Complete #genome analysis of a #SARS-like #bat #coronavirus identified in the Republic of #Korea (Virus Genes, abstract)

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

Virus Genes. 2019 May 10. doi: 10.1007/s11262-019-01668-w. [Epub ahead of print]

Complete genome analysis of a SARS-like bat coronavirus identified in the Republic of Korea.

Kim Y1,2, Son K1, Kim YS2, Lee SY2, Jheong W1, Oem JK3.

Author information: 1 Environmental Health Research Department, National Institute of Environmental Research, Hwangyeong-ro 42, Seo-gu, Incheon, Republic of Korea. 2 Department of Veterinary Infectious Diseases, College of Veterinary Medicine, Chonbuk National University, Jeonju, Republic of Korea. 3 Department of Veterinary Infectious Diseases, College of Veterinary Medicine, Chonbuk National University, Jeonju, Republic of Korea. jku0623@jbnu.ac.kr.

 

Abstract

Bats have been widely known as natural reservoir hosts of zoonotic diseases, such as severe acute respiratory syndrome (SARS) and Middle East respiratory syndrome (MERS) caused by coronaviruses (CoVs). In the present study, we investigated the whole genomic sequence of a SARS-like bat CoV (16BO133) and found it to be 29,075 nt in length with a 40.9% G+C content. Phylogenetic analysis using amino acid sequences of the ORF 1ab and the spike gene showed that the bat coronavirus strain 16BO133 was grouped with the Beta-CoV lineage B and was closely related to the JTMC15 strain isolated from Rhinolophus ferrumequinum in China. However, 16BO133 was distinctly located in the phylogenetic topology of the human SARS CoV strain (Tor2). Interestingly, 16BO133 showed complete elimination of ORF8 regions induced by a frame shift of the stop codon in ORF7b. The lowest amino acid identity of 16BO133 was identified at the spike region among various ORFs. The spike region of 16BO133 showed 84.7% and 75.2% amino acid identity with Rf1 (SARS-like bat CoV) and Tor2 (human SARS CoV), respectively. In addition, the S gene of 16BO133 was found to contain the amino acid substitution of two critical residues (N479S and T487 V) associated with human infection. In conclusion, we firstly carried out whole genome characterization of the SARS-like bat coronavirus discovered in the Republic of Korea; however, it presumably has no human infectivity. However, continuous surveillance and genomic characterization of coronaviruses from bats are necessary due to potential risks of human infection induced by genetic mutation.

KEYWORDS: Bat; Frame shift; SARS-like coronavirus; Whole genome; Zoonotic disease

PMID: 31076983 DOI: 10.1007/s11262-019-01668-w

Keywords: Coronavirus; SARS; Bats; S. Korea.

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#Discovery and Characterization of Novel #Bat #Coronavirus Lineages from #Kazakhstan (Viruses, abstract)

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

Viruses. 2019 Apr 17;11(4). pii: E356. doi: 10.3390/v11040356.

Discovery and Characterization of Novel Bat Coronavirus Lineages from Kazakhstan.

Mendenhall IH1, Kerimbayev AA2, Strochkov VM3, Sultankulova KT4, Kopeyev SK5, Su YCF6, Smith GJD7,8,9, Orynbayev MB10.

Author information: 1 Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore 169857, Singapore. ian.mendenhall@duke-nus.edu.sg. 2 Research Institute for Biological Safety Problems, 080409 Gvardeiskiy, Kordaiskiy rayon, Zhambylskaya oblast, Kazakhstan. aslan_kerim@mail.ru. 3 Research Institute for Biological Safety Problems, 080409 Gvardeiskiy, Kordaiskiy rayon, Zhambylskaya oblast, Kazakhstan. vstrochkov@gmail.com. 4 Research Institute for Biological Safety Problems, 080409 Gvardeiskiy, Kordaiskiy rayon, Zhambylskaya oblast, Kazakhstan. sultankul70@mail.ru. 5 Research Institute for Biological Safety Problems, 080409 Gvardeiskiy, Kordaiskiy rayon, Zhambylskaya oblast, Kazakhstan. kopeyev85@mail.ru. 6 Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore 169857, Singapore. yvonne.su@duke-nus.edu.sg. 7 Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore 169857, Singapore. gavin.smith@duke-nus.edu.sg. 8 SingHealth Duke-NUS Global Health Institute, SingHealth Duke-NUS Academic Medical Centre, Singapore 168753, Singapore. gavin.smith@duke-nus.edu.sg. 9 Duke Global Health Institute, Duke University, Durham, NC 27710, USA. gavin.smith@duke-nus.edu.sg. 10 Research Institute for Biological Safety Problems, 080409 Gvardeiskiy, Kordaiskiy rayon, Zhambylskaya oblast, Kazakhstan. omb65@mail.ru.

 

Abstract

Coronaviruses are positive-stranded RNA viruses that infect a variety of hosts, resulting in a range of symptoms from gastrointestinal illness to respiratory distress. Bats are reservoirs for a high diversity of coronaviruses, and focused surveillance detected several strains genetically similar to MERS-coronavirus, SARS-coronavirus, and the human coronaviruses 229E and NL63. The bat fauna of central Asia, which link China to eastern Europe, are relatively less studied than other regions of the world. Kazakhstan is the world’s ninth largest country; however, little is understood about the prevalence and diversity of bat-borne viruses. In this study, bat guano was collected from bat caves in three different sites of southern Kazakhstan that tested positive for coronaviruses. Our phylogenetic reconstruction indicates these are novel bat coronaviruses that belong to the genus Alphacoronavirus. In addition, two distinct lineages of Kazakhstan bat coronaviruses were detected. Both lineages are closely related to bat coronaviruses from China, France, Spain, and South Africa, suggesting that co-circulation of coronaviruses is common in multiple bat species with overlapping geographical distributions. Our study highlights the need for collaborative efforts in understudied countries to increase integrated surveillance capabilities toward better monitoring and detection of infectious diseases.

KEYWORDS: Hypsugo savii; Kazakhstan; Myotis blythii; coronavirus; phylogeny; virus discovery

PMID: 30999711 DOI: 10.3390/v11040356

Keywords: Coronavirus; Alphacoronavirus; Bats; Kazakhstan.

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#Genome Organization of Canada #Goose #Coronavirus, A Novel #Species Identified in a Mass Die-off of Canada Geese (Sci Rep., abstract)

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

Sci Rep. 2019 Apr 11;9(1):5954. doi: 10.1038/s41598-019-42355-y.

Genome Organization of Canada Goose Coronavirus, A Novel Species Identified in a Mass Die-off of Canada Geese.

Papineau A1,2, Berhane Y1, Wylie TN3,4, Wylie KM3,4, Sharpe S5, Lung O6,7.

Author information: 1 National Centre for Foreign Animal Disease, Canadian Food Inspection Agency, Winnipeg, MB, Canada. 2 Department of Biological Sciences, University of Manitoba, Winnipeg, MB, Canada. 3 Department of Pediatrics, Washington University School of Medicine, St. Louis, St. Louis, MO, USA. 4 McDonnell Genome Institute, Washington University School of Medicine in St. Louis, St. Louis, MO, USA. 5 Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada. 6 National Centre for Foreign Animal Disease, Canadian Food Inspection Agency, Winnipeg, MB, Canada. Oliver.Lung@canada.ca. 7 Department of Biological Sciences, University of Manitoba, Winnipeg, MB, Canada. Oliver.Lung@canada.ca.

 

Abstract

The complete genome of a novel coronavirus was sequenced directly from the cloacal swab of a Canada goose that perished in a die-off of Canada and Snow geese in Cambridge Bay, Nunavut, Canada. Comparative genomics and phylogenetic analysis indicate it is a new species of Gammacoronavirus, as it falls below the threshold of 90% amino acid similarity in the protein domains used to demarcate Coronaviridae. Additional features that distinguish the genome of Canada goose coronavirus include 6 novel ORFs, a partial duplication of the 4 gene and a presumptive change in the proteolytic processing of polyproteins 1a and 1ab.

PMID: 30976080 DOI: 10.1038/s41598-019-42355-y

Keywords: Coronavirus; Gammacoronavirus; Canada Goose Coronavirus; Canada; Wild Birds.

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High-throughput #Screening and #Identification of Potent Broad-spectrum #Inhibitors of #Coronaviruses (J Virol., abstract)

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

High-throughput Screening and Identification of Potent Broad-spectrum Inhibitors of Coronaviruses

Liang Shen, Junwei Niu, Chunhua Wang, Baoying Huang, Wenling Wang, Na Zhu, Yao Deng, Huijuan Wang, Fei Ye, Shan Cen, Wenjie Tan

DOI: 10.1128/JVI.00023-19

 

ABSTRACT

Coronaviruses (CoVs) act as cross-species viruses and have the potential to spread rapidly into new host species and cause epidemic diseases. Despite the severe public health threat of severe acute respiratory syndrome coronavirus and Middle East respiratory syndrome CoV (MERS-CoV), there are currently no drugs available for their treatment; therefore, broad-spectrum inhibitors of emerging and endemic CoVs are urgently needed. To search for effective inhibitory agents, we performed high-throughput screening (HTS) of a 2,000-compound library of approved drugs and pharmacologically active compounds using the established genetically engineered human CoV OC43 (HCoV-OC43) strain expressing Renilla luciferase (rOC43-ns2Del-Rluc) and validated the inhibitors using multiple genetically distinct CoVs in vitro. We screened 56 hits from the HTS data and validated 36 compounds in vitro using wild-type HCoV-OC43. Furthermore, we identified seven compounds (lycorine, emetine, monensin sodium, mycophenolate mofeti, mycophenolic acid, phenazopyridine, and pyrvinium pamoate) as broad-spectrum inhibitors according to their strong inhibition of replication by four CoVs in vitro at low-micromolar concentrations. Additionally, we found that emetine blocked MERS-CoV entry according to pseudovirus-entry assays, and that lycorine protected BALB/c mice against HCoV-OC43-induced lethality by decreasing viral load in the central nervous system. This represents the first demonstration of in vivo real-time bioluminescence imaging to monitor the effect of lycorine on the spread and distribution of HCoV-OC43 in a mouse model. These results offer critical information supporting the development of an effective therapeutic strategy against CoV infection.

 

IMPORTANCE

Currently, there is no approved therapy to treat coronavirus infection; therefore, broad-spectrum inhibitors of emerging and endemic CoVs are needed. Based on our high-throughput screening assay using a compound library, we identified seven compounds with broad-spectrum efficacy against the replication of four CoVs in vitro. Additionally, one compound (lycorine) was found to protect BALB/c mice against HCoV-OC43-induced lethality by decreasing viral load in the central nervous system. This inhibitor might offer promising therapeutic possibilities for combatting novel CoV infections in the future.

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

Keywords: Antivirals; Coronavirus; Animal models.

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Anti-spike #IgG causes severe acute #lung #injury by skewing #macrophage responses during acute #SARS-CoV infection (JCI Insight, abstract)

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

JCI Insight. 2019 Feb 21;4(4). pii: 123158. doi: 10.1172/jci.insight.123158. eCollection 2019 Feb 21.

Anti-spike IgG causes severe acute lung injury by skewing macrophage responses during acute SARS-CoV infection.

Liu L1,2, Wei Q3, Lin Q1, Fang J1, Wang H1, Kwok H1, Tang H1, Nishiura K1, Peng J1, Tan Z1, Wu T1, Cheung KW1, Chan KH1, Alvarez X4, Qin C3, Lackner A4, Perlman S5,6, Yuen KY1, Chen Z1,2.

Author information: 1 AIDS Institute and Department of Microbiology, State Key Laboratory of Emerging Infectious Disease, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China. 2 HKU-AIDS Institute Shenzhen Research Laboratory and AIDS Clinical Research Laboratory, Shenzhen Key Laboratory of Infection and Immunity, Shenzhen Key Clinical Department of Emerging Infectious Diseases, Shenzhen Third People’s Hospital, Shenzhen, China. 3 Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences (CAMS) and Peking Union Medical College (PUMC), Beijing, China. 4 Division of Comparative Pathology, Tulane National Primate Research Center, Covington, Louisiana, USA. 5 Department of Microbiology and Immunology, University of Iowa, Iowa City, Iowa, USA. 6 State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.

 

Abstract

Newly emerging viruses, such as severe acute respiratory syndrome coronavirus (SARS-CoV), Middle Eastern respiratory syndrome CoVs (MERS-CoV), and H7N9, cause fatal acute lung injury (ALI) by driving hypercytokinemia and aggressive inflammation through mechanisms that remain elusive. In SARS-CoV/macaque models, we determined that anti-spike IgG (S-IgG), in productively infected lungs, causes severe ALI by skewing inflammation-resolving response. Alveolar macrophages underwent functional polarization in acutely infected macaques, demonstrating simultaneously both proinflammatory and wound-healing characteristics. The presence of S-IgG prior to viral clearance, however, abrogated wound-healing responses and promoted MCP1 and IL-8 production and proinflammatory monocyte/macrophage recruitment and accumulation. Critically, patients who eventually died of SARS (hereafter referred to as deceased patients) displayed similarly accumulated pulmonary proinflammatory, absence of wound-healing macrophages, and faster neutralizing antibody responses. Their sera enhanced SARS-CoV-induced MCP1 and IL-8 production by human monocyte-derived wound-healing macrophages, whereas blockade of FcγR reduced such effects. Our findings reveal a mechanism responsible for virus-mediated ALI, define a pathological consequence of viral specific antibody response, and provide a potential target for treatment of SARS-CoV or other virus-mediated lung injury.

KEYWORDS: Cytokines; Immunoglobulins; Infectious disease; Macrophages; Pulmonology

PMID: 30830861 DOI: 10.1172/jci.insight.123158

Keywords: Coronavirus; SARS-CoV; Acute Lung Injury; Immunoglobulins.

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Potential Intermediate #Hosts for #Coronavirus Transmission: No Evidence of Clade 2c Coronaviruses in Domestic #Livestock from #Ghana (Trop Med Infect Dis., abstract)

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

Trop Med Infect Dis. 2019 Feb 10;4(1). pii: E34. doi: 10.3390/tropicalmed4010034.

Potential Intermediate Hosts for Coronavirus Transmission: No Evidence of Clade 2c Coronaviruses in Domestic Livestock from Ghana.

El-Duah P1,2, Sylverken A3,4, Owusu M5,6, Yeboah R7,8, Lamptey J9,10, Frimpong YO11,12, Burimuah V13,14, Antwi C15, Folitse R16, Agbenyega O17, Oppong S18, Adu-Sarkodie Y19.

Author information: 1 Department of Clinical Microbiology, Kwame Nkrumah University of Science and Technology, PMB, UPO, Kumasi 00233, Ghana. elduahphilip9@gmail.com. 2 Kumasi Centre for Collaborative Research in Tropical Medicine, PMB, UPO, Kumasi 00233, Ghana. elduahphilip9@gmail.com. 3 Kumasi Centre for Collaborative Research in Tropical Medicine, PMB, UPO, Kumasi 00233, Ghana. annan@kccr.de. 4 Department of Theoretical and Applied Biology, Kwame Nkrumah University of Science and Technology, PMB, UPO, Kumasi 00233, Ghana. annan@kccr.de. 5 Kumasi Centre for Collaborative Research in Tropical Medicine, PMB, UPO, Kumasi 00233, Ghana. owusumichael-gh@hotmail.com. 6 Department of Medical Laboratory Technology, Kwame Nkrumah University of Science and Technology, PMB, UPO, Kumasi 00233, Ghana. owusumichael-gh@hotmail.com. 7 Department of Clinical Microbiology, Kwame Nkrumah University of Science and Technology, PMB, UPO, Kumasi 00233, Ghana. Yeboahrichmond82@yahoo.com. 8 Kumasi Centre for Collaborative Research in Tropical Medicine, PMB, UPO, Kumasi 00233, Ghana. Yeboahrichmond82@yahoo.com. 9 Department of Clinical Microbiology, Kwame Nkrumah University of Science and Technology, PMB, UPO, Kumasi 00233, Ghana. jlamptey80@gmail.com. 10 Kumasi Centre for Collaborative Research in Tropical Medicine, PMB, UPO, Kumasi 00233, Ghana. jlamptey80@gmail.com. 11 Kumasi Centre for Collaborative Research in Tropical Medicine, PMB, UPO, Kumasi 00233, Ghana. oppongfrimpong1@gmail.com. 12 Department of Animal Science, Kwame Nkrumah University of Science and Technology, PMB, UPO, Kumasi 00233, Ghana. oppongfrimpong1@gmail.com. 13 Kumasi Centre for Collaborative Research in Tropical Medicine, PMB, UPO, Kumasi 00233, Ghana. vitus7uk@yahoo.co.uk. 14 School of Veterinary Medicine, Kwame Nkrumah University of Science and Technology, PMB, UPO, Kumasi 00233, Ghana. vitus7uk@yahoo.co.uk. 15 Department of Animal Science, Kwame Nkrumah University of Science and Technology, PMB, UPO, Kumasi 00233, Ghana. cantwi@icloud.com. 16 School of Veterinary Medicine, Kwame Nkrumah University of Science and Technology, PMB, UPO, Kumasi 00233, Ghana. raphfolitse@yahoo.com. 17 Department of Agroforestry, Kwame Nkrumah University of Science and Technology, PMB, UPO, Kumasi 00233, Ghana. olivia_agbenyega@yahoo.com. 18 Department of Wildlife and Range Management, Kwame Nkrumah University of Science and Technology, PMB, UPO, Kumasi 00233, Ghana. kobbyoppong@yahoo.com. 19 Department of Clinical Microbiology, Kwame Nkrumah University of Science and Technology, PMB, UPO, Kumasi 00233, Ghana. yasax@hotmail.co.uk.

 

Abstract

The emergence of Middle East Respiratory Syndrome Coronavirus (MERS-CoV), nearly a decade ago with worldwide distribution, was believed to be of zoonotic origin from bats with dromedary camels as intermediate hosts. There is a likelihood of other domestic livestock serving as intermediate hosts for this virus. The presence of coronaviruses, closely related to MERS-CoV in Ghanaian bats, presented the opportunity to test the hypothesis of transmissibility of this virus through domestic livestock species. The possible interactions between livestock and bats in 31 household farms were accessed by observation and interviews with farmers. Rectal swabs and serum from cattle, sheep, goats, donkeys, and swine from commercial and household farms were tested for MERS-CoV and a Nycteris sp. bat coronavirus, previously detected in Ghana. A pan-PCR assay to detect clade 2c viruses and recombinant immunofluorescence assay to detect anti-spike IgG antibodies against the target viruses were used. Likely contact between livestock and bats was determined for 13 farms (41.9%) that reported confining their livestock and also observing bats in their homes. Livestock were left unconfined on eight farms (25.8%) that also observed bats roosting in trees close to their homes. No viral RNA or antibodies against the two coronaviruses were detected in any of the livestock species tested. Cattle, sheep, goats, donkeys, and swine are not likely hosts of clade 2c coronaviruses.

KEYWORDS: bats; coronavirus; intermediate host; livestock

PMID: 30744201 DOI: 10.3390/tropicalmed4010034 Free full text

Keywords: Coronavirus; MERS-CoV; Bats; Cattle; Pigs; Ghana.

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#Bat-Origin #Coronaviruses Expand Their #Host Range to #Pigs (Front Microbiol., abstract)

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

Trends Microbiol. 2018 Jun;26(6):466-470. doi: 10.1016/j.tim.2018.03.001. Epub 2018 Apr 18.

Bat-Origin Coronaviruses Expand Their Host Range to Pigs.

Wang L1, Su S2, Bi Y3, Wong G4, Gao GF5.

Author information: 1 CAS Key Laboratory of Pathogenic Microbiology and Immunology, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Disease, Institute of Microbiology, Center for Influenza Research and Early-warning (CASCIRE), Chinese Academy of Sciences, Beijing 100101, China. 2 MOE Joint International Research Laboratory of Animal Health and Food Safety, Jiangsu Engineering Laboratory of Animal Immunology, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China. 3 CAS Key Laboratory of Pathogenic Microbiology and Immunology, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Disease, Institute of Microbiology, Center for Influenza Research and Early-warning (CASCIRE), Chinese Academy of Sciences, Beijing 100101, China; Shenzhen Key Laboratory of Pathogen and Immunity, Guangdong Key Laboratory for Diagnosis and Treatment of Emerging Infectious Diseases, Shenzhen Third People’s Hospital, Shenzhen 518112, China. 4 Shenzhen Key Laboratory of Pathogen and Immunity, Guangdong Key Laboratory for Diagnosis and Treatment of Emerging Infectious Diseases, Shenzhen Third People’s Hospital, Shenzhen 518112, China. 5 CAS Key Laboratory of Pathogenic Microbiology and Immunology, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Disease, Institute of Microbiology, Center for Influenza Research and Early-warning (CASCIRE), Chinese Academy of Sciences, Beijing 100101, China; Shenzhen Key Laboratory of Pathogen and Immunity, Guangdong Key Laboratory for Diagnosis and Treatment of Emerging Infectious Diseases, Shenzhen Third People’s Hospital, Shenzhen 518112, China; National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), Beijing 102206, China. Electronic address: gaof@im.ac.cn.

 

Abstract

Infections with bat-origin coronaviruses have caused severe illness in humans by ‘host jump’. Recently, novel bat-origin coronaviruses were found in pigs. The large number of mutations on the receptor-binding domain allowed the viruses to infect the new host, posing a potential threat to both agriculture and public health.

Copyright © 2018 Elsevier Ltd. All rights reserved.

KEYWORDS: SeACoV; bat-origin; host jump; public health; swine enteric alphacoronaviruses

PMID: 29680361 DOI: 10.1016/j.tim.2018.03.001 [Indexed for MEDLINE]

Keywords: Coronavirus; Bats; Pigs; Alphacoronavirus.

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