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Xu L, Song M, Tian X, Sun J, Wang Y, Bie M, Bi Y, Holmes EC, Guan Y, Chen J, Li J, Shi W. Five-year longitudinal surveillance reveals the continual circulation of both alpha- and beta-coronaviruses in Plateau and Gansu pikas ( Ochotona spp.) at Qinghai Lake, China 1. Emerg Microbes Infect 2024; 13:2392693. [PMID: 39137298 PMCID: PMC11346322 DOI: 10.1080/22221751.2024.2392693] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2024] [Revised: 08/03/2024] [Accepted: 08/11/2024] [Indexed: 08/15/2024]
Abstract
The discovery of alphacoronaviruses and betacoronaviruses in plateau pikas (Ochotona curzoniae) expanded the host range of mammalian coronavirus (CoV) to a new order - Lagomorpha. However, the diversity and evolutionary relationships of CoVs in these plateau-region-specific animal population remains uncertain. We conducted a five-year longitudinal surveillance of CoVs harboured by pikas around Qinghai Lake, China. CoVs were identified in 33 of 236 plateau pikas and 2 of 6 Gansu pikas (Ochotona cansus), with a total positivity rate of 14.5%, and exhibiting a wide spatiotemporal distribution across seven sampling sites and six time points. Through meta-transcriptomic sequencing and RT-PCR, we recovered 16 near-complete viral genome sequences. Phylogenetic analyses classified the viruses as variants of either pika alphacoronaviruses or betacoronaviruses endemic to plateau pikas from the Qinghai-Tibet Plateau region. Of particular note, the pika-associated betacoronaviruses may represent a novel subgenus within the genus Betacoronavirus. Tissue tropism, evaluated using quantitative real-time PCR, revealed the presence of CoV in the rectal and/or lung tissues, with the highest viral loads at 103.55 or 102.80 RNA copies/μL. Surface plasmon resonance (SPR) assays indicated that the newly identified betacoronavirus did not bind to human or pika Angiotensin-converting enzyme 2 (ACE2) or Dipeptidyl peptidase 4 (DPP4). The findings highlight the ongoing circulation and broadening host spectrum of CoVs among pikas, emphasizing the necessity for further investigation to evaluate their potential public health risks.
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Affiliation(s)
- Lin Xu
- School of Public Health, Shandong First Medical University & Shandong Academy of Medical Sciences, Ji'nan, People’s Republic of China
- Key Laboratory of Emerging Infectious Diseases in Universities of Shandong, Shandong First Medical University & Shandong Academy of Medical Sciences, Ji'nan, People’s Republic of China
| | - Meiqing Song
- School of Public Health, Shandong First Medical University & Shandong Academy of Medical Sciences, Ji'nan, People’s Republic of China
- Key Laboratory of Emerging Infectious Diseases in Universities of Shandong, Shandong First Medical University & Shandong Academy of Medical Sciences, Ji'nan, People’s Republic of China
| | - Xianzhi Tian
- School of Public Health, Shandong First Medical University & Shandong Academy of Medical Sciences, Ji'nan, People’s Republic of China
- Key Laboratory of Emerging Infectious Diseases in Universities of Shandong, Shandong First Medical University & Shandong Academy of Medical Sciences, Ji'nan, People’s Republic of China
| | - Ju Sun
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Center for Influenza Research and Early-warning (CASCIRE), CAS-TWAS Center of Excellence for Emerging Infectious Diseases (CEEID), Chinese Academy of Sciences (CAS), Beijing, People’s Republic of China
| | - Yanjun Wang
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Center for Influenza Research and Early-warning (CASCIRE), CAS-TWAS Center of Excellence for Emerging Infectious Diseases (CEEID), Chinese Academy of Sciences (CAS), Beijing, People’s Republic of China
| | - Mengyu Bie
- School of Public Health, Shandong First Medical University & Shandong Academy of Medical Sciences, Ji'nan, People’s Republic of China
- Key Laboratory of Emerging Infectious Diseases in Universities of Shandong, Shandong First Medical University & Shandong Academy of Medical Sciences, Ji'nan, People’s Republic of China
| | - Yuhai Bi
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Center for Influenza Research and Early-warning (CASCIRE), CAS-TWAS Center of Excellence for Emerging Infectious Diseases (CEEID), Chinese Academy of Sciences (CAS), Beijing, People’s Republic of China
- University of Chinese Academy of Sciences, Beijing, People’s Republic of China
| | - Edward C. Holmes
- School of Medical Sciences, The University of Sydney, Sydney, Australia
| | - Yi Guan
- Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, People’s Republic of China
- Shanghai Institute of Virology, Shanghai Jiao Tong University School of Medicine, Shanghai, People’s Republic of China
| | - Jianjun Chen
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, People’s Republic of China
| | - Juan Li
- Key Laboratory of Emerging Infectious Diseases in Universities of Shandong, Shandong First Medical University & Shandong Academy of Medical Sciences, Ji'nan, People’s Republic of China
| | - Weifeng Shi
- Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, People’s Republic of China
- Shanghai Institute of Virology, Shanghai Jiao Tong University School of Medicine, Shanghai, People’s Republic of China
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Guo J, He J, Liang Z, Huang S, Wen F. Birds as reservoirs: unraveling the global spread of Gamma- and Deltacoronaviruses. mBio 2024:e0232424. [PMID: 39230281 DOI: 10.1128/mbio.02324-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/05/2024] Open
Abstract
Avian migration is a global phenomenon that transcends geographical boundaries. These migratory birds serve as unwitting carriers of diverse Gammacoronaviruses (γ-CoVs) and Deltacoronaviruses (δ-CoVs). While recombination events have been documented among γ-CoVs in avian species and β-CoVs in mammals, evidence for recombination between CoVs of distinct genera remains limited. This minireview examines the prevalence of CoVs in both domestic waterfowl (ducks and geese) and wild bird populations inhabiting various regions. We investigate the dissemination patterns of γ-CoVs and δ-CoVs among these populations, highlighting their shared characteristics. Furthermore, the review explores the intricate web of cross-species transmission of δ-CoVs from wild birds to mammals, with a particular focus on pigs. Understanding the distinct features of CoVs harbored by waterfowl and wild birds and their potential for cross-species transmission is crucial for preparedness and response to future CoV epidemics.
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Affiliation(s)
- Jinyue Guo
- College of Life Science and Engineering, Foshan University, Foshan, Guangdong, China
| | - Jieheng He
- College of Life Science and Engineering, Foshan University, Foshan, Guangdong, China
| | - Zhaoping Liang
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, Guangdong, China
| | - Shujian Huang
- College of Life Science and Engineering, Foshan University, Foshan, Guangdong, China
| | - Feng Wen
- College of Life Science and Engineering, Foshan University, Foshan, Guangdong, China
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Tian Y, Yu T, Wang J, Zhang H, Jian Y, Li X, Wang G, Wang G, Hu Y, Lu C, Zhou J, Ma L, Liao M. Genetic characterization of the first Deltacoronavirus from wild birds around Qinghai Lake. Front Microbiol 2024; 15:1423367. [PMID: 38933020 PMCID: PMC11199898 DOI: 10.3389/fmicb.2024.1423367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2024] [Accepted: 05/15/2024] [Indexed: 06/28/2024] Open
Abstract
Deltacoronavirus, widely distributed among pigs and wild birds, pose a significant risk of cross-species transmission, including potential human epidemics. Metagenomic analysis of bird samples from Qinghai Lake, China in 2021 reported the presence of Deltacoronavirus. A specific gene fragment of Deltacoronavirus was detected in fecal samples from wild birds at a positive rate of 5.94% (6/101). Next-generation sequencing (NGS) identified a novel Deltacoronavirus strain, which was closely related to isolates from the United Arab Emirates (2018), China (2022), and Poland (2023). Subsequently the strain was named A/black-headed gull/Qinghai/2021(BHG-QH-2021) upon confirmation of the Cytochrome b gene of black-headed gull in the sample. All available genome sequences of avian Deltacoronavirus, including the newly identified BHG-QH-2021 and 5 representative strains of porcine Deltacoronavirus (PDCoV), were classified according to ICTV criteria. In contrast to Coronavirus HKU15, which infects both mammals and birds and shows the possibility of cross-species transmission from bird to mammal host, our analysis revealed that BHG-QH-2021 is classified as Putative species 4. Putative species 4 has been reported to infect 5 species of birds but not mammals, suggesting that cross-species transmission of Putative species 4 is more prevalent among birds. Recombination analysis traced BHG-QH-2021 origin to dut148cor1 and MW01_1o strains, with MW01_1o contributing the S gene. Surprisingly, SwissModle prediction showed that the optimal template for receptor-binding domain (RBD) of BHG-QH-2021 is derived from the human coronavirus 229E, a member of the Alphacoronavirus, rather than the anticipated RBD structure of PDCoV of Deltacoronavirus. Further molecular docking analysis revealed that substituting the loop 1-2 segments of HCoV-229E significantly enhanced the binding capability of BHG-QH-2021 with human Aminopeptidase N (hAPN), surpassing its native receptor-binding domain (RBD). Most importantly, this finding was further confirmed by co-immunoprecipitation experiment that loop 1-2 segments of HCoV-229E enable BHG-QH-2021 RBD binding to hAPN, indicating that the loop 1-2 segment of the RBD in Putative species 4 is a probable key determinant for the virus ability to spill over into humans. Our results summarize the phylogenetic relationships among known Deltacoronavirus, reveal an independent putative avian Deltacoronavirus species with inter-continental and inter-species transmission potential, and underscore the importance of continuous surveillance of wildlife Deltacoronavirus.
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Affiliation(s)
- Ye Tian
- Key Laboratory of Animal Virology, Ministry of Agriculture and Rural Affairs, Zhejiang University, Hangzhou, China
| | - Tianqi Yu
- Key Laboratory of Animal Virology, Ministry of Agriculture and Rural Affairs, Zhejiang University, Hangzhou, China
| | - Jun Wang
- Animal Husbandry and Veterinary Workstation of the Third Division, Xinjiang Production and Construction Corps, Tumushuke, China
| | - Haoxiang Zhang
- Key Laboratory of Animal Virology, Ministry of Agriculture and Rural Affairs, Zhejiang University, Hangzhou, China
| | - Yingna Jian
- Qinghai Provincial Key Laboratory of Pathogen Diagnosis for Animal Disease and Green Technical Research for Prevention and Control, Qinghai Academy of Animal Sciences and Veterinary Medicine, Qinghai University, Xining, Qinghai, China
| | - Xiuping Li
- Qinghai Provincial Key Laboratory of Pathogen Diagnosis for Animal Disease and Green Technical Research for Prevention and Control, Qinghai Academy of Animal Sciences and Veterinary Medicine, Qinghai University, Xining, Qinghai, China
| | - Geping Wang
- Qinghai Provincial Key Laboratory of Pathogen Diagnosis for Animal Disease and Green Technical Research for Prevention and Control, Qinghai Academy of Animal Sciences and Veterinary Medicine, Qinghai University, Xining, Qinghai, China
| | - Guanghua Wang
- Qinghai Provincial Key Laboratory of Pathogen Diagnosis for Animal Disease and Green Technical Research for Prevention and Control, Qinghai Academy of Animal Sciences and Veterinary Medicine, Qinghai University, Xining, Qinghai, China
| | - Yong Hu
- Qinghai Provincial Key Laboratory of Pathogen Diagnosis for Animal Disease and Green Technical Research for Prevention and Control, Qinghai Academy of Animal Sciences and Veterinary Medicine, Qinghai University, Xining, Qinghai, China
| | - Chenhe Lu
- Key Laboratory of Animal Virology, Ministry of Agriculture and Rural Affairs, Zhejiang University, Hangzhou, China
| | - Jiyong Zhou
- Key Laboratory of Animal Virology, Ministry of Agriculture and Rural Affairs, Zhejiang University, Hangzhou, China
| | - Liqing Ma
- Qinghai Provincial Key Laboratory of Pathogen Diagnosis for Animal Disease and Green Technical Research for Prevention and Control, Qinghai Academy of Animal Sciences and Veterinary Medicine, Qinghai University, Xining, Qinghai, China
| | - Min Liao
- Key Laboratory of Animal Virology, Ministry of Agriculture and Rural Affairs, Zhejiang University, Hangzhou, China
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Dong L, Li Y, Yang C, Gong J, Zhu W, Huang Y, Kong M, Zhao L, Wang F, Lu S, Pu J, Yang J. Species-level microbiota of ticks and fleas from Marmota himalayana in the Qinghai-Tibet Plateau. Front Microbiol 2023; 14:1188155. [PMID: 37415819 PMCID: PMC10320725 DOI: 10.3389/fmicb.2023.1188155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Accepted: 05/31/2023] [Indexed: 07/08/2023] Open
Abstract
Introduction Ticks and fleas, as blood-sucking arthropods, carry and transmit various zoonotic diseases. In the natural plague foci of China, monitoring of Yersinia pestis has been continuously conducted in Marmota himalayana and other host animals, whereas other pathogens carried by vectors are rarely concerned in the Qinghai-Tibet Plateau. Methods In this study, we investigated the microbiota of ticks and fleas sampling from M. himalayana in the Qinghai-Tibet Plateau, China by metataxonomics combined with metagenomic methods. Results By metataxonomic approach based on full-length 16S rDNA amplicon sequencing and operational phylogenetic unit (OPU) analyses, we described the microbiota community of ticks and fleas at the species level, annotated 1,250 OPUs in ticks, including 556 known species and 492 potentially new species, accounting for 48.50% and 41.71% of the total reads in ticks, respectively. A total of 689 OPUs were detected in fleas, consisting of 277 known species (40.62% of the total reads in fleas) and 294 potentially new species (56.88%). At the dominant species categories, we detected the Anaplasma phagocytophilum (OPU 421) and potentially pathogenic new species of Wolbachia, Ehrlichia, Rickettsia, and Bartonella. Using shotgun sequencing, we obtained 10 metagenomic assembled genomes (MAGs) from vector samples, including a known species (Providencia heimbachae DFT2), and six new species affliated to four known genera, i.e., Wolbachia, Mumia, Bartonella, and Anaplasma. By the phylogenetic analyses based on full-length 16S rRNA genes and core genes, we identified that ticks harbored pathogenic A. phagocytophilum. Moreover, these potentially pathogenic novel species were more closely related to Ehrlichia muris, Ehrlichia muris subsp. eauclairensis, Bartonella rochalimae, and Rickettsia limoniae, respectively. The OPU 422 Ehrlichia sp1 was most related to Ehrlichia muris and Ehrlichia muris subsp. eauclairensis. The OPU 230 Bartonella sp1 and Bartonella spp. (DTF8 and DTF9) was clustered with Bartonella rochalimae. The OPU 427 Rickettsia sp1 was clustered with Rickettsia limoniae. Discussion The findings of the study have advanced our understanding of the potential pathogen groups of vectors in marmot (Marmota himalayana) in the Qinghai-Tibet Plateau.
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Affiliation(s)
- Lingzhi Dong
- Department of Epidemiology, School of Public Health, Shanxi Medical University, Taiyuan, China
- State Key Laboratory of Infectious Disease Prevention and Control, Chinese Center for Disease Control and Prevention, National Institute for Communicable Disease Control and Prevention, Beijing, China
| | - Yaben Li
- Department of Epidemiology, School of Public Health, Shanxi Medical University, Taiyuan, China
- State Key Laboratory of Infectious Disease Prevention and Control, Chinese Center for Disease Control and Prevention, National Institute for Communicable Disease Control and Prevention, Beijing, China
| | - Caixin Yang
- Department of Epidemiology, School of Public Health, Shanxi Medical University, Taiyuan, China
- State Key Laboratory of Infectious Disease Prevention and Control, Chinese Center for Disease Control and Prevention, National Institute for Communicable Disease Control and Prevention, Beijing, China
| | - Jian Gong
- Department of Epidemiology, School of Public Health, Shanxi Medical University, Taiyuan, China
- State Key Laboratory of Infectious Disease Prevention and Control, Chinese Center for Disease Control and Prevention, National Institute for Communicable Disease Control and Prevention, Beijing, China
| | - Wentao Zhu
- Department of Infectious Diseases and Clinical Microbiology, Beijing Chao-Yang Hospital, Capital Medical University, Beijing, China
| | - Yuyuan Huang
- State Key Laboratory of Infectious Disease Prevention and Control, Chinese Center for Disease Control and Prevention, National Institute for Communicable Disease Control and Prevention, Beijing, China
| | - Mimi Kong
- Department of Epidemiology, School of Public Health, Shanxi Medical University, Taiyuan, China
- State Key Laboratory of Infectious Disease Prevention and Control, Chinese Center for Disease Control and Prevention, National Institute for Communicable Disease Control and Prevention, Beijing, China
| | - Lijun Zhao
- Department of Epidemiology, School of Public Health, Shanxi Medical University, Taiyuan, China
- State Key Laboratory of Infectious Disease Prevention and Control, Chinese Center for Disease Control and Prevention, National Institute for Communicable Disease Control and Prevention, Beijing, China
| | - Feifei Wang
- Department of Epidemiology, School of Public Health, Shanxi Medical University, Taiyuan, China
- State Key Laboratory of Infectious Disease Prevention and Control, Chinese Center for Disease Control and Prevention, National Institute for Communicable Disease Control and Prevention, Beijing, China
| | - Shan Lu
- Department of Epidemiology, School of Public Health, Shanxi Medical University, Taiyuan, China
- State Key Laboratory of Infectious Disease Prevention and Control, Chinese Center for Disease Control and Prevention, National Institute for Communicable Disease Control and Prevention, Beijing, China
- Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing, China
| | - Ji Pu
- Department of Epidemiology, School of Public Health, Shanxi Medical University, Taiyuan, China
- State Key Laboratory of Infectious Disease Prevention and Control, Chinese Center for Disease Control and Prevention, National Institute for Communicable Disease Control and Prevention, Beijing, China
| | - Jing Yang
- Department of Epidemiology, School of Public Health, Shanxi Medical University, Taiyuan, China
- State Key Laboratory of Infectious Disease Prevention and Control, Chinese Center for Disease Control and Prevention, National Institute for Communicable Disease Control and Prevention, Beijing, China
- Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing, China
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Wang X, Zhu X, Lin Y, He L, Yang J, Wang C, Zhu W. Tracking the first SARS-CoV-2 Omicron BA.5.1.3 outbreak in China. Front Microbiol 2023; 14:1183633. [PMID: 37275159 PMCID: PMC10232789 DOI: 10.3389/fmicb.2023.1183633] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 04/28/2023] [Indexed: 06/07/2023] Open
Abstract
The SARS-CoV-2 is still undergoing rapid evolution, resulting in the emergence of several variants of concern, especially the Omicron variants (B.1.1.529), which are surging worldwide. In this study, we tracked Omicron subvariant BA.5.1.3 as the causative agent in the Hainan Province wave in China, which started on 1 August 2022. This was China's first case of Omicron subvariant BA.5.1.3 and led to an indefinite total lockdown in Hainan with more than 8,500 confirmed cases. We obtained 391 whole genomes from positive nasopharyngeal swab samples in the city of Sanya in Hainan Province, which was the center of this outbreak. More than half of the infected cases were female (58%, 227/391) with a median age of 37.0 years (IQR 23.0-53.0). Median Ct values were 24.9 (IQR 22.6-27.3) and 25.2 (IQR 22.9-27.6) for ORF1ab and N genes, respectively. The total single-nucleotide polymorphism (SNP) numbers of Omicron BA.5.1.3 sampled in Sanya (median 69.0, IQR = 69.0-70.0) compared to those worldwide (median 63.0, IQR = 61.0-64.0) showed a significant difference (p < 0.05). Unique core mutations, including three non-synonymous mutations in ORF1ab (Y1064N, S2844G, and R3574K) and one synonymous mutation in ORF3a (S74S), were found. Phylogenetic analysis showed that virus from Sanya formed an independent sub-clade within the BA.5.1.3 subvariant, and could be divided into 15 haplotypes based on the S gene. The most recent common ancestor for the virus from Sanya was estimated as appearing on 5 July 2022, with 95% HPD ranging from 15 May to 20 September 2022. Thanks to our results, we were also able to delineate the mutational profile of this outbreak and highlight the importance of global genomic surveillance and data sharing.
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Affiliation(s)
- Xiaoxia Wang
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, Sichuan, China
- Central and Clinical Laboratory of Sanya People's Hospital, Sanya, Hainan, China
| | - Xiong Zhu
- Central and Clinical Laboratory of Sanya People's Hospital, Sanya, Hainan, China
| | - Yujin Lin
- Central and Clinical Laboratory of Sanya People's Hospital, Sanya, Hainan, China
| | - Lvfen He
- Central and Clinical Laboratory of Sanya People's Hospital, Sanya, Hainan, China
| | - Jing Yang
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Chuan Wang
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Wentao Zhu
- Department of Infectious Diseases and Clinical Microbiology, Beijing Institute of Respiratory Medicine and Beijing Chao-Yang Hospital, Capital Medical University, Beijing, China
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Zhu W, Huang Y, Gong J, Dong L, Yu X, Chen H, Li D, Zhou L, Yang J, Lu S. A Novel Bat Coronavirus with a Polybasic Furin-like Cleavage Site. Virol Sin 2023:S1995-820X(23)00047-0. [PMID: 37141989 PMCID: PMC10151251 DOI: 10.1016/j.virs.2023.04.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2023] [Accepted: 04/24/2023] [Indexed: 05/06/2023] Open
Abstract
The current pandemic of COVID-19 caused by a novel coronavirus, severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), threatens human health around the world. Of particular concern is that bats are recognized as one of the most potential natural hosts of SARS-CoV-2; however, coronavirus ecology in bats is still nascent. Here, we performed a degenerate primer screening and next-generation sequencing analysis of 112 bats, collected from Hainan Province, China. Three coronaviruses, namely bat betacoronavirus (Bat CoV) CD35, Bat CoV CD36 and bat alphacoronavirus CD30 were identified. Bat CoV CD35 genome had 99.5% identity with Bat CoV CD36, both sharing the highest nucleotide identity with Bat Hp-betacoronavirus Zhejiang2013 (71.4%), followed by SARS-CoV-2 (54.0%). Phylogenetic analysis indicated that Bat CoV CD35 formed a distinct clade, and together with Bat Hp-betacoronavirus Zhejiang2013, was basal to the lineage of SARS-CoV-1 and SARS-CoV-2. Notably, Bat CoV CD35 harbored a canonical furin-like S1/S2 cleavage site that resembles the corresponding sites of SARS-CoV-2. The furin cleavage sites between CD35 and CD36 are identical. In addition, the receptor-binding domain of Bat CoV CD35 showed a highly similar structure to that of SARS-CoV-1 and SARS-CoV-2, especially in one binding loop. In conclusion, this study deepens our understanding of the diversity of coronaviruses and provides clues about the natural origin of the furin cleavage site of SARS-CoV-2.
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Affiliation(s)
- Wentao Zhu
- Department of Infectious Diseases and Clinical Microbiology, Beijing Institute of Respiratory Medicine and Beijing Chao-Yang Hospital, Capital Medical University, Beijing, 100020, China
| | - Yuyuan Huang
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Jian Gong
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Lingzhi Dong
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Xiaojie Yu
- Hainan Provincial Center for Disease Control and Prevention, Haikou 570203, China
| | - Haiyun Chen
- Hainan Provincial Center for Disease Control and Prevention, Haikou 570203, China
| | - Dandan Li
- Hainan Provincial Center for Disease Control and Prevention, Haikou 570203, China
| | - Libo Zhou
- Hainan Provincial Center for Disease Control and Prevention, Haikou 570203, China
| | - Jing Yang
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China; Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing 100730, China.
| | - Shan Lu
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China; Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing 100730, China.
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González-Parra G, Arenas AJ. Mathematical Modeling of SARS-CoV-2 Omicron Wave under Vaccination Effects. COMPUTATION (BASEL, SWITZERLAND) 2023; 11:36. [PMID: 38957648 PMCID: PMC11218807 DOI: 10.3390/computation11020036] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 07/04/2024]
Abstract
Over the course of the COVID-19 pandemic millions of deaths and hospitalizations have been reported. Different SARS-CoV-2 variants of concern have been recognized during this pandemic and some of these variants of concern have caused uncertainty and changes in the dynamics. The Omicron variant has caused a large amount of infected cases in the US and worldwide. The average number of deaths during the Omicron wave toll increased in comparison with previous SARS-CoV-2 waves. We studied the Omicron wave by using a highly nonlinear mathematical model for the COVID-19 pandemic. The novel model includes individuals who are vaccinated and asymptomatic, which influences the dynamics of SARS-CoV-2. Moreover, the model considers the waning of the immunity and efficacy of the vaccine against the Omicron strain. This study uses the facts that the Omicron strain has a higher transmissibility than the previous circulating SARS-CoV-2 strain but is less deadly. Preliminary studies have found that Omicron has a lower case fatality rate compared to previous circulating SARS-CoV-2 strains. The simulation results show that even if the Omicron strain is less deadly it might cause more deaths, hospitalizations and infections. We provide a variety of scenarios that help to obtain insight about the Omicron wave and its consequences. The proposed mathematical model, in conjunction with the simulations, provides an explanation for a large Omicron wave under various conditions related to vaccines and transmissibility. These results provide an awareness that new SARS-CoV-2 variants can cause more deaths even if their fatality rate is lower.
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Affiliation(s)
- Gilberto González-Parra
- Department of Mathematics, New Mexico Tech, New Mexico Institute of Mining and Technology, Socorro, NM 87801, USA
| | - Abraham J. Arenas
- Departamento de Matematicas y Estadistica, Universidad de Cordoba, Monteria 230002, Colombia
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He X, Wang X, Fan G, Li F, Wu W, Wang Z, Fu M, Wei X, Ma S, Ma X. Metagenomic analysis of viromes in tissues of wild Qinghai vole from the eastern Tibetan Plateau. Sci Rep 2022; 12:17239. [PMID: 36241909 PMCID: PMC9562062 DOI: 10.1038/s41598-022-22134-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Accepted: 10/10/2022] [Indexed: 01/06/2023] Open
Abstract
Rodents are natural reservoirs of diverse zoonotic viruses and widely distributed on the Tibetan Plateau. A comprehensive understanding of the virome in local rodent species could provide baseline of viral content and assist in efforts to reduce the risk for future emergence of rodent related zoonotic diseases. A total of 205 tissue and fecal samples from 41 wild Qinghai voles were collected. Metagenomic analyses were performed to outline the characteristics of the viromes, and phylogenetic analyses were used to identify the novel viral genomes. The virome distribution among five tissues (liver, lung, spleen, small intestine with content and feces) was also compared. We identified sequences related to 46 viral families. Novel viral genomes from distinct evolutionary lineages with known viruses were characterized for their genomic and evolutionary characteristics, including Hepatovirus, Hepacivirus, Rotavirus, and Picobirnavirus. Further analyses revealed that the core virome harbored by rodent internal tissues were quite different from the virome found in intestine and fecal samples. These findings provide an overview of the viromes in wild Qinghai voles, which are unique and the most common rodent species in the eastern Tibetan Plateau. A high diversity of viruses is likely present in rodent species in this area.
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Affiliation(s)
- Xiaozhou He
- grid.198530.60000 0000 8803 2373NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People’s Republic of China ,grid.9227.e0000000119573309Chinese Center for Disease Control and Prevention - Wuhan Institute of Virology, Chinese Academy of Sciences Joint Research Center for Emerging Infectious Diseases and Biosafety, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, People’s Republic of China
| | - Xu Wang
- grid.508378.1National Institute of Parasitic Diseases, Chinese Center for Diseases Control and Prevention (Chinese Center for Tropical Diseases Research), NHC Key Laboratory of Parasite and Vector Biology, WHO Collaborating Centre for Tropical Diseases, National Center for International Research on Tropical Diseases, Shanghai, People’s Republic of China
| | - Guohao Fan
- grid.198530.60000 0000 8803 2373NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People’s Republic of China ,grid.9227.e0000000119573309Chinese Center for Disease Control and Prevention - Wuhan Institute of Virology, Chinese Academy of Sciences Joint Research Center for Emerging Infectious Diseases and Biosafety, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, People’s Republic of China
| | - Fan Li
- grid.198530.60000 0000 8803 2373NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People’s Republic of China
| | - Weiping Wu
- grid.508378.1National Institute of Parasitic Diseases, Chinese Center for Diseases Control and Prevention (Chinese Center for Tropical Diseases Research), NHC Key Laboratory of Parasite and Vector Biology, WHO Collaborating Centre for Tropical Diseases, National Center for International Research on Tropical Diseases, Shanghai, People’s Republic of China
| | - Zhenghuan Wang
- grid.22069.3f0000 0004 0369 6365School of Life Sciences, East China Normal University, Shanghai, People’s Republic of China
| | - Meihua Fu
- grid.430328.eShanghai Municipal Center for Disease Control and Prevention, Shanghai, People’s Republic of China
| | - Xu Wei
- grid.22069.3f0000 0004 0369 6365School of Life Sciences, East China Normal University, Shanghai, People’s Republic of China
| | - Shuo Ma
- grid.22069.3f0000 0004 0369 6365School of Life Sciences, East China Normal University, Shanghai, People’s Republic of China
| | - Xuejun Ma
- grid.198530.60000 0000 8803 2373NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People’s Republic of China ,grid.9227.e0000000119573309Chinese Center for Disease Control and Prevention - Wuhan Institute of Virology, Chinese Academy of Sciences Joint Research Center for Emerging Infectious Diseases and Biosafety, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, People’s Republic of China
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9
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Wernike K, Drewes S, Mehl C, Hesse C, Imholt C, Jacob J, Ulrich RG, Beer M. No Evidence for the Presence of SARS-CoV-2 in Bank Voles and Other Rodents in Germany, 2020–2022. Pathogens 2022; 11:pathogens11101112. [PMID: 36297169 PMCID: PMC9610409 DOI: 10.3390/pathogens11101112] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 09/23/2022] [Accepted: 09/26/2022] [Indexed: 11/16/2022] Open
Abstract
Rodentia is the most speciose mammalian order, found across the globe, with some species occurring in close proximity to humans. Furthermore, rodents are known hosts for a variety of zoonotic pathogens. Among other animal species, rodents came into focus when the severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2) spread through human populations across the globe, initially as laboratory animals to study the viral pathogenesis and to test countermeasures. Under experimental conditions, some rodent species including several cricetid species are susceptible to SARS-CoV-2 infection and a few of them can transmit the virus to conspecifics. To investigate whether SARS-CoV-2 is also spreading in wild rodent populations in Germany, we serologically tested samples of free-ranging bank voles (Myodes glareolus, n = 694), common voles (Microtus arvalis, n = 2), house mice (Mus musculus, n = 27), brown or Norway rats (Rattus norvegicus, n = 97) and Apodemus species (n = 8) for antibodies against the virus. The samples were collected from 2020 to 2022 in seven German federal states. All but one sample tested negative by a multispecies ELISA based on the receptor-binding domain (RBD) of SARS-CoV-2. The remaining sample, from a common vole collected in 2021, was within the inconclusive range of the RBD-ELISA, but this result could not be confirmed by a surrogate virus neutralization test as the sample gave a negative result in this test. These results indicate that SARS-CoV-2 has not become highly prevalent in wild rodent populations in Germany.
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Affiliation(s)
- Kerstin Wernike
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, 17493 Greifswald-Insel Riems, Germany
- Correspondence:
| | - Stephan Drewes
- Institute of Novel and Emerging Infectious Diseases, Friedrich-Loeffler-Institut, 17493 Greifswald-Insel Riems, Germany
| | - Calvin Mehl
- Institute of Novel and Emerging Infectious Diseases, Friedrich-Loeffler-Institut, 17493 Greifswald-Insel Riems, Germany
- German Centre for Infection Research (DZIF), Site Hamburg-Lübeck-Borstel-Riems, 17493 Greifswald-Insel Riems, Germany
| | - Christin Hesse
- Rodent Research, Institute for Epidemiology and Pathogen Diagnostics, Julius Kühn-Institute (JKI), Federal Research Centre for Cultivated Plants, 48161 Münster, Germany
| | - Christian Imholt
- Rodent Research, Institute for Epidemiology and Pathogen Diagnostics, Julius Kühn-Institute (JKI), Federal Research Centre for Cultivated Plants, 48161 Münster, Germany
| | - Jens Jacob
- Rodent Research, Institute for Epidemiology and Pathogen Diagnostics, Julius Kühn-Institute (JKI), Federal Research Centre for Cultivated Plants, 48161 Münster, Germany
| | - Rainer G. Ulrich
- Institute of Novel and Emerging Infectious Diseases, Friedrich-Loeffler-Institut, 17493 Greifswald-Insel Riems, Germany
- German Centre for Infection Research (DZIF), Site Hamburg-Lübeck-Borstel-Riems, 17493 Greifswald-Insel Riems, Germany
| | - Martin Beer
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, 17493 Greifswald-Insel Riems, Germany
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10
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Wang X, Ren Z, Wang L, Chen J, Zhang P, Chen JP, Chen X, Li L, Lin X, Qi N, Luo S, Xiang R, Yuan Z, Zhang J, Wang G, Sun MH, Huang Y, Hua Y, Zou J, Hou F, Huang Z, Du S, Xiang H, Sun M, Liu Q, Liao M. Identification of coronaviruses in farmed wild animals reveals their evolutionary origins in Guangdong, southern China. Virus Evol 2022; 8:veac049. [PMID: 35795295 PMCID: PMC9252129 DOI: 10.1093/ve/veac049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 05/15/2022] [Accepted: 06/19/2022] [Indexed: 11/16/2022] Open
Abstract
Coronavirus infections cause diseases that range from mild to severe in mammals and birds. In this study, we detected coronavirus infections in 748 farmed wild animals of 23 species in Guangdong, southern China, by RT-PCR and metagenomic analysis. We identified four coronaviruses in these wild animals and analysed their evolutionary origins. Coronaviruses detected in Rhizomys sinensis were genetically grouped into canine and rodent coronaviruses, which were likely recombinants of canine and rodent coronaviruses. The coronavirus found in Phasianus colchicus was a recombinant pheasant coronavirus of turkey coronavirus and infectious bronchitis virus. The coronavirus in Paguma larvata had a high nucleotide identity (94.6-98.5 per cent) with a coronavirus of bottlenose dolphin (Tursiops truncates). These findings suggested that the wildlife coronaviruses may have experienced homologous recombination and/or crossed the species barrier, likely resulting in the emergence of new coronaviruses. It is necessary to reduce human-animal interactions by prohibiting the eating and raising of wild animals, which may contribute to preventing the emergence of the next coronavirus pandemic.
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Affiliation(s)
- Xiaohu Wang
- Key Laboratory of Livestock Disease Prevention of Guangdong Province, Scientific Observation and Key Laboratory for prevention and control of Avian Influenza and Other Major Poultry Diseases, Ministry of Agriculture and Rural Affairs, Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Baishigang, Wushan Street, Tianhe District, Guangzhou 510640, China
| | - Zhaowen Ren
- Key Laboratory of Livestock Disease Prevention of Guangdong Province, Scientific Observation and Key Laboratory for prevention and control of Avian Influenza and Other Major Poultry Diseases, Ministry of Agriculture and Rural Affairs, Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Baishigang, Wushan Street, Tianhe District, Guangzhou 510640, China
- College of Veterinary Medicine, South China Agricultural University, No. 483 Wushan Road, Tianhe District, Guangzhou 510600, China
| | - Lu Wang
- Key Laboratory of Livestock Disease Prevention of Guangdong Province, Scientific Observation and Key Laboratory for prevention and control of Avian Influenza and Other Major Poultry Diseases, Ministry of Agriculture and Rural Affairs, Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Baishigang, Wushan Street, Tianhe District, Guangzhou 510640, China
- College of Veterinary Medicine, South China Agricultural University, No. 483 Wushan Road, Tianhe District, Guangzhou 510600, China
| | - Jing Chen
- Key Laboratory of Livestock Disease Prevention of Guangdong Province, Scientific Observation and Key Laboratory for prevention and control of Avian Influenza and Other Major Poultry Diseases, Ministry of Agriculture and Rural Affairs, Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Baishigang, Wushan Street, Tianhe District, Guangzhou 510640, China
| | - Pian Zhang
- Key Laboratory of Livestock Disease Prevention of Guangdong Province, Scientific Observation and Key Laboratory for prevention and control of Avian Influenza and Other Major Poultry Diseases, Ministry of Agriculture and Rural Affairs, Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Baishigang, Wushan Street, Tianhe District, Guangzhou 510640, China
- College of Veterinary Medicine, South China Agricultural University, No. 483 Wushan Road, Tianhe District, Guangzhou 510600, China
| | - Jin-Ping Chen
- Institute of Zoology, Guangdong Academy of Sciences, No. 105 Xingang West Road, Haizhu District, Guangzhou 510260, China
| | - Xiaofan Chen
- Key Laboratory of Livestock Disease Prevention of Guangdong Province, Scientific Observation and Key Laboratory for prevention and control of Avian Influenza and Other Major Poultry Diseases, Ministry of Agriculture and Rural Affairs, Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Baishigang, Wushan Street, Tianhe District, Guangzhou 510640, China
- College of Veterinary Medicine, South China Agricultural University, No. 483 Wushan Road, Tianhe District, Guangzhou 510600, China
| | - Linmiao Li
- Institute of Zoology, Guangdong Academy of Sciences, No. 105 Xingang West Road, Haizhu District, Guangzhou 510260, China
| | - Xuhui Lin
- Key Laboratory of Livestock Disease Prevention of Guangdong Province, Scientific Observation and Key Laboratory for prevention and control of Avian Influenza and Other Major Poultry Diseases, Ministry of Agriculture and Rural Affairs, Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Baishigang, Wushan Street, Tianhe District, Guangzhou 510640, China
| | - Nanshan Qi
- Key Laboratory of Livestock Disease Prevention of Guangdong Province, Scientific Observation and Key Laboratory for prevention and control of Avian Influenza and Other Major Poultry Diseases, Ministry of Agriculture and Rural Affairs, Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Baishigang, Wushan Street, Tianhe District, Guangzhou 510640, China
| | - Shengjun Luo
- Key Laboratory of Livestock Disease Prevention of Guangdong Province, Scientific Observation and Key Laboratory for prevention and control of Avian Influenza and Other Major Poultry Diseases, Ministry of Agriculture and Rural Affairs, Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Baishigang, Wushan Street, Tianhe District, Guangzhou 510640, China
| | - Rong Xiang
- Key Laboratory of Livestock Disease Prevention of Guangdong Province, Scientific Observation and Key Laboratory for prevention and control of Avian Influenza and Other Major Poultry Diseases, Ministry of Agriculture and Rural Affairs, Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Baishigang, Wushan Street, Tianhe District, Guangzhou 510640, China
| | - Ziguo Yuan
- College of Veterinary Medicine, South China Agricultural University, No. 483 Wushan Road, Tianhe District, Guangzhou 510600, China
| | - Jianfeng Zhang
- Key Laboratory of Livestock Disease Prevention of Guangdong Province, Scientific Observation and Key Laboratory for prevention and control of Avian Influenza and Other Major Poultry Diseases, Ministry of Agriculture and Rural Affairs, Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Baishigang, Wushan Street, Tianhe District, Guangzhou 510640, China
| | - Gang Wang
- Key Laboratory of Livestock Disease Prevention of Guangdong Province, Scientific Observation and Key Laboratory for prevention and control of Avian Influenza and Other Major Poultry Diseases, Ministry of Agriculture and Rural Affairs, Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Baishigang, Wushan Street, Tianhe District, Guangzhou 510640, China
| | - Min-Hua Sun
- Key Laboratory of Livestock Disease Prevention of Guangdong Province, Scientific Observation and Key Laboratory for prevention and control of Avian Influenza and Other Major Poultry Diseases, Ministry of Agriculture and Rural Affairs, Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Baishigang, Wushan Street, Tianhe District, Guangzhou 510640, China
| | - Yuan Huang
- Key Laboratory of Livestock Disease Prevention of Guangdong Province, Scientific Observation and Key Laboratory for prevention and control of Avian Influenza and Other Major Poultry Diseases, Ministry of Agriculture and Rural Affairs, Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Baishigang, Wushan Street, Tianhe District, Guangzhou 510640, China
| | - Yan Hua
- Guangdong Provincial Wildlife Rescue Center, No. 139 Yuxi Road, Tianhe District, Guangzhou 510520, China
| | - Jiejian Zou
- Guangdong Provincial Wildlife Rescue Center, No. 139 Yuxi Road, Tianhe District, Guangzhou 510520, China
| | - Fanghui Hou
- Guangdong Provincial Wildlife Rescue Center, No. 139 Yuxi Road, Tianhe District, Guangzhou 510520, China
| | - Zhong Huang
- Key Laboratory of Livestock Disease Prevention of Guangdong Province, Scientific Observation and Key Laboratory for prevention and control of Avian Influenza and Other Major Poultry Diseases, Ministry of Agriculture and Rural Affairs, Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Baishigang, Wushan Street, Tianhe District, Guangzhou 510640, China
| | - Shouwen Du
- Department of Infectious Diseases, The Second Clinical Medical College (Shenzhen People’s Hospital) of Jinan University, No. 1017 Dongmen North Road, Luohu District, Shenzhen 518020, China
| | - Hua Xiang
- Key Laboratory of Livestock Disease Prevention of Guangdong Province, Scientific Observation and Key Laboratory for prevention and control of Avian Influenza and Other Major Poultry Diseases, Ministry of Agriculture and Rural Affairs, Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Baishigang, Wushan Street, Tianhe District, Guangzhou 510640, China
- College of Veterinary Medicine, South China Agricultural University, No. 483 Wushan Road, Tianhe District, Guangzhou 510600, China
| | - Mingfei Sun
- Key Laboratory of Livestock Disease Prevention of Guangdong Province, Scientific Observation and Key Laboratory for prevention and control of Avian Influenza and Other Major Poultry Diseases, Ministry of Agriculture and Rural Affairs, Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Baishigang, Wushan Street, Tianhe District, Guangzhou 510640, China
| | - Quan Liu
- Key Laboratory of Livestock Disease Prevention of Guangdong Province, Scientific Observation and Key Laboratory for prevention and control of Avian Influenza and Other Major Poultry Diseases, Ministry of Agriculture and Rural Affairs, Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Baishigang, Wushan Street, Tianhe District, Guangzhou 510640, China
- School of Life Sciences and Engineering, Foshan University, No. 33 Guangyun Road, Shishan Town, Nanhai District, Foshan 528225, China
| | - Ming Liao
- Key Laboratory of Livestock Disease Prevention of Guangdong Province, Scientific Observation and Key Laboratory for prevention and control of Avian Influenza and Other Major Poultry Diseases, Ministry of Agriculture and Rural Affairs, Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Baishigang, Wushan Street, Tianhe District, Guangzhou 510640, China
- College of Veterinary Medicine, South China Agricultural University, No. 483 Wushan Road, Tianhe District, Guangzhou 510600, China
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11
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Zhu W, Yang J, Lu S, Jin D, Pu J, Wu S, Luo XL, Liu L, Li Z, Xu J. RNA Virus Diversity in Birds and Small Mammals From Qinghai–Tibet Plateau of China. Front Microbiol 2022; 13:780651. [PMID: 35250920 PMCID: PMC8894885 DOI: 10.3389/fmicb.2022.780651] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Accepted: 01/12/2022] [Indexed: 12/20/2022] Open
Abstract
Most emerging and re-emerging viruses causing infectious diseases in humans and domestic animals have originated from wildlife. However, current knowledge of the spectrum of RNA viruses in the Qinghai-Tibet Plateau in China is still limited. Here, we performed metatranscriptomic sequencing on fecal samples from 56 birds and 91 small mammals in Tibet and Qinghai Provinces, China, to delineate their viromes and focused on vertebrate RNA viruses. A total of 184 nearly complete genome RNA viruses belonging to 28 families were identified. Among these, 173 new viruses shared <90% amino acid identity with previously known viral sequences. Several of these viruses, such as those belonging to genera Orthonairovirus and Hepatovirus, could be zoonotic viruses. In addition, host taxonomy and geographical location of these viruses showed new hosts and distribution of several previously discovered viruses. Moreover, 12 invertebrate RNA viruses were identified with <40% amino acid identity to known viruses, indicating that they belong to potentially new taxa. The detection and characterization of RNA viruses from wildlife will broaden our knowledge of virus biodiversity and possible viral diseases in the Qinghai–Tibet Plateau.
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Affiliation(s)
- Wentao Zhu
- State Key Laboratory of Infectious Disease Prevention and Control, Chinese Center for Disease Control and Prevention, National Institute for Communicable Disease Control and Prevention, Beijing, China
| | - Jing Yang
- State Key Laboratory of Infectious Disease Prevention and Control, Chinese Center for Disease Control and Prevention, National Institute for Communicable Disease Control and Prevention, Beijing, China
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
- Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing, China
| | - Shan Lu
- State Key Laboratory of Infectious Disease Prevention and Control, Chinese Center for Disease Control and Prevention, National Institute for Communicable Disease Control and Prevention, Beijing, China
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
- Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing, China
| | - Dong Jin
- State Key Laboratory of Infectious Disease Prevention and Control, Chinese Center for Disease Control and Prevention, National Institute for Communicable Disease Control and Prevention, Beijing, China
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
- Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing, China
| | - Ji Pu
- State Key Laboratory of Infectious Disease Prevention and Control, Chinese Center for Disease Control and Prevention, National Institute for Communicable Disease Control and Prevention, Beijing, China
| | - Shusheng Wu
- Yushu Prefecture Center for Disease Control and Prevention, Yushu, China
| | - Xue-Lian Luo
- State Key Laboratory of Infectious Disease Prevention and Control, Chinese Center for Disease Control and Prevention, National Institute for Communicable Disease Control and Prevention, Beijing, China
| | - Liyun Liu
- State Key Laboratory of Infectious Disease Prevention and Control, Chinese Center for Disease Control and Prevention, National Institute for Communicable Disease Control and Prevention, Beijing, China
| | - Zhenjun Li
- State Key Laboratory of Infectious Disease Prevention and Control, Chinese Center for Disease Control and Prevention, National Institute for Communicable Disease Control and Prevention, Beijing, China
| | - Jianguo Xu
- State Key Laboratory of Infectious Disease Prevention and Control, Chinese Center for Disease Control and Prevention, National Institute for Communicable Disease Control and Prevention, Beijing, China
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
- Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing, China
- Research Institute of Public Heath, Nankai University, Tianjin, China
- *Correspondence: Jianguo Xu,
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12
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Zhu W, Huang Y, Yu X, Chen H, Li D, Zhou L, Huang Q, Liu L, Yang J, Lu S. Discovery and Evolutionary Analysis of a Novel Bat-Borne Paramyxovirus. Viruses 2022; 14:288. [PMID: 35215881 PMCID: PMC8879077 DOI: 10.3390/v14020288] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 01/24/2022] [Accepted: 01/28/2022] [Indexed: 12/04/2022] Open
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.
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Affiliation(s)
- Wentao Zhu
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China; (W.Z.); (Y.H.); (Q.H.); (L.L.)
| | - Yuyuan Huang
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China; (W.Z.); (Y.H.); (Q.H.); (L.L.)
| | - Xiaojie Yu
- Hainan Provincial Center for Disease Control and Prevention, Haikou 570203, China; (X.Y.); (H.C.); (D.L.); (L.Z.)
| | - Haiyun Chen
- Hainan Provincial Center for Disease Control and Prevention, Haikou 570203, China; (X.Y.); (H.C.); (D.L.); (L.Z.)
| | - Dandan Li
- Hainan Provincial Center for Disease Control and Prevention, Haikou 570203, China; (X.Y.); (H.C.); (D.L.); (L.Z.)
| | - Libo Zhou
- Hainan Provincial Center for Disease Control and Prevention, Haikou 570203, China; (X.Y.); (H.C.); (D.L.); (L.Z.)
| | - Qianni Huang
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China; (W.Z.); (Y.H.); (Q.H.); (L.L.)
| | - Liyun Liu
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China; (W.Z.); (Y.H.); (Q.H.); (L.L.)
| | - Jing Yang
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China; (W.Z.); (Y.H.); (Q.H.); (L.L.)
- Shanghai Public Health Clinical Center, Fudan University, Shanghai 201508, China
- Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Shan Lu
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China; (W.Z.); (Y.H.); (Q.H.); (L.L.)
- Shanghai Public Health Clinical Center, Fudan University, Shanghai 201508, China
- Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing 100730, China
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13
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Zhu W, Yang J, Lu S, Huang Y, Jin D, Pu J, Liu L, Li Z, Shi M, Xu J. Novel pegiviruses infecting wild birds and rodents. Virol Sin 2022; 37:208-214. [PMID: 35234631 PMCID: PMC9170927 DOI: 10.1016/j.virs.2022.01.013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Accepted: 11/04/2021] [Indexed: 11/18/2022] Open
Abstract
Pegivirus (family Flaviviridae) is a genus of small enveloped RNA viruses that mainly causes blood infections in various mammals including human. Herein, we carried out an extensive survey of pegiviruses from a wide range of wild animals mainly sampled in the Qinghai-Tibet Plateau of China. Three novel pegiviruses, namely Passer montanus pegivirus, Leucosticte brandti pegivirus and Montifringilla taczanowskii pegivirus, were identified from different wild birds, and one new rodent pegivirus, namely Phaiomys leucurus pegivirus, was identified from Blyth's vole. Interestingly, the pegiviruses of non-mammalian origin discovered in this study substantially broaden the host range of Pegivirus to avian species. Co-evolutionary analysis showed virus-host co-divergence over long evolutionary timescales, and indicated that pegiviruses largely followed a virus-host co-divergence relationship. Overall, this work extends the biodiversity of the Pegivirus genus to those infecting wild birds and hence revises the host range and evolutionary history of genus Pegivirus. Novel pegiviruses were identified from wild-life animals in Qinghai-Tibet Plateau. The three divergent species of bird pegiviruses substantially broaden the host range of Pegivirus. A long-term evolutionary relationship was established between pegiviruses and their vertebrate hosts.
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Affiliation(s)
- Wentao Zhu
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Jing Yang
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China; Shanghai Public Health Clinical Center, Fudan University, Shanghai, 201508, China; Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Shan Lu
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China; Shanghai Public Health Clinical Center, Fudan University, Shanghai, 201508, China; Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Yuyuan Huang
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Dong Jin
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China; Shanghai Public Health Clinical Center, Fudan University, Shanghai, 201508, China; Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Ji Pu
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Liyun Liu
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China; Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Zhenjun Li
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Mang Shi
- School of Medicine, Sun Yat-sen University, Shenzhen, 510006, China.
| | - Jianguo Xu
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China; Shanghai Public Health Clinical Center, Fudan University, Shanghai, 201508, China; Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing, 100730, China; Research Institute of Public Heath, Nankai University, Tianjin, 300071, China.
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14
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Zanganeh S, Goodarzi N, Doroudian M, Movahed E. Potential COVID-19 therapeutic approaches targeting angiotensin-converting enzyme 2; An updated review. Rev Med Virol 2021; 32:e2321. [PMID: 34958163 DOI: 10.1002/rmv.2321] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 11/24/2021] [Accepted: 11/30/2021] [Indexed: 12/14/2022]
Abstract
COVID-19 has spread swiftly throughout the world posing a global health emergency. The significant numbers of deaths attributed to this pandemic have researchers battling to understand this new, dangerous virus. Researchers are looking to find possible treatment regimens and develop effective therapies. This study aims to provide an overview of published scientific information on potential treatments, emphasizing angiotensin-converting enzyme II (ACE2) inhibitors as one of the most important drug targets. SARS-CoV-2 receptor-binding domain (RBD); as a viral attachment or entry inhibitor against SARS-CoV-2, human recombinant soluble ACE2; as a genetically modified soluble form of ACE2 to compete with membrane-bound ACE2, and microRNAs (miRNAs); as a negative regulator of the expression of ACE2/TMPRSS2 to inhibit SARS-CoV2 entry into cells, are the potential therapeutic approaches discussed thoroughly in this article. This review provides the groundwork for the ongoing development of therapeutic agents and effective treatments against SARS-COV-2.
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Affiliation(s)
- Saba Zanganeh
- Department of Cell and Molecular Sciences, Faculty of Biological Sciences, Kharazmi University, Tehran, Iran
| | - Nima Goodarzi
- Department of Cell and Molecular Sciences, Faculty of Biological Sciences, Kharazmi University, Tehran, Iran
| | - Mohammad Doroudian
- Department of Cell and Molecular Sciences, Faculty of Biological Sciences, Kharazmi University, Tehran, Iran
| | - Elaheh Movahed
- Wadsworth Center, New York State Department of Health, Albany, New Year, USA
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15
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Zhu W, Zhou J, Lu S, Yang J, Lai XH, Jin D, Pu J, Huang Y, Liu L, Li Z, Xu J. Isolation and characterization of tick-borne Roseomonas haemaphysalidis sp. nov. and rodent-borne Roseomonas marmotae sp. nov. J Microbiol 2021; 60:137-146. [PMID: 34826100 PMCID: PMC8622105 DOI: 10.1007/s12275-022-1428-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 10/26/2021] [Accepted: 10/27/2021] [Indexed: 12/02/2022]
Abstract
Four novel Gram-negative, mesophilic, aerobic, motile, and cocci-shaped strains were isolated from tick samples (strains 546T and 573) and respiratory tracts of marmots (strains 1318T and 1311). The 16S rRNA gene sequencing revealed that strains 546T and 573 were 97.8% identical to Roseomonas wenyumeiae Z23T, whereas strains 1311 and 1318T were 98.3% identical to Roseomonas ludipueritiae DSM 14915T. In addition, a 98.0% identity was observed between strains 546T and 1318T. Phylogenetic and phylogenomic analyses revealed that strains 546T and 573 clustered with R. wenyumeiae Z23T, whereas strains 1311 and 1318T grouped with R. ludipueritiae DSM 14915T. The average nucleotide identity between our isolates and members of the genus Roseomonas was below 95%. The genomic G+C content of strains 546T and 1318T was 70.9% and 69.3%, respectively. Diphosphatidylglycerol (DPG) and phosphatidylethanolamine (PE) were the major polar lipids, with Q-10 as the predominant respiratory quinone. According to all genotypic, phenotypic, phylogenetic, and phylogenomic analyses, the four strains represent two novel species of the genus Roseomonas, for which the names Roseomonas haemaphysalidis sp. nov. and Roseomonas marmotae sp. nov. are proposed, with 546T (= GDMCC 1.1780T = JCM 34187T) and 1318T (= GDMCC 1.1781T = JCM 34188T) as type strains, respectively.
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Affiliation(s)
- Wentao Zhu
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing, 102206, P. R. China
| | - Juan Zhou
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing, 102206, P. R. China
| | - Shan Lu
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing, 102206, P. R. China.,Shanghai Public Health Clinical Center, Fudan University, Shanghai, 201508, P. R. China.,Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing, 100730, P. R. China
| | - Jing Yang
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing, 102206, P. R. China.,Shanghai Public Health Clinical Center, Fudan University, Shanghai, 201508, P. R. China.,Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing, 100730, P. R. China
| | - Xin-He Lai
- Henan Key Laboratory of Biomolecular Recognition and Sensing, College of Chemistry and Chemical Engineering, Henan Joint International Research Laboratory of Chemo/Biosensing and Early Diagnosis of Major Diseases, Shangqiu Normal University, Shangqiu, 476000, P. R. China
| | - Dong Jin
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing, 102206, P. R. China.,Shanghai Public Health Clinical Center, Fudan University, Shanghai, 201508, P. R. China.,Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing, 100730, P. R. China
| | - Ji Pu
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing, 102206, P. R. China
| | - Yuyuan Huang
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing, 102206, P. R. China
| | - Liyun Liu
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing, 102206, P. R. China
| | - Zhenjun Li
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing, 102206, P. R. China
| | - Jianguo Xu
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing, 102206, P. R. China. .,Shanghai Public Health Clinical Center, Fudan University, Shanghai, 201508, P. R. China. .,Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing, 100730, P. R. China.
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16
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Zhu W, Yang J, Lu S, Jin D, Wu S, Pu J, Luo XL, Liu L, Li Z, Xu J. Discovery and Evolution of a Divergent Coronavirus in the Plateau Pika From China That Extends the Host Range of Alphacoronaviruses. Front Microbiol 2021; 12:755599. [PMID: 34691006 PMCID: PMC8529330 DOI: 10.3389/fmicb.2021.755599] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Accepted: 09/14/2021] [Indexed: 12/26/2022] Open
Abstract
Although plateau pikas are the keystone species in the plateau ecosystem of the Qinghai Province of China, little is known about their role in the evolution and transmission of viral pathogens, especially coronaviruses. Here, we describe the characterization and evolution of a novel alphacoronavirus, termed plateau pika coronavirus (PPCoV) P83, which has a prevalence of 4.5% in plateau pika fecal samples. In addition to classical gene order, the complete viral genome contains a unique nonstructural protein (NS2), several variable transcription regulatory sequences and a highly divergent spike protein. Phylogenetic analysis indicates that the newly discovered PPCoV falls into the genus Alphacoronavirus and is most closely related to rodent alphacoronaviruses. The co-speciation analysis shows that the phylogenetic trees of the alphacoronaviruses and their hosts are not always matched, suggesting inter-species transmission is common in alphacoronaviruses. And, PPCoV origin was estimated by molecular clock based on membrane and RNA-dependent RNA polymerase encoding genes, respectively, which revealed an apparent discrepancy with that of co-speciation analysis. PPCoV was detected mainly in intestinal samples, indicating a potential enteric tropism for the virus. Overall, this study extends the host range of alphacoronaviruses to a new order (Lagomorpha), indicating that plateau pikas may be the natural reservoir of PPCoV and play an important and long-term role in alphacoronavirus evolution.
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Affiliation(s)
- Wentao Zhu
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Jing Yang
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China.,Shanghai Public Health Clinical Center, Fudan University, Shanghai, China.,Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing, China
| | - Shan Lu
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China.,Shanghai Public Health Clinical Center, Fudan University, Shanghai, China.,Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing, China
| | - Dong Jin
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China.,Shanghai Public Health Clinical Center, Fudan University, Shanghai, China.,Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing, China
| | - Shusheng Wu
- Yushu Prefecture Center for Disease Control and Prevention, Yushu, China
| | - Ji Pu
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Xue-Lian Luo
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Liyun Liu
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Zhenjun Li
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Jianguo Xu
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China.,Shanghai Public Health Clinical Center, Fudan University, Shanghai, China.,Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing, China.,Research Institute of Public Heath, Nankai University, Tianjin, China
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17
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Zhu W, Song W, Fan G, Yang J, Lu S, Jin D, Luo XL, Pu J, Chen H, Xu J. Genomic Characterization of a New Coronavirus from Migratory Birds in Jiangxi Province of China. Virol Sin 2021; 36:1656-1659. [PMID: 34236588 PMCID: PMC8264173 DOI: 10.1007/s12250-021-00402-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 03/29/2021] [Indexed: 12/11/2022] Open
Affiliation(s)
- Wentao Zhu
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Wentao Song
- The Collaboration Unit for Field Epidemiology of State Key Laboratory of Infectious Disease Prevention and Control, Jiangxi Provincial Key Laboratory of Animal-Origin and Vector-Borne Diseases, Nanchang Center for Disease Control and Prevention, Nanchang, 330038, China
| | - Guoyin Fan
- The Collaboration Unit for Field Epidemiology of State Key Laboratory of Infectious Disease Prevention and Control, Jiangxi Provincial Key Laboratory of Animal-Origin and Vector-Borne Diseases, Nanchang Center for Disease Control and Prevention, Nanchang, 330038, China
| | - Jing Yang
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, 201508, China
- Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Shan Lu
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, 201508, China
- Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Dong Jin
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, 201508, China
- Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Xue-Lian Luo
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Ji Pu
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Haiying Chen
- The Collaboration Unit for Field Epidemiology of State Key Laboratory of Infectious Disease Prevention and Control, Jiangxi Provincial Key Laboratory of Animal-Origin and Vector-Borne Diseases, Nanchang Center for Disease Control and Prevention, Nanchang, 330038, China.
| | - Jianguo Xu
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China.
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, 201508, China.
- Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing, 100730, China.
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18
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Modular Evolution of Coronavirus Genomes. Viruses 2021; 13:v13071270. [PMID: 34209881 PMCID: PMC8310335 DOI: 10.3390/v13071270] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 06/22/2021] [Accepted: 06/23/2021] [Indexed: 12/13/2022] Open
Abstract
The viral family Coronaviridae comprises four genera, termed Alpha-, Beta-, Gamma-, and Deltacoronavirus. Recombination events have been described in many coronaviruses infecting humans and other animals. However, formal analysis of the recombination patterns, both in terms of the involved genome regions and the extent of genetic divergence between partners, are scarce. Common methods of recombination detection based on phylogenetic incongruences (e.g., a phylogenetic compatibility matrix) may fail in cases where too many events diminish the phylogenetic signal. Thus, an approach comparing genetic distances in distinct genome regions (pairwise distance deviation matrix) was set up. In alpha, beta, and delta-coronaviruses, a low incidence of recombination between closely related viruses was evident in all genome regions, but it was more extensive between the spike gene and other genome regions. In contrast, avian gammacoronaviruses recombined extensively and exist as a global cloud of genes with poorly corresponding genetic distances in different parts of the genome. Spike, but not other structural proteins, was most commonly exchanged between coronaviruses. Recombination patterns differed between coronavirus genera and corresponded to the modular structure of the spike: recombination traces were more pronounced between spike domains (N-terminal and C-terminal parts of S1 and S2) than within domains. The variability of possible recombination events and their uneven distribution over the genome suggest that compatibility of genes, rather than mechanistic or ecological limitations, shapes recombination patterns in coronaviruses.
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19
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Martínez-Rodríguez D, Gonzalez-Parra G, Villanueva RJ. Analysis of Key Factors of a SARS-CoV-2 Vaccination Program: A Mathematical Modeling Approach. EPIDEMIOLOGIA 2021; 2:140-161. [PMID: 35141702 PMCID: PMC8824484 DOI: 10.3390/epidemiologia2020012] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 03/25/2021] [Indexed: 02/07/2023] Open
Abstract
The administration of vaccines against the coronavirus disease 2019 (COVID-19) started in early December of 2020. Currently, there are only a few approved vaccines, each with different efficacies and mechanisms of action. Moreover, vaccination programs in different regions may vary due to differences in implementation, for instance, simply the availability of the vaccine. In this article, we study the impact of the pace of vaccination and the intrinsic efficacy of the vaccine on prevalence, hospitalizations, and deaths related to the SARS-CoV-2 virus. Then we study different potential scenarios regarding the burden of the COVID-19 pandemic in the near future. We construct a compartmental mathematical model and use computational methodologies to study these different scenarios. Thus, we are able to identify some key factors to reach the aims of the vaccination programs. We use some metrics related to the outcomes of the COVID-19 pandemic in order to assess the impact of the efficacy of the vaccine and the pace of the vaccine inoculation. We found that both factors have a high impact on the outcomes. However, the rate of vaccine administration has a higher impact in reducing the burden of the COVID-19 pandemic. This result shows that health institutions need to focus on increasing the vaccine inoculation pace and create awareness in the population about the importance of COVID-19 vaccines.
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Affiliation(s)
- David Martínez-Rodríguez
- Insituto Universitario de Matemática Multidisciplinar, Universitat Politècnica de València, 46022 Valencia, Spain; (D.M.-R.); (R.-J.V.)
| | | | - Rafael-J. Villanueva
- Insituto Universitario de Matemática Multidisciplinar, Universitat Politècnica de València, 46022 Valencia, Spain; (D.M.-R.); (R.-J.V.)
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20
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Impact of a New SARS-CoV-2 Variant on the Population: A Mathematical Modeling Approach. MATHEMATICAL AND COMPUTATIONAL APPLICATIONS 2021. [DOI: 10.3390/mca26020025] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Several SARS-CoV-2 variants have emerged around the world, and the appearance of other variants depends on many factors. These new variants might have different characteristics that can affect the transmissibility and death rate. The administration of vaccines against the coronavirus disease 2019 (COVID-19) started in early December of 2020 and in some countries the vaccines will not soon be widely available. For this article, we studied the impact of a new more transmissible SARS-CoV-2 strain on prevalence, hospitalizations, and deaths related to the SARS-CoV-2 virus. We studied different scenarios regarding the transmissibility in order to provide a scientific support for public health policies and bring awareness of potential future situations related to the COVID-19 pandemic. We constructed a compartmental mathematical model based on differential equations to study these different scenarios. In this way, we are able to understand how a new, more infectious strain of the virus can impact the dynamics of the COVID-19 pandemic. We studied several metrics related to the possible outcomes of the COVID-19 pandemic in order to assess the impact of a higher transmissibility of a new SARS-CoV-2 strain on these metrics. We found that, even if the new variant has the same death rate, its high transmissibility can increase the number of infected people, those hospitalized, and deaths. The simulation results show that health institutions need to focus on increasing non-pharmaceutical interventions and the pace of vaccine inoculation since a new variant with higher transmissibility, such as, for example, VOC-202012/01 of lineage B.1.1.7, may cause more devastating outcomes in the population.
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21
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González-Parra G, Arenas AJ. Qualitative analysis of a mathematical model with presymptomatic individuals and two SARS-CoV-2 variants. COMPUTATIONAL AND APPLIED MATHEMATICS 2021; 40:199. [PMCID: PMC8325548 DOI: 10.1007/s40314-021-01592-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 07/01/2021] [Accepted: 07/22/2021] [Indexed: 05/31/2023]
Abstract
The SARS-CoV-2 continues to spread across the world. During this COVID-19 pandemic, several variants of the SARS-CoV-2 have been found. Some of these new variants like the VOC-202012/01 of lineage B.1.1.7 or the most recently B.1.617 emerging in India have a higher infectiousness than those previously prevalent. We propose a mathematical model based on ordinary differential equations to investigate potential consequences of the appearance of a new more transmissible SARS-CoV-2 strain in a given region. The proposed mathematical model incorporates the presymptomatic and asymptomatic subpopulations in addition to the more usual susceptible, exposed, infected, and recovered subpopulations. This is important from a realistic point of view since it has been found recently that presymptomatic and asymptomatic individuals are relevant spreaders of the SARS-CoV-2. Using the next-generation matrix method, we find the basic reproduction number, \documentclass[12pt]{minimal}
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\begin{document}$${\mathcal {R}}_{0}$$\end{document}R0, an important threshold parameter that provides insight regarding the evolution and outcome of a certain instance of the COVID-19 pandemic. The local and global stability of system equilibria are also presented. In particular, for the global stability we construct a Lyapunov functional and use the LaSalle invariant principle to prove that if the basic reproduction ratio is less than unity, the infection-free equilibrium is globally asymptotically stable. On the other hand, if \documentclass[12pt]{minimal}
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\begin{document}$${\mathcal {R}}_{0}>1$$\end{document}R0>1 the endemic equilibrium is globally asymptotically stable. Finally, we present numerical simulations to numerically support the analytic results and to show the impact of the introduction of a new more contagious SARS-CoV-2 variant in a population.
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Affiliation(s)
| | - Abraham J. Arenas
- Departamento de Matemáticas y Estadística, Universidad de Córdoba, Montería, Colombia
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