese FiV DH04 or antigenically-related one being the most widely and the most highly prevalent. Further viral metagenomic analysis of fruit bat tissues also identified the gene sequence of a novel FiV. These results indicate the likely prevalence of other so far unidentified FiVs within Chinese bat population, with frugivorous Rousettus leschenaulti and Eonycteris spelaea bats and insectivorous Myotis horsfieldii and M. schreibersi bats being their major reservoirs.



Bats are natural hosts of many FiVs, from which diverse FiVs were serologically or virologically detected in Africa, Europe and East Asia. Recently, very divergent FiVs were identified in Chinese bat population, but their antigenic relationship with other known FiVs remains unknown. Here we conducted serological characterization and investigation of Chinese indigenous FiVs and prototypes of other viruses in bats. Results indicated that Chinese indigenous FiVs are antigenically distant to other FiVs and infection of novel or multiple FiVs occurred in Chinese bats with FiV DH04 or antigenically-related one being the most widely and the most highly prevalent. Additionally, besides Rousettus leschenaulti and Eonycteris spelaea bats, the insectivorous Myotis horsfieldii and M. schreibersi bats are highly preferential hosts of FiVs. Seroreactive and viral metagenomic results indicated that more as yet unknown bat-borne FiVs circulate in the Southern China, and to uncover them further investigation and timely surveillance is needed.

Copyright © 2020 American Society for Microbiology. All Rights Reserved.

Keywords: Mononegavirales; Filovirus; Bats; China.


High #Pathogenicity of #Nipah Virus from Pteropus lylei Fruit #Bats, #Cambodia (Emerg Infect Dis., abstract)

[Source: US Centers for Disease Control and Prevention (CDC), Emerging Infectious Diseases Journal, full page: (LINK). Abstract, edited.]

Volume 26, Number 1—January 2020 / Research

High Pathogenicity of Nipah Virus from Pteropus lylei Fruit Bats, Cambodia

Maria Gaudino, Noémie Aurine, Claire Dumont, Julien Fouret, Marion Ferren, Cyrille Mathieu, Olivier Reynard, Viktor E. Volchkov, Catherine Legras-Lachuer, Marie-Claude Georges-Courbot, and Branka Horvat

Author affiliations: Centre International de Recherche en Infectiologie, CIRI, INSERM U1111, CNRS, UMR5308, Univ Lyon, University Claude Bernard Lyon 1, École Normale Supérieure de Lyon, Lyon, France (M. Gaudino, N. Aurine, C. Dumont, J. Fouret, M. Ferren, C. Mathieu, O. Reynard, V.E. Volchkov, M.-C. Georges-Courbot, B. Horvat); ViroScan 3D, Trévoux, France (J. Fouret, C. Legras-Lachuer); University Claude Bernard Lyon 1, LEM, UMR5557, CNRS, INRA, VetAgro Sup, Lyon (C. Legras-Lachuer); Unité de Biologie des Infections Virales Emergentes, Institute Pasteur, INSERM P4, Jean Mérieux, Lyon (M.-C. Georges-Courbot)



We conducted an in-depth characterization of the Nipah virus (NiV) isolate previously obtained from a Pteropus lylei bat in Cambodia in 2003 (CSUR381). We performed full-genome sequencing and phylogenetic analyses and confirmed CSUR381 is part of the NiV-Malaysia genotype. In vitro studies revealed similar cell permissiveness and replication of CSUR381 (compared with 2 other NiV isolates) in both bat and human cell lines. Sequence alignments indicated conservation of the ephrin-B2 and ephrin-B3 receptor binding sites, the glycosylation site on the G attachment protein, as well as the editing site in phosphoprotein, suggesting production of nonstructural proteins V and W, known to counteract the host innate immunity. In the hamster animal model, CSUR381 induced lethal infections. Altogether, these data suggest that the Cambodia bat-derived NiV isolate has high pathogenic potential and, thus, provide insight for further studies and better risk assessment for future NiV outbreaks in Southeast Asia.

Keywords: Nipah virus; Bats; Animal models.


#Coronaviruses Detected in #Bats in Close Contact with Humans in #Rwanda (Ecohealth, abstract)

[Source: US National Library of Medicine, full page: (LINK). Abstract, edited.]

Ecohealth. 2019 Dec 6. doi: 10.1007/s10393-019-01458-8. [Epub ahead of print]

Coronaviruses Detected in Bats in Close Contact with Humans in Rwanda.

Nziza J1, Goldstein T2, Cranfield M3, Webala P4, Nsengimana O5, Nyatanyi T6, Mudakikwa A7, Tremeau-Bravard A2, Byarugaba D8, Tumushime JC3, Mwikarago IE9, Gafarasi I10, Mazet J3,2, Gilardi K3,2.

Author information: 1 Gorilla Doctors, P.O. Box 115, Musanze, Rwanda. nzizavet@gmail.com. 2 Karen C. Drayer Wildlife Health Center, One Health Institute, School of Veterinary Medicine, University of California Davis, Davis, CA, USA. 3 Gorilla Doctors, P.O. Box 115, Musanze, Rwanda. 4 Department of Forestry and Wildlife Management, Maasai Mara University, P.O. Box 861, Narok, 20500, Kenya. 5 Rwanda Wildlife Conservation Association, P.O. Box 5427, Kigali, Rwanda. 6 Department of Global Health and Social Medicine, School of Medicine, Harvard University, Boston, USA. 7 Rwanda Development Board, P.O. Box 6932, Kigali, Rwanda. 8 Makerere University Walter Reed Project, College of Veterinary Medicine, Animal Resources and Biosecurity, Makerere University, Kampala, Uganda. 9 National Reference Laboratory, Rwanda Biomedical Center, P.O. Box 83, Kigali, Rwanda. 10 Rwanda Agriculture Board, P.O. Box 5016, Kigali, Rwanda.



Bats living in close contact with people in Rwanda were tested for evidence of infection with viruses of zoonotic potential. Mucosal swabs from 503 bats representing 17 species were sampled from 2010 to 2014 and screened by consensus PCR for 11 viral families. Samples were negative for all viral families except coronaviruses, which were detected in 27 bats belonging to eight species. Known coronaviruses detected included the betacorona viruses: Kenya bat coronaviruses, Eidolon bat coronavirus, and Bat coronavirus HKU9, as well as an alphacoronavirus, Chaerephon Bat coronavirus. Novel coronaviruses included two betacorona viruses clustering with SARS-CoV, a 2d coronavirus, and an alphacoronavirus.

KEYWORDS: Bats; Coronaviruses; Human–wildlife interfaces; Rwanda

PMID: 31811597 DOI: 10.1007/s10393-019-01458-8

Keywords: Coronavirus; Alphacoronavirus; Betacoronavirus; Bats; Rwanda.


#Mutations in the NA-like #protein of #bat #influenza #H18N11 virus enhance virus #replication in #mammalian cells, mice, and ferrets (J Virol., abstract)

[Source: Journal of Virology, full page: (LINK). Abstract, edited.]

Mutations in the NA-like protein of bat influenza H18N11 virus enhance virus replication in mammalian cells, mice, and ferrets

Gongxun Zhong, Shufang Fan, Masato Hatta, Sumiho Nakatsu, Kevin B. Walters, Tiago J.S. Lopes, Jessica I-Hsuan Wang, Makoto Ozawa, Alexander Karasin, Yan Li, Suxiang Tong, Ruben O. Donis, Gabriele Neumann, Yoshihiro Kawaoka

DOI: 10.1128/JVI.01416-19



To characterize bat influenza H18N11 virus, we propagated a reverse genetics-generated H18N11 virus in MDCK II cells and detected two adapting mutations in the neuraminidase (NA)-like protein (NA-F144C and NA-T342A, N2 numbering) that increased virus titers in three mammalian cell lines (i.e., Madin-Darby canine kidney, Madin-Darby canine kidney II, and human lung adenocarcinoma Calu-3 cells). In mice, wild-type H18N11 virus replicated only in the lungs of the infected animals, whereas the NA-T342A and NA-F144C/T342A mutant viruses were detected in the nasal turbinates in addition to the lungs. Bat influenza viruses have not been tested for their virulence and organ tropism in ferrets. We detected wild-type and single mutant viruses each possessing NA-F144C or NA-T342A in the nasal turbinates of one or several infected ferret(s), respectively. A mutant virus possessing both NA-F144C and T342A was isolated from both the lung and trachea, suggesting broader organ tropism compared with wild-type virus. However, none of the H18N11 viruses caused symptoms in mice or ferrets. The NA-F144C/T342A double mutation did not substantially affect virion morphology or the release of virions from cells. Collectively, our data demonstrate that propagation of bat influenza H18N11 virus in mammalian cells can result in mammalian-adapting mutations that could increase virus replicative ability and/or organ tropism; overall, however, these viruses did not replicate to high titers throughout the respiratory tract of mice and ferrets.



Bats are reservoirs for several severe zoonotic pathogens. The genomes of influenza A viruses of the H17N10 and H18N11 subtypes were identified in bats, but no live virus has been isolated. The characterization of artificially generated bat influenza H18N11 virus in mammalian cell lines and animal models revealed that this virus can acquire mammalian-adapting mutations that could increase its zoonotic potential; however, the wild-type and mutant viruses did not replicate in the lungs of all infected animals.

Copyright © 2019 American Society for Microbiology. All Rights Reserved.

Keywords: Influenza A; Bat Influenza; H18N11; Animal models.


Molecular basis of binding between #MERS-CoV and CD26s from seven #bat species (J Virol., abstract)

[Source: Journal of Virology, full page: (LINK). Abstract, edited.]

Molecular basis of binding between MERS-CoV and CD26s from seven bat species

Yuan Yuan, Jianxun Qi, Ruchao Peng, Chunrui Li, Guangwen Lu, Jinghua Yan, Qihui Wang, George Fu Gao

DOI: 10.1128/JVI.01387-19



Continued reports of Middle East respiratory syndrome coronavirus (MERS-CoV) infecting human have occurred since its identification in 2012. MERS-CoV is prone to cause endemic disease in the Middle East, with several dozens of spill-over infections to other continents. It is hypothesized that MERS-CoV originated from bat coronaviruses and that dromedary camels are its natural reservoir. Although gene segments identical to MERS-CoV were sequenced from certain species of bats, and one species experimentally shed the virus, it is still unknown whether other bats can transmit the virus. Here, at the molecular level, we found that all purified bat CD26s (bCD26s) from a diverse range of species interact with the receptor binding domain (RBD) of MERS-CoV, with KD values ranging from several to hundreds of micromolar level. Moreover, all bCD26s expressed in this study mediated the entry of pseudotyped MERS-CoV to receptor-expressing cells, indicating the broad potential engagement of bCD26s as MERS-CoV receptors. Further structural analysis indicated that in the bat receptor, compared to the human receptor, substitutions of key residues and their adjacent amino acids leads to decreased binding affinity to the MERS-RBD. These results add more evidence to the existing belief that bats are the original source of MERS-CoV and suggest that bCD26s in many species can mediate the entry of the virus, which has significant implications for the surveillance and control of MERS-CoV infection.



In this study, we found that bat CD26s (bCD26s) from different species exhibit large diversities, especially in the region responsible for binding to the receptor binding domain of Middle East respiratory syndrome coronavirus (MERS-CoV). However, they maintain the interaction with MERS-RBD at varied affinities and support the entry of pseudotyped MERS-CoV. These bat receptors polymorphisms seem to confer evolutionary pressure for the adaptation of CD26-binding virus, such as the ancestor of MERS-CoV, and led to the generation of diversified CD26-engaging CoV strains. Thus, our data add more evidence to support that bats are the reservoir of MERS-CoV and similar viruses, as well as further emphasize the necessity to survey MERS-CoV and other CoVs among bats.

Copyright © 2019 American Society for Microbiology. All Rights Reserved.

Keywords: Coronavirus; Bats; Camels; MERS-CoV.