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Lu X, Ji L, Wang H, Zhang Q, Wang X, Liu Y, Shen Q, Yang S, Ma X, Zhang W, Shan T. Highly diverse RNA viruses and phage sequences concealed within birds. Microbiol Spectr 2024; 12:e0080224. [PMID: 38860816 PMCID: PMC11218532 DOI: 10.1128/spectrum.00802-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Accepted: 04/30/2024] [Indexed: 06/12/2024] Open
Abstract
The diversity of birds in most parts of the world is very high, and thus, they may carry different types of highly differentiated and unknown viruses. Thanks to advanced sequencing technologies, studies on the diversity of bird-associated viruses have increased over the past few years. In this study, a large-scale viral metagenomics survey was performed on cloacal swabs of 2,990 birds from nine provinces of the Chinese mainland. To detect undescribed RNA viruses in birds, more than 1,800 sequences sharing relatively low (<60%) amino acid sequence identity with the best match in the GenBank database were screened. Potentially novel viruses related to vertebrates have been identified, and several potential recombination signals were found. Additionally, hundreds of RNA viral sequences related to plants, fungi, and insects were detected, including previously unknown viruses. Furthermore, we investigated the novelty, functionality, and classification of the phages examined in this study. These viruses occupied topological positions on the evolutionary trees to a certain extent and might form novel putative families, genera, or species, thus providing information to fill the phylogenetic gaps of related viruses. These findings provided new insights into bird-associated viruses, but the interactions among these viruses remain unknown and require further investigation.IMPORTANCEStudying the diversity of RNA viruses in birds and mammals is crucial due to their potential impact on human health and the global ecosystem. Many RNA viruses, such as influenza and coronaviruses, have been shown to cross the species barrier and cause zoonotic diseases. In this metagenomics study involving 2,990 birds from at least 82 species, we identified over 1,800 RNA sequences with distant relationships to known viruses, some of which are rare in birds. The study highlights the scope and diversity of RNA viruses in birds, providing data to predict disease risks and monitor potential viral threats to wildlife, livestock, and human health. This information can aid in the development of strategies for disease prevention and control.
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Affiliation(s)
- Xiang Lu
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Likai Ji
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Haoning Wang
- School of Geography and Tourism, Harbin University, Harbin, Heilongjiang, China
| | - Qing Zhang
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China
- Qinghai Institute of Endemic Disease Prevention and Control, Xining, Qinghai, China
| | - Xiaochun Wang
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Yuwei Liu
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Quan Shen
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Shixing Yang
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Xiao Ma
- Qinghai Institute of Endemic Disease Prevention and Control, Xining, Qinghai, China
| | - Wen Zhang
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Tongling Shan
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
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Ji C, Zhang Y, Feng Y, Zhang X, Ma J, Pan Z, Kawaguchi A, Yao H. Systematic Surveillance of an Emerging Picornavirus among Cattle and Sheep in China. Microbiol Spectr 2023; 11:e0504022. [PMID: 37162348 PMCID: PMC10269770 DOI: 10.1128/spectrum.05040-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 03/09/2023] [Indexed: 05/11/2023] Open
Abstract
Emerging viruses are a constant threat to human and animal health. Boosepivirus is a novel picornavirus considered a gastrointestinal pathogen and has broken out in recent years. In 2020, we identified a strain of boosepivirus NX20-1 from Chinese calf feces and performed genetic characterization and evolutionary analysis. NX20-1 was closely related to the Japanese strain Bo-12-38/2009/JPN and belonged to Boosepivirus B. We found that 64 of 603 samples (10.6%) from 20 different provinces across the country were positive for boosepivirus by reverse transcription (RT)-PCR. Further, coinfection with other diarrheal pathogens was also present in 35 of these positive samples. Importantly, we found the prevalence of boosepivirus in sheep as well, indicating that Boosepivirus can infect different domestic animals. Our data suggest that boosepivirus is a potential diarrheal pathogen, but the pathogenicity and the mechanism of pathogenesis need further study. IMPORTANCE We identified a novel picornavirus, boosepivirus, for the first time in China. Genetic evolutionary analysis revealed that NX20-1 strain was closely related to the Japanese strain Bo-12-38/2009/JPN and belonged to Boosepivirus B. In addition, we found that the virus was prevalent in China with an overall positivity rate of 10.6% (64 of 603 samples), and there was significant coinfection with other pathogens. Importantly, we found the prevalence of boosepivirus in sheep as well, suggesting that boosepivirus has a risk of spillover and can be transmitted across species.
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Affiliation(s)
- Chengyuan Ji
- Ministry of Education Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Yao Zhang
- Ministry of Education Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Yiqiu Feng
- Ministry of Education Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Xinqin Zhang
- Ministry of Education Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Jiale Ma
- Ministry of Education Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Zihao Pan
- Ministry of Education Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Atsushi Kawaguchi
- Department of Infection Biology, Faculty of Medicine and Graduate School of Comprehensive Human Sciences, University of Tsukuba, Tsukuba, Japan
| | - Huochun Yao
- Ministry of Education Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
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Zhou L, Lu X, Zhao C, Zhang Y, Ning S, Zhang W. Characterization of a novel picornavirus prevalent in experimental rabbits ( Oryctolagus cuniculus). Heliyon 2023; 9:e15702. [PMID: 37159695 PMCID: PMC10163628 DOI: 10.1016/j.heliyon.2023.e15702] [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: 12/20/2022] [Revised: 04/18/2023] [Accepted: 04/20/2023] [Indexed: 05/11/2023] Open
Abstract
Here, using viral metagenomic method a novel picornavirus (named UJS-2019picorna, GenBank accession number OP821762) was discovered in fecal and blood samples of experimental rabbits (Oryctolagus cuniculus). The complete genome size of UJS-2019picorna is 7832 bp excluding the poly(A)-tail, with GC content of 44.00% and a nucleotide composition of 28.0% A, 28.0% U, 21.5% G, and 22.5% C. The viral genome has a typical picornavirus organization pattern from the 5'-3' direction: VPg-5' UTR-(L)-P1, (VP4-VP2-VP3-VP1)-P2, (2 A-2B-2C)-P3, (3 A-3B-3C-3D)-3' UTR-poly(A). The P1 region of UJS-2019picorna is related to Erbovirus with amino acid identity of 37.31%, while the P2 and P3 regions are the closest to Bopivirus with amino acid identity of 35.66%-39.53%. According to the Picornaviridae Study Group guidelines, UJS-2019picorna should be presumed to be a new genus belonging to the Picornaviridae family. Epidemiologic study revealed that this novel picornavirus was prevalent in a cohort of experimental rabbits, with prevalence rate of 23.68% (9/38) in feces and 18.4% (7/38) in blood samples. Further work is required to elucidate whether this virus is pathogenic to rabbits and whether it has influence on studies using rabbits as experimental animal.
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Affiliation(s)
- Liye Zhou
- School of Basic Medical Sciences, Shanxi Medical University, Taiyuan, China
| | - Xiang Lu
- School of Medicine, Jiangsu University, Zhenjiang, China
| | - Chunyan Zhao
- Medical School, Wuxi Taihu University, Wuxi, Jiangsu, China
| | - Yu Zhang
- Key Laboratory of Cellular Physiology, Ministry of Education, and the Department of Physiology, Shanxi Medical University, Taiyuan, China
| | - Songyi Ning
- School of Medicine, Jiangsu University, Zhenjiang, China
- Corresponding author.
| | - Wen Zhang
- School of Medicine, Jiangsu University, Zhenjiang, China
- Corresponding author.
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An Emerging Duck Egg-Reducing Syndrome Caused by a Novel Picornavirus Containing Seven Putative 2A Peptides. Viruses 2022; 14:v14050932. [PMID: 35632674 PMCID: PMC9144743 DOI: 10.3390/v14050932] [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: 03/02/2022] [Revised: 04/20/2022] [Accepted: 04/28/2022] [Indexed: 02/04/2023] Open
Abstract
Since 2016, frequent outbreaks of egg-reducing syndromes caused by an unknown virus in duck farms have resulted in huge economic losses in China. The causative virus was isolated and identified as a novel species in Avihepatovirus of the picornavirus family according to the current guidelines of the International Committee on Taxonomy of Viruses (ICVT), and was named the duck egg-reducing syndrome virus (DERSV). The DERSV was most closely related to wild duck avihepatovirus-like virus (WDALV) with 64.0%, 76.8%, 77.5%, and 70.7% of amino acid identities of P1, 2C, 3C, and 3D proteins, respectively. The DERSV had a typical picornavirus-like genomic structure, but with the longest 2A region in the reported picornaviruses so far. Importantly, the clinical symptoms were successfully observed by artificially infecting ducks with DERSV, even in the contact exposed ducks, which suggested that DERSV transmitted among ducks by direct contact. The antibody levels of DERSV were correlated with the emergence of the egg-reducing syndromes in ducks in field. These results indicate that DERSV is a novel emerging picornavirus causing egg-reducing syndrome in ducks.
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Identification and genome analysis of a novel picornavirus from captive belugas (Delphinapterus leucas) in China. Sci Rep 2021; 11:21018. [PMID: 34697355 PMCID: PMC8549006 DOI: 10.1038/s41598-021-00605-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Accepted: 10/13/2021] [Indexed: 11/18/2022] Open
Abstract
The discovery of new viruses is important for predicting their potential threats to the health of humans and other animals. A novel picornavirus was identified from oral, throat, and anal swab samples collected from belugas (Delphinapterus leucas), from Dalian Sun Asia Tourism Holding Co., China, between January and December 2018, using a metagenomics approach. The genome of this novel PicoV-HMU-1 strain was 8197 nucleotides (nt) in length, with a open reading frame (from 1091 to 8074 nt) that encoded a polyprotein precursor of 2328 amino acids. Moreover, the genomic length and GC content of PicoV-HMU-1 were within the ranges found in other picornaviruses, and the genome organization was also similar. Nevertheless, PicoV-HMU-1 had a lower amino acid identity and distinct host species compared with other members of the Picornaviridae family. Phylogenetic trees were constructed based on the P1 and 3D amino acid sequences of PicoV-HMU-1 along with representative members of the Picornaviridae family, which showed that PicoV-HMU-1 was related to unclassified bat picornaviruses groups. These findings suggest that the PicoV-HMU-1 strain represents a potentially novel genus of picornavirus. These data can enhance our understanding of the picornavirus genetic diversity and evolution.
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Chen P, Li Z, Cui S. Picornaviral 2C proteins: A unique ATPase family critical in virus replication. Enzymes 2021; 49:235-264. [PMID: 34696834 DOI: 10.1016/bs.enz.2021.06.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
The 2C proteins of Picornaviridae are unique members of AAA+ protein family. Although picornavirus 2C shares many conserved motifs with Super Family 3 DNA helicases, duplex unwinding activity of many 2C proteins remains undetected, and high-resolution structures of 2C hexamers are unavailable. All characterized 2C proteins exhibit ATPase activity, but the purpose of ATP hydrolysis is not fully understood. 2C is highly conserved among picornaviruses and plays crucial roles in nearly all steps of the virus lifecycle. It is therefore considered as an effective target for broad-spectrum antiviral drug development. Crystallographic investigation of enterovirus 2C proteins provide structural details important for the elucidation of 2C function and development of antiviral drugs. This chapter summarizes not only the findings of enzymatic activities, biochemical and structural characterizations of the 2C proteins, but also their role in virus replication, immune evasion and morphogenesis. The linkage between structure and function of the 2C proteins is discussed in detail. Inhibitors targeting the 2C proteins are also summarized to provide an overview of drug development. Finally, we raise several key questions to be addressed in this field and provide future research perspective on this unique class of ATPases.
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Affiliation(s)
- Pu Chen
- Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Zhijian Li
- Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Sheng Cui
- Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China.
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Wacharapluesadee S, Buathong R, Iamsirithawon S, Chaifoo W, Ponpinit T, Ruchisrisarod C, Sonpee C, Katasrila P, Yomrat S, Ghai S, Sirivichayakul S, Okada P, Mekha N, Karnkawinpong O, Uttayamakul S, Vachiraphan A, Plipat T, Hemachudha T. Identification of a Novel Pathogen Using Family-Wide PCR: Initial Confirmation of COVID-19 in Thailand. Front Public Health 2020; 8:555013. [PMID: 33134237 PMCID: PMC7579402 DOI: 10.3389/fpubh.2020.555013] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Accepted: 09/03/2020] [Indexed: 11/13/2022] Open
Abstract
In resource-limited countries, early detection of novel pathogens is often challenging, due to financial and technical constraints. This study reports the efficacy of family-wide polymerase chain reaction (PCR) in screening, detecting, and identifying initial cases of the novel SARS-CoV-2 in Thailand. Respiratory secretions were collected from suspected individuals traveling from Wuhan, China to Thailand at the beginning of January 2020. Family-wide PCR assays yielded positive results for coronavirus in one traveler within 12 h on January 8, 2020. Nucleotide sequences (290 bp) showed 100% similarity to SARS-CoV-2. The whole genome sequence was further characterized by Next Generation Sequencing (NGS) for confirmation. Combining family-wide PCR, as a rapid screening tool, with NGS, for full genome characterization, could facilitate early detection and confirmation of a novel pathogen and enable early containment of a disease outbreak.
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Affiliation(s)
- Supaporn Wacharapluesadee
- Thai Red Cross Emerging Infectious Diseases Health Science Centre, World Health Organization Collaborating Centre for Research and Training on Viral Zoonoses, King Chulalongkorn University, Pathumwan, Thailand.,Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Rome Buathong
- Department of Disease Control, Ministry of Public Health, Nonthaburi, Thailand
| | - Sopon Iamsirithawon
- Department of Disease Control, Ministry of Public Health, Nonthaburi, Thailand
| | - Walairat Chaifoo
- Department of Disease Control, Ministry of Public Health, Nonthaburi, Thailand
| | - Teerada Ponpinit
- Thai Red Cross Emerging Infectious Diseases Health Science Centre, World Health Organization Collaborating Centre for Research and Training on Viral Zoonoses, King Chulalongkorn University, Pathumwan, Thailand.,Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Chanida Ruchisrisarod
- Thai Red Cross Emerging Infectious Diseases Health Science Centre, World Health Organization Collaborating Centre for Research and Training on Viral Zoonoses, King Chulalongkorn University, Pathumwan, Thailand.,Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Chanikarn Sonpee
- Thai Red Cross Emerging Infectious Diseases Health Science Centre, World Health Organization Collaborating Centre for Research and Training on Viral Zoonoses, King Chulalongkorn University, Pathumwan, Thailand.,Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Panticha Katasrila
- Thai Red Cross Emerging Infectious Diseases Health Science Centre, World Health Organization Collaborating Centre for Research and Training on Viral Zoonoses, King Chulalongkorn University, Pathumwan, Thailand.,Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Siriporn Yomrat
- Thai Red Cross Emerging Infectious Diseases Health Science Centre, World Health Organization Collaborating Centre for Research and Training on Viral Zoonoses, King Chulalongkorn University, Pathumwan, Thailand.,Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Siriporn Ghai
- Thai Red Cross Emerging Infectious Diseases Health Science Centre, World Health Organization Collaborating Centre for Research and Training on Viral Zoonoses, King Chulalongkorn University, Pathumwan, Thailand.,Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | | | - Pilailuk Okada
- Department of Medical Sciences, Ministry of Public Health, Nonthaburi, Thailand
| | - Nanthawan Mekha
- Department of Medical Sciences, Ministry of Public Health, Nonthaburi, Thailand
| | - Opart Karnkawinpong
- Department of Medical Sciences, Ministry of Public Health, Nonthaburi, Thailand
| | - Sumonmal Uttayamakul
- Department of Disease Control, Bamrasnaradura Infectious Disease Institute, Ministry of Public Health, Nonthaburi, Thailand
| | - Apichart Vachiraphan
- Department of Disease Control, Bamrasnaradura Infectious Disease Institute, Ministry of Public Health, Nonthaburi, Thailand
| | - Tanarak Plipat
- Department of Disease Control, Ministry of Public Health, Nonthaburi, Thailand
| | - Thiravat Hemachudha
- Thai Red Cross Emerging Infectious Diseases Health Science Centre, World Health Organization Collaborating Centre for Research and Training on Viral Zoonoses, King Chulalongkorn University, Pathumwan, Thailand.,Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
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