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Shum MHH, Lee Y, Tam L, Xia H, Chung OLW, Guo Z, Lam TTY. Binding affinity between coronavirus spike protein and human ACE2 receptor. Comput Struct Biotechnol J 2024; 23:759-770. [PMID: 38304547 PMCID: PMC10831124 DOI: 10.1016/j.csbj.2024.01.009] [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: 09/15/2023] [Revised: 01/14/2024] [Accepted: 01/15/2024] [Indexed: 02/03/2024] Open
Abstract
Coronaviruses (CoVs) pose a major risk to global public health due to their ability to infect diverse animal species and potential for emergence in humans. The CoV spike protein mediates viral entry into the cell and plays a crucial role in determining the binding affinity to host cell receptors. With particular emphasis on α- and β-coronaviruses that infect humans and domestic animals, current research on CoV receptor use suggests that the exploitation of the angiotensin-converting enzyme 2 (ACE2) receptor poses a significant threat for viral emergence with pandemic potential. This review summarizes the approaches used to study binding interactions between CoV spike proteins and the human ACE2 (hACE2) receptor. Solid-phase enzyme immunoassays and cell binding assays allow qualitative assessment of binding but lack quantitative evaluation of affinity. Surface plasmon resonance, Bio-layer interferometry, and Microscale Thermophoresis on the other hand, provide accurate affinity measurement through equilibrium dissociation constants (KD). In silico modeling predicts affinity through binding structure modeling, protein-protein docking simulations, and binding energy calculations but reveals inconsistent results due to the lack of a standardized approach. Machine learning and deep learning models utilize simulated and experimental protein-protein interaction data to elucidate the critical residues associated with CoV binding affinity to hACE2. Further optimization and standardization of existing approaches for studying binding affinity could aid pandemic preparedness. Specifically, prioritizing surveillance of CoVs that can bind to human receptors stands to mitigate the risk of zoonotic spillover.
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Affiliation(s)
- Marcus Ho-Hin Shum
- State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong, China
- School of Public Health, The University of Hong Kong, Hong Kong, China
- Laboratory of Data Discovery for Health (D24H), Hong Kong Science Park, Hong Kong, China
| | - Yang Lee
- School of Public Health, The University of Hong Kong, Hong Kong, China
- Centre for Immunology and Infection (C2i), Hong Kong Science Park, Hong Kong, China
| | - Leighton Tam
- School of Public Health, The University of Hong Kong, Hong Kong, China
- Laboratory of Data Discovery for Health (D24H), Hong Kong Science Park, Hong Kong, China
| | - Hui Xia
- Department of Chemistry, South University of Science and Technology of China, China
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
| | - Oscar Lung-Wa Chung
- Department of Chemistry, South University of Science and Technology of China, China
| | - Zhihong Guo
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
| | - Tommy Tsan-Yuk Lam
- State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong, China
- School of Public Health, The University of Hong Kong, Hong Kong, China
- Laboratory of Data Discovery for Health (D24H), Hong Kong Science Park, Hong Kong, China
- Centre for Immunology and Infection (C2i), Hong Kong Science Park, Hong Kong, China
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Goraichuk IV, Harden M, Spackman E, Suarez DL. The 28S rRNA RT-qPCR assay for host depletion evaluation to enhance avian virus detection in Illumina and Nanopore sequencing. Front Microbiol 2024; 15:1328987. [PMID: 38351914 PMCID: PMC10864109 DOI: 10.3389/fmicb.2024.1328987] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Accepted: 01/09/2024] [Indexed: 02/16/2024] Open
Abstract
Abundant host and bacterial sequences can obscure the detection of less prevalent viruses in untargeted next-generation sequencing (NGS). Efficient removal of these non-targeted sequences is vital for accurate viral detection. This study presents a novel 28S ribosomal RNA (rRNA) RT-qPCR assay designed to assess the efficiency of avian rRNA depletion before conducting costly NGS for the detection of avian RNA viruses. The comprehensive evaluation of this 28S-test focuses on substituting DNase I with alternative DNases in our established depletion protocols and finetuning essential parameters for reliable host rRNA depletion. To validate the effectiveness of the 28S-test, we compared its performance with NGS results obtained from both Illumina and Nanopore sequencing platforms. This evaluation utilized swab samples from chickens infected with highly pathogenic avian influenza virus, subjected to established and modified depletion protocols. Both methods significantly reduced host rRNA levels, but using the alternative DNase had superior performance. Additionally, utilizing the 28S-test, we explored cost- and time-effective strategies, such as reduced probe concentrations and other alternative DNase usage, assessed the impact of filtration pre-treatment, and evaluated various experimental parameters to further optimize the depletion protocol. Our findings underscore the value of the 28S-test in optimizing depletion methods for advancing improvements in avian disease research through NGS.
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Affiliation(s)
- Iryna V. Goraichuk
- Southeast Poultry Research Laboratory, U.S. National Poultry Research Center, Agriculture Research Service, U.S. Department of Agriculture, Athens, GA, United States
| | - Mark Harden
- College of Veterinary Medicine, Tuskegee University, Tuskegee, AL, United States
| | - Erica Spackman
- Southeast Poultry Research Laboratory, U.S. National Poultry Research Center, Agriculture Research Service, U.S. Department of Agriculture, Athens, GA, United States
| | - David L. Suarez
- Southeast Poultry Research Laboratory, U.S. National Poultry Research Center, Agriculture Research Service, U.S. Department of Agriculture, Athens, GA, United States
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3
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Li L, Quan J, Liu H, Yu H, Chen H, Xia C, Zhao S, Gao C. Identification of the genetic characteristics of copy number variations in experimental specific pathogen-free ducks using whole-genome resequencing. BMC Genomics 2024; 25:17. [PMID: 38166615 PMCID: PMC10759622 DOI: 10.1186/s12864-023-09928-8] [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: 08/31/2023] [Accepted: 12/19/2023] [Indexed: 01/05/2024] Open
Abstract
BACKGROUND Specific pathogen-free ducks are a valuable laboratory resource for waterfowl disease research and poultry vaccine development. High throughput sequencing allows the systematic identification of structural variants in genomes. Copy number variation (CNV) can explain the variation of important duck genetic traits. Herein, the genome-wide CNVs of the three experimental duck species in China (Jinding ducks (JD), Shaoxing ducks (SX), and Fujian Shanma ducks (SM)) were characterized using resequencing to determine their genetic characteristics and selection signatures. RESULTS We obtained 4,810 CNV regions (CNVRs) by merging 73,012 CNVs, covering 4.2% of the duck genome. Functional analysis revealed that the shared CNVR-harbored genes were significantly enriched for 31 gene ontology terms and 16 Kyoto Encyclopedia of Genes and Genomes pathways (e.g., olfactory transduction and immune system). Based on the genome-wide fixation index for each CNVR, growth (SPAG17 and PTH1R), disease resistance (CATHL3 and DMBT1), and thermoregulation (TRPC4 and SLIT3) candidate genes were identified in strongly selected signatures specific to JD, SM, and SX, respectively. CONCLUSIONS In conclusion, we investigated the genome-wide distribution of experimental duck CNVs, providing a reference to establish the genetic basis of different phenotypic traits, thus contributing to the management of experimental animal genetic resources.
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Affiliation(s)
- Lanlan Li
- College of Animal Science & Technology, Gansu Agricultural University, Lanzhou, 730070, P.R. China
- College of Animal Science & Technology, Ningxia University, Yinchuan, 750021, P.R. China
| | - Jinqiang Quan
- College of Animal Science & Technology, Gansu Agricultural University, Lanzhou, 730070, P.R. China.
| | - Hongyi Liu
- State Key Laboratory of Veterinary Biotechnology, Heilongjiang Provincial Key Laboratory of Laboratory Animal and Comparative Medicine, National Poultry Laboratory Animal Resource Center, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Harbin, 150069, P.R. China
| | - Haibo Yu
- State Key Laboratory of Veterinary Biotechnology, Heilongjiang Provincial Key Laboratory of Laboratory Animal and Comparative Medicine, National Poultry Laboratory Animal Resource Center, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Harbin, 150069, P.R. China
| | - Hongyan Chen
- State Key Laboratory of Veterinary Biotechnology, Heilongjiang Provincial Key Laboratory of Laboratory Animal and Comparative Medicine, National Poultry Laboratory Animal Resource Center, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Harbin, 150069, P.R. China
| | - Changyou Xia
- State Key Laboratory of Veterinary Biotechnology, Heilongjiang Provincial Key Laboratory of Laboratory Animal and Comparative Medicine, National Poultry Laboratory Animal Resource Center, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Harbin, 150069, P.R. China
| | - Shengguo Zhao
- College of Animal Science & Technology, Gansu Agricultural University, Lanzhou, 730070, P.R. China
| | - Caixia Gao
- State Key Laboratory of Veterinary Biotechnology, Heilongjiang Provincial Key Laboratory of Laboratory Animal and Comparative Medicine, National Poultry Laboratory Animal Resource Center, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Harbin, 150069, P.R. China.
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Zhao J, Zhao Y, Zhang G. Key Aspects of Coronavirus Avian Infectious Bronchitis Virus. Pathogens 2023; 12:pathogens12050698. [PMID: 37242368 DOI: 10.3390/pathogens12050698] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 05/01/2023] [Accepted: 05/03/2023] [Indexed: 05/28/2023] Open
Abstract
Infectious bronchitis virus (IBV) is an enveloped and positive-sense single-stranded RNA virus. IBV was the first coronavirus to be discovered and predominantly causes respiratory disease in commercial poultry worldwide. This review summarizes several important aspects of IBV, including epidemiology, genetic diversity, antigenic diversity, and multiple system disease caused by IBV as well as vaccination and antiviral strategies. Understanding these areas will provide insight into the mechanism of pathogenicity and immunoprotection of IBV and may improve prevention and control strategies for the disease.
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Affiliation(s)
- Jing Zhao
- National Key Laboratory of Veterinary Public Health Security, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
- Key Laboratory of Animal Epidemiology of the Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
| | - Ye Zhao
- Key Laboratory of Animal Epidemiology of the Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
| | - Guozhong Zhang
- National Key Laboratory of Veterinary Public Health Security, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
- Key Laboratory of Animal Epidemiology of the Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
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5
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Li L, Quan J, Gao C, Liu H, Yu H, Chen H, Xia C, Zhao S. Whole-genome resequencing to unveil genetic characteristics and selection signatures of specific pathogen-free ducks. Poult Sci 2023; 102:102748. [PMID: 37209656 DOI: 10.1016/j.psj.2023.102748] [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: 02/23/2023] [Revised: 04/11/2023] [Accepted: 04/19/2023] [Indexed: 05/22/2023] Open
Abstract
Specific pathogen-free ducks are important high-grade laboratory animals, with a key role in research related to poultry biosecurity, production, and breeding. However, the genetic characteristics of experimental duck varieties remain poorly explored. Herein we performed whole-genome resequencing to construct a single nucleotide polymorphism genetic map of the genomes of 3 experimental duck varieties [Jinding ducks (JD), Shaoxing ducks (SX), and Fujian Shanma ducks (SM)] to determine their genetic characteristics and identify selection signatures. Subsequent analyses of population structure and genetic diversity revealed that each duck variety formed a monophyletic group, with SM showing richer genetic diversity than JD and SX. Further, on exploring shared selection signatures, we found 2 overlapping genomic regions on chromosome Z of all experimental ducks, which comprised immune response-related genes (IL7R and IL6ST). Moreover, growth and skeletal development (IGF1R and GDF5), meat quality (FoxO1), and stress resistance (HSP90B1 and Gpx8-b) candidate gene loci were identified in strongly selected signatures specific to JD, SM, and SX, respectively. Our results identified the population genetic basis of experimental ducks at the whole-genome level, providing a framework for future molecular investigations of genetic variations and phenotypic changes. We believe that such studies will eventually contribute to the management of experimental animal resources.
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Affiliation(s)
- Lanlan Li
- State Key Laboratory of Veterinary Biotechnology, Heilongjiang Provincial Key Laboratory of Laboratory Animal and Comparative Medicine, National Poultry Laboratory Animal Resource Center, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Harbin 150069, PR China; College of Animal Science & Technology, Gansu Agricultural University, Lanzhou 730070, PR China
| | - Jinqiang Quan
- College of Animal Science & Technology, Gansu Agricultural University, Lanzhou 730070, PR China
| | - Caixia Gao
- State Key Laboratory of Veterinary Biotechnology, Heilongjiang Provincial Key Laboratory of Laboratory Animal and Comparative Medicine, National Poultry Laboratory Animal Resource Center, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Harbin 150069, PR China.
| | - Hongyi Liu
- State Key Laboratory of Veterinary Biotechnology, Heilongjiang Provincial Key Laboratory of Laboratory Animal and Comparative Medicine, National Poultry Laboratory Animal Resource Center, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Harbin 150069, PR China
| | - Haibo Yu
- State Key Laboratory of Veterinary Biotechnology, Heilongjiang Provincial Key Laboratory of Laboratory Animal and Comparative Medicine, National Poultry Laboratory Animal Resource Center, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Harbin 150069, PR China
| | - Hongyan Chen
- State Key Laboratory of Veterinary Biotechnology, Heilongjiang Provincial Key Laboratory of Laboratory Animal and Comparative Medicine, National Poultry Laboratory Animal Resource Center, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Harbin 150069, PR China
| | - Changyou Xia
- State Key Laboratory of Veterinary Biotechnology, Heilongjiang Provincial Key Laboratory of Laboratory Animal and Comparative Medicine, National Poultry Laboratory Animal Resource Center, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Harbin 150069, PR China
| | - Shengguo Zhao
- College of Animal Science & Technology, Gansu Agricultural University, Lanzhou 730070, PR China
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6
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Liu Z, Ding X, Haider MS, Ali F, Yu H, Chen X, Tan S, Zu Y, Liu W, Ding B, Zheng A, Zheng J, Qian Z, Ashfaq H, Yu D, Li K. A metagenomic insight into the Yangtze finless porpoise virome. Front Vet Sci 2022; 9:922623. [PMID: 36118360 PMCID: PMC9478467 DOI: 10.3389/fvets.2022.922623] [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: 04/18/2022] [Accepted: 08/15/2022] [Indexed: 11/13/2022] Open
Abstract
The Yangtze finless porpoise (Neophocaena phocaenoides asiaeorientalis) inhabiting the Yantze River, China is critically endangered because of the influences of infectious disease, human activity, and water contamination. Viral diseases are one of the crucial factors that threatening the health of Yangtze finless porpoise. However, there are few studies which elaborate the viral diversity of Yangtze finless. Therefore, this study was performed to investigate the viral diversity of Yangtze finless by metagenomics. Results indicated that a total of 12,686,252 high-quality valid sequences were acquired and 2,172 virus reads were recognized. Additionally, we also obtained a total of 10,600 contigs. Phages was the most abundant virus in the samples and the ratio of DNA and RNA viruses were 69.75 and 30.25%, respectively. Arenaviridae, Ackermannviridae and Siphoviridae were the three most predominant families in all the samples. Moreover, the majority of viral genus were Mammarenavirus, Limestonevirus and Lambdavirus. The results of gene prediction indicated that these viruses play vital roles in biological process, cellular component, molecular function, and disease. To the best of our knowledge, this is the first report on the viral diversity of Yangtze finless porpoise, which filled the gaps in its viral information. Meanwhile, this study can also provide a theoretical basis for the establishment of the prevention and protection system for virus disease of Yangtze finless porpoise.
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Affiliation(s)
- Zhigang Liu
- College of Life Science, Anqing Normal University, Anqing, China
- Research Center of Aquatic Organism Conservation and Water Ecosystem Restoration in Anhui Province, Anqing Normal University, Anqing, China
- Zhigang Liu
| | - Xin Ding
- College of Life Science, Anqing Normal University, Anqing, China
| | | | - Farah Ali
- Department of Theriogenology, Faculty of Veterinary and Animal Sciences, The Islamia University of Bahawalpur, Bahawalpur, Pakistan
| | - Han Yu
- College of Life Science, Anqing Normal University, Anqing, China
| | - Xin Chen
- College of Life Science, Anqing Normal University, Anqing, China
| | - Shuaishuai Tan
- College of Life Science, Anqing Normal University, Anqing, China
| | - Yuan Zu
- College of Life Science, Anqing Normal University, Anqing, China
| | - Wenlong Liu
- College of Life Science, Anqing Normal University, Anqing, China
| | - Bangzhi Ding
- College of Life Science, Anqing Normal University, Anqing, China
| | - Aifang Zheng
- College of Life Science, Anqing Normal University, Anqing, China
| | - Jinsong Zheng
- Institute of Hydrobiology, Chinese Academy of Sciences, Beijing, China
| | - Zhengyi Qian
- Hubei Yangtze River Ecological Protection Foundation, Wuhan, China
| | - Hassan Ashfaq
- Institute of Continuing Education and Extension, University of Veterinary Animal Sciences, Lahore, Pakistan
| | - Daoping Yu
- College of Life Science, Anqing Normal University, Anqing, China
- Research Center of Aquatic Organism Conservation and Water Ecosystem Restoration in Anhui Province, Anqing Normal University, Anqing, China
| | - Kun Li
- Institute of Traditional Chinese Veterinary Medicine, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
- MOE Joint International Research Laboratory of Animal Health and Food Safety, Nanjing Agricultural University, Nanjing, China
- *Correspondence: Kun Li
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Shehata AA, Attia YA, Rahman MT, Basiouni S, El-Seedi HR, Azhar EI, Khafaga AF, Hafez HM. Diversity of Coronaviruses with Particular Attention to the Interspecies Transmission of SARS-CoV-2. Animals (Basel) 2022; 12:ani12030378. [PMID: 35158701 PMCID: PMC8833600 DOI: 10.3390/ani12030378] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2022] [Revised: 01/30/2022] [Accepted: 02/01/2022] [Indexed: 11/30/2022] Open
Abstract
Simple Summary Coronaviruses are a broad group of viruses that may infect a wide range of animals, including humans. Despite the fact that each coronavirus has a limited host range, frequent interspecies transmission of coronaviruses across diverse hosts has resulted in a complex ecology. The recently discovered SARS-CoV-2 virus is the clearest evidence of the danger of a global pandemic spreading. Natural infection with SARS-CoV-2 has been reported in a variety of domestic and wild animals, which may complicate the virus’s epidemiology and influence its development. In this review, we discussed the potential determinants of SARS-CoV-2 interspecies transmission. Additionally, despite the efforts that have been made to control this pandemic and to implement the One Health policy, several problems, such as the role of animals in SARS-CoV-2 evolution and the dynamics of interspecies transmission, are still unanswered. Abstract In December 2019, the outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was reported in China with serious impacts on global health and economy that is still ongoing. Although interspecies transmission of coronaviruses is common and well documented, each coronavirus has a narrowly restricted host range. Coronaviruses utilize different receptors to mediate membrane fusion and replication in the cell cytoplasm. The interplay between the receptor-binding domain (RBD) of coronaviruses and their coevolution are determinants for host susceptibility. The recently emerged SARS-CoV-2 caused the coronavirus disease 2019 (COVID-19) pandemic and has also been reported in domestic and wild animals, raising the question about the responsibility of animals in virus evolution. Additionally, the COVID-19 pandemic might also substantially have an impact on animal production for a long time. In the present review, we discussed the diversity of coronaviruses in animals and thus the diversity of their receptors. Moreover, the determinants of the susceptibility of SARS-CoV-2 in several animals, with special reference to the current evidence of SARS-CoV-2 in animals, were highlighted. Finally, we shed light on the urgent demand for the implementation of the One Health concept as a collaborative global approach to mitigate the threat for both humans and animals.
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Affiliation(s)
- Awad A. Shehata
- Birds and Rabbit Medicine Department, Faculty of Veterinary Medicine, University of Sadat City, Sadat City 32897, Egypt;
- Research and Development Section, PerNaturam GmbH, 56290 Gödenroth, Germany
| | - Youssef A. Attia
- Department of Agriculture, Faculty of Environmental Sciences, King Abdulaziz University, P.O. Box 80208, Jeddah 21589, Saudi Arabia;
- The Strategic Center to Kingdom Vision Realization, King Abdulaziz University, P.O. Box 80200, Jeddah 21589, Saudi Arabia
- Animal and Poultry Production Department, Faculty of Agriculture, Damanhour University, Damanhour 22516, Egypt
| | - Md. Tanvir Rahman
- Department of Microbiology and Hygiene, Faculty of Veterinary Science, Bangladesh Agricultural University, Mymensingh 2202, Bangladesh;
| | - Shereen Basiouni
- Clinical Pathology Department, Faculty of Veterinary Medicine, Benha University, Benha 13736, Egypt;
| | - Hesham R. El-Seedi
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, China;
- Department of Chemistry, Faculty of Science, Menoufia University, Shebin El-Kom 32512, Egypt
| | - Esam I. Azhar
- Special Infectious Agents Unit—BSL3, King Fahd Medical Research Center and Department of Medical Laboratory Science, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah 21362, Saudi Arabia;
| | - Asmaa F. Khafaga
- Department of Pathology, Faculty of Veterinary Medicine, Alexandria University, Edfina 22758, Egypt;
| | - Hafez M. Hafez
- Institute of Poultry Diseases, Faculty of Veterinary Medicine, Free University of Berlin, 14163 Berlin, Germany
- Correspondence:
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Abbas G, Zhang Y, Sun X, Chen H, Ren Y, Wang X, Ahmad MZ, Huang X, Li G. Molecular Characterization of Infectious Bronchitis Virus Strain HH06 Isolated in a Poultry Farm in Northeastern China. Front Vet Sci 2022; 8:794228. [PMID: 34977225 PMCID: PMC8716591 DOI: 10.3389/fvets.2021.794228] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 11/25/2021] [Indexed: 11/13/2022] Open
Abstract
Spike (S) glycoprotein is an important virulent factor for coronaviruses (CoVs), and variants of CoVs have been characterized based on S gene analysis. We present phylogenetic relationship of an isolated infectious bronchitis virus (IBV) strain with reference to the available genome and protein sequences based on network, multiple sequence, selection pressure, and evolutionary fingerprinting analysis in People's Republic of China. One hundred and elven strains of CoVs i.e., Alphacoronaviruses (Alpha-CoVs; n = 12), Betacoronaviruses (Beta-CoVs; n = 37), Gammacoronaviruses (Gamma-CoVs; n = 46), and Deltacoronaviruses (Delta-CoVs; n = 16) were selected for this purpose. Phylogenetically, SARS-CoV-2 and SARS-CoVs clustered together with Bat-CoVs and MERS-CoV of Beta-CoVs (C). The IBV HH06 of Avian-CoVs was closely related to Duck-CoV and partridge S14, LDT3 (teal and chicken host). Beluga whale-CoV (SW1) and Bottlenose dolphin-CoVs of mammalian origin branched distantly from other animal origin viruses, however, making group with Avian-CoVs altogether into Gamma-CoVs. The motif analysis indicated well-conserved domains on S protein, which were similar within the same phylogenetic class and but variable at different domains of different origins. Recombination network tree indicated SARS-CoV-2, SARS-CoV, and Bat-CoVs, although branched differently, shared common clades. The MERS-CoVs of camel and human origin spread branched into a different clade, however, was closely associated closely with SARS-CoV-2, SARS-CoV, and Bat-CoVs. Whereas, HCoV-OC43 has human origin and branched together with bovine CoVs with but significant distant from other CoVs like SARS CoV-2 and SARS-CoV of human origin. These findings explain that CoVs' constant genetic recombination and evolutionary process that might maintain them as a potential veterinary and human epidemic threat.
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Affiliation(s)
- Ghulam Abbas
- Heilongjiang Key Laboratory for Animal and Comparative Medicine, College of Veterinary Medicine, Northeast Agricultural University, Harbin, China
| | - Yue Zhang
- Heilongjiang Key Laboratory for Animal and Comparative Medicine, College of Veterinary Medicine, Northeast Agricultural University, Harbin, China
| | - Xiaowei Sun
- Heilongjiang Key Laboratory for Animal and Comparative Medicine, College of Veterinary Medicine, Northeast Agricultural University, Harbin, China
| | - Huijie Chen
- College of Pharmaceutical Engineering, Jilin Agriculture Science and Technology University, Jilin, China
| | - Yudong Ren
- Department of Computer Science and Technology, College of Electrical and Information Technology, Northeast Agricultural University, Harbin, China
| | - Xiurong Wang
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Science, Harbin, China
| | - Muhammad Zulfiqar Ahmad
- Department of Plant Breeding and Genetics, Faculty of Agriculture, Gomal University, Dera Ismail Khan, Pakistan
| | - Xiaodan Huang
- Heilongjiang Key Laboratory for Animal and Comparative Medicine, College of Veterinary Medicine, Northeast Agricultural University, Harbin, China
| | - Guangxing Li
- Heilongjiang Key Laboratory for Animal and Comparative Medicine, College of Veterinary Medicine, Northeast Agricultural University, Harbin, China
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Liang Y, Ma Y, Zhang Y, Chen Z, Wang Z, Li X, Cui L, Xu L, Liu S, Li H. Single-Cell Analysis of the In Vivo Dynamics of Host Circulating Immune Cells Highlights the Importance of Myeloid Cells in Avian Flaviviral Infection. THE JOURNAL OF IMMUNOLOGY 2021; 207:2878-2891. [PMID: 34697228 DOI: 10.4049/jimmunol.2100116] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Accepted: 09/24/2021] [Indexed: 01/26/2023]
Abstract
Ducks are an economically important waterfowl but a natural reservoir for some zoonotic pathogens, such as influenza virus and flaviviruses. Our understanding of the duck immune system and its interaction with viruses remains incomplete. In this study, we constructed the transcriptomic landscape of duck circulating immune cells, the first line of defense in the arthropod-borne transmission of arboviruses, using high-throughput single-cell transcriptome sequencing, which defined 14 populations of peripheral blood leukocytes (PBLks) based on distinct molecular signatures and revealed differences in the clustering of PBLks between ducks and humans. Taking advantage of in vivo sex differences in the susceptibility of duck PBLks to avian tembusu virus (TMUV) infection, a mosquito-borne flavivirus newly emerged from ducks with a broad host range from mosquitos to mammals, a comprehensive comparison of the in vivo dynamics of duck PBLks upon TMUV infection between sexes was performed at the single-cell level. Using this in vivo model, we discovered that TMUV infection reprogrammed duck PBLks differently between sexes, driving the expansion of granulocytes and priming granulocytes and monocytes for antiviral immune activation in males but decreasing the antiviral immune activity of granulocytes and monocytes by restricting their dynamic transitions from steady states to antiviral states with a decrease in the abundance of circulating monocytes in females. This study provides insights into the initial immune responses of ducks to arthropod-borne flaviviral infection and provides a framework for studying duck antiviral immunity.
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Affiliation(s)
- Yumeng Liang
- State Key Laboratory of Veterinary Biotechnology, National Poultry Laboratory Animal Resource Center, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, People's Republic of China; and
| | - Yong Ma
- School of Public Health (Shenzhen), Sun Yat-sen University, Shenzhen, People's Republic of China
| | - Yanhui Zhang
- State Key Laboratory of Veterinary Biotechnology, National Poultry Laboratory Animal Resource Center, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, People's Republic of China; and
| | - Zhijie Chen
- State Key Laboratory of Veterinary Biotechnology, National Poultry Laboratory Animal Resource Center, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, People's Republic of China; and
| | - Zhitao Wang
- State Key Laboratory of Veterinary Biotechnology, National Poultry Laboratory Animal Resource Center, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, People's Republic of China; and
| | - Xuefeng Li
- State Key Laboratory of Veterinary Biotechnology, National Poultry Laboratory Animal Resource Center, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, People's Republic of China; and
| | - Lu Cui
- State Key Laboratory of Veterinary Biotechnology, National Poultry Laboratory Animal Resource Center, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, People's Republic of China; and
| | - Li Xu
- State Key Laboratory of Veterinary Biotechnology, National Poultry Laboratory Animal Resource Center, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, People's Republic of China; and
| | - Shengwang Liu
- State Key Laboratory of Veterinary Biotechnology, National Poultry Laboratory Animal Resource Center, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, People's Republic of China; and
| | - Hai Li
- State Key Laboratory of Veterinary Biotechnology, National Poultry Laboratory Animal Resource Center, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, People's Republic of China; and
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10
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Traceable surveillance and genetic diversity analysis of coronaviruses in poultry from China in 2019. Virus Res 2021; 306:198566. [PMID: 34582833 PMCID: PMC8464398 DOI: 10.1016/j.virusres.2021.198566] [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: 03/10/2021] [Revised: 09/13/2021] [Accepted: 09/15/2021] [Indexed: 11/20/2022]
Abstract
Coronavirus disease 2019 (COVID-19), caused by Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), was first reported in Wuhan, China, and rapidly spread throughout the world. This newly emerging pathogen is highly transmittable and can cause fatal disease. More than 35 million cases have been confirmed, with a fatality rate of about 2.9% to October 9, 2020. However, the original and intermediate hosts of SARS-CoV-2 remain unknown. Here, 3160 poultry samples collected from 14 provinces of China between September and December 2019 were tested for SARS-CoV-2 infection. All the samples were SARS-CoV-2 negative, but 593 avian coronaviruses were detected, including 485 avian infectious bronchitis viruses, 72 duck coronaviruses, and 36 pigeon coronaviruses, with positivity rates of 15.35%, 2.28%, and 1.14%, respectively. Our surveillance demonstrates the diversity of avian coronaviruses in China, with higher prevalence rates in some regions. Furthermore, the possibility that SARS-CoV-2 originated from a known avian-origin coronavirus can be preliminarily ruled out. More surveillance of and research into avian coronaviruses are required to better understand the diversity, distribution, cross-species transmission, and clinical significance of these viruses.
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11
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Domańska-Blicharz K, Miłek-Krupa J, Pikuła A. Diversity of Coronaviruses in Wild Representatives of the Aves Class in Poland. Viruses 2021; 13:v13081497. [PMID: 34452362 PMCID: PMC8402903 DOI: 10.3390/v13081497] [Citation(s) in RCA: 12] [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: 05/31/2021] [Revised: 07/15/2021] [Accepted: 07/23/2021] [Indexed: 02/06/2023] Open
Abstract
The revealed prevalence of coronaviruses in wild bird populations in Poland was 4.15% and the main reservoirs were birds from orders Anseriformes and Charadriiformes, with a prevalence of 3.51% and 5.59%, respectively. Gammacoronaviruses were detected more often than deltacoronaviruses, with detection rates of 3.5% and 0.7%, respectively. Gammacoronaviruses were detected in birds belonging to six orders, including Anseriformes, Charadriiformes, Columbiformes, Galliformes, Gruiformes, and Passeriformes, indicating a relatively wide host range. Interestingly, this was the only coronavirus detected in Anseriformes (3.51%), while in Charadriiformes, the prevalence was 3.1%. The identified gammacoronaviruses belonged to the Igacovirus and Brangacovirus subgeneras. Most of these were igacoviruses and formed a common phylogenetic group with a Duck Coronavirus 2714 and two with an Avian Coronavirus/Avian Coronavirus9203, while the viruses from the pigeons formed a distinct “pigeon-like” group, not yet officially represented. The presence of deltacoronaviruses was detected in birds belonging to three orders, Charadriiformes, Galliformes, and Suliformes indicating a narrower host range. Most identified deltacoronaviruses belonged to the Buldecovirus subgenus, while only one belonged to Herdecovirus. Interestingly, the majority of buldecoviruses were identified in gulls, and they formed a distinct phylogenetic lineage not represented by any officially ratified virus species. Another separate group of buldecoviruses, also not represented by the official species, was formed by a virus identified in a common snipe. Only one identified buldecovirus (from common pheasant) formed a group with the ratified species Coronavirus HKU15. The results obtained indicate the high diversity of detected coronaviruses, and thus also the need to update their taxonomy (establishing new representative virus species). The serological studies performed revealed antibodies against an infectious bronchitis virus in the sera of white storks and mallards.
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12
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Zhang X, Chen T, Chen S, Nie Y, Xie Z, Feng K, Zhang H, Xie Q. The Efficacy of a Live Attenuated TW I-Type Infectious Bronchitis Virus Vaccine Candidate. Virol Sin 2021; 36:1431-1442. [PMID: 34251605 PMCID: PMC8273854 DOI: 10.1007/s12250-021-00419-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Accepted: 04/26/2021] [Indexed: 11/17/2022] Open
Abstract
Infectious bronchitis (IB) is a highly contagious avian disease caused by infection with infectious bronchitis virus (IBV), which seriously affects the development of the global poultry industry. The distribution of TW I-type IBV in China has increased in recent years, becoming a widespread genotype. We previously isolated a TW I-type IBV strain termed CK/CH/GD/GZ14 in 2014, but its pathogenicity and possibility for vaccine development were not explored. Therefore, this research aimed to develop a live-attenuated virus vaccine based on the CK/CH/GD/GZ14 strain. The wild type IBV CK/CH/GD/GZ14 strain was serially passaged in SPF embryos for 145 generations. The morbidity and mortality rate of wild-type strain in 14 day-old chickens is 100% and 80% respectively, while the morbidity rate in the attenuated strain was 20% in the 95th and 105th generations and there was no death. Histopathological observations showed that the pathogenicity of the 95th and 105th generations in chickens was significantly weakened. Further challenge experiments confirmed that the attenuated CK/CH/GD/GZ14 strain in the 95th and 105th generations could resist CK/CH/GD/GZ14 (5th generation) infection and the protection rate was 80%. Tracheal cilia stagnation, virus shedding, and viral load experiments confirmed that the 95th and 105th generations provide good immune protection in chickens, and the immunogenicity of the 105th generation is better than that of the 95th generation. These data suggest that the attenuated CK/CH/GD/GZ14 strain in the 105th generation may be applied as a vaccine candidate against TW I-type IBV.
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Affiliation(s)
- Xinheng Zhang
- Lingnan Guangdong Laboratory of Modern Agriculture, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China.,Guangdong Engineering Research Center for Vector Vaccine of Animal Virus, Guangzhou, 510642, China.,South China Collaborative Innovation Center for Poultry Disease Control and Product Safety, Guangzhou, 510642, China
| | - Tong Chen
- Lingnan Guangdong Laboratory of Modern Agriculture, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China.,Guangdong Engineering Research Center for Vector Vaccine of Animal Virus, Guangzhou, 510642, China.,South China Collaborative Innovation Center for Poultry Disease Control and Product Safety, Guangzhou, 510642, China
| | - Sheng Chen
- Lingnan Guangdong Laboratory of Modern Agriculture, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China.,Guangdong Engineering Research Center for Vector Vaccine of Animal Virus, Guangzhou, 510642, China
| | - Yu Nie
- Lingnan Guangdong Laboratory of Modern Agriculture, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China.,Guangdong Engineering Research Center for Vector Vaccine of Animal Virus, Guangzhou, 510642, China
| | - Zi Xie
- Lingnan Guangdong Laboratory of Modern Agriculture, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China.,Guangdong Engineering Research Center for Vector Vaccine of Animal Virus, Guangzhou, 510642, China
| | - Keyu Feng
- Lingnan Guangdong Laboratory of Modern Agriculture, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China.,Guangdong Engineering Research Center for Vector Vaccine of Animal Virus, Guangzhou, 510642, China
| | - Huanmin Zhang
- United States Department of Agriculture, Agriculture Research Service, Avian Disease and Oncology Laboratory, East Lansing, MI, 48823, USA
| | - Qingmei Xie
- Lingnan Guangdong Laboratory of Modern Agriculture, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China. .,Guangdong Engineering Research Center for Vector Vaccine of Animal Virus, Guangzhou, 510642, China. .,South China Collaborative Innovation Center for Poultry Disease Control and Product Safety, Guangzhou, 510642, China.
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13
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Shi Y, Tao J, Li B, Shen X, Cheng J, Liu H. The Gut Viral Metagenome Analysis of Domestic Dogs Captures Snapshot of Viral Diversity and Potential Risk of Coronavirus. Front Vet Sci 2021; 8:695088. [PMID: 34307533 PMCID: PMC8292670 DOI: 10.3389/fvets.2021.695088] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Accepted: 06/10/2021] [Indexed: 11/13/2022] Open
Abstract
The close relations between dogs (Canis lupus familiaris) and humans lay a foundation for cross species transmissions of viruses. The co-existence of multiplex viruses in the host accelerate viral variations. For effective prediction and prevention of potential epidemic or even pandemic, the metagenomics method was used to investigate the gut virome status of 45 domestic healthy dogs which have extensive contact with human beings. A total of 248.6 GB data (505, 203, 006 valid reads, 150 bp in length) were generated and 325, 339 contigs, which were best matched with viral genes, were assembled from 46, 832, 838 reads. In the aggregate, 9,834 contigs (3.02%) were confirmed for viruses. The top 30 contigs with the most reads abundance were mapped to DNA virus families Circoviridae, Parvoviridae and Herpesviridae; and RNA virus families Astroviridae, Coronaviridae and Picornaviridae, respectively. Numerous sequences were assigned to animal virus families of Astroviridae, Coronaviridae, Circoviridae, etc.; and phage families of Microviridae, Siphoviridae, Ackermannviridae, Podoviridae, Myoviridae and the unclassified phages. Further, several sequences were homologous with the insect and plant viruses, which reflects the diet and habitation of dogs. Significantly, canine coronavirus was uniquely identified in all the samples with high abundance, and the phylogenetic analysis therefore showed close relationship with the human coronavirus strain 229E and NL63, indicating the potential risk of canine coronavirus to infect humans by obtaining the ability of cross-species transmission. This study emphasizes the high detection frequency of virus harbored in the enteric tract of healthy contacted animal, and expands the knowledge of the viral diversity and the spectrum for further disease-association studies, which is meaningful for elucidating the epidemiological and biological role of companion animals in public health.
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Affiliation(s)
- Ying Shi
- Department of Animal Infectious Diseases, Institute of Animal Husbandry and Veterinary Sciences, Shanghai Academy of Agricultural Sciences, Shanghai, China.,Shanghai Key Laboratory of Agricultural Genetic Breeding, Shanghai, China.,Shanghai Engineering Research Center of Pig Breeding, Shanghai, China
| | - Jie Tao
- Department of Animal Infectious Diseases, Institute of Animal Husbandry and Veterinary Sciences, Shanghai Academy of Agricultural Sciences, Shanghai, China.,Shanghai Key Laboratory of Agricultural Genetic Breeding, Shanghai, China.,Shanghai Engineering Research Center of Pig Breeding, Shanghai, China
| | - Benqiang Li
- Department of Animal Infectious Diseases, Institute of Animal Husbandry and Veterinary Sciences, Shanghai Academy of Agricultural Sciences, Shanghai, China.,Shanghai Key Laboratory of Agricultural Genetic Breeding, Shanghai, China.,Shanghai Engineering Research Center of Pig Breeding, Shanghai, China
| | - Xiaohui Shen
- Department of Animal Infectious Diseases, Institute of Animal Husbandry and Veterinary Sciences, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Jinghua Cheng
- Department of Animal Infectious Diseases, Institute of Animal Husbandry and Veterinary Sciences, Shanghai Academy of Agricultural Sciences, Shanghai, China.,Shanghai Key Laboratory of Agricultural Genetic Breeding, Shanghai, China.,Shanghai Engineering Research Center of Pig Breeding, Shanghai, China
| | - Huili Liu
- Department of Animal Infectious Diseases, Institute of Animal Husbandry and Veterinary Sciences, Shanghai Academy of Agricultural Sciences, Shanghai, China.,Shanghai Key Laboratory of Agricultural Genetic Breeding, Shanghai, China.,Shanghai Engineering Research Center of Pig Breeding, Shanghai, China
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14
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Mohamadian M, Chiti H, Shoghli A, Biglari S, Parsamanesh N, Esmaeilzadeh A. COVID-19: Virology, biology and novel laboratory diagnosis. J Gene Med 2021; 23:e3303. [PMID: 33305456 PMCID: PMC7883242 DOI: 10.1002/jgm.3303] [Citation(s) in RCA: 150] [Impact Index Per Article: 50.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 11/15/2020] [Accepted: 12/04/2020] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND At the end of December 2019, a novel coronavirus tentatively named SARS-CoV-2 in Wuhan, a central city in China, was announced by the World Health Organization. SARS-CoV-2 is an RNA virus that has become a major public health concern after the outbreak of the Middle East Respiratory Syndrome-CoV (MERS-CoV) and Severe Acute Respiratory Syndrome-CoV (SARS-CoV) in 2002 and 2012, respectively. As of 29 October 2020, the total number of COVID-19 cases had reached over 44 million worldwide, with more than 1.17 million confirmed deaths. DISCUSSION SARS-CoV-2 infected patients usually present with severe viral pneumonia. Similar to SARS-CoV, the virus enters respiratory tract cells via the angiotensin-converting enzyme receptor 2. The structural proteins play an essential role in budding the virus particles released from different host cells. To date, an approved vaccine or treatment option of a preventive character to avoid severe courses of COVID-19 is still not available. CONCLUSIONS In the present study, we provide a brief review of the general biological features of CoVs and explain the pathogenesis, clinical symptoms and diagnostic approaches regarding monitoring future infectivity and prevent emerging COVID-19 infections.
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Affiliation(s)
- Malihe Mohamadian
- Department of Molecular MedicineBirjand University of Medical SciencesBirjandIran
- Cellular and Molecular Research CenterBirjand University of Medical SciencesBirjandIran
| | - Hossein Chiti
- Zanjan Metabolic Diseases Research CenterZanjan University of Medical SciencesZanjanIran
| | - Alireza Shoghli
- Social Determinants of Health Research CenterZanjan University of Medical SciencesZanjanIran
| | - Sajjad Biglari
- School of MedicineZanjan University of Medical SciencesZanjanIran
| | - Negin Parsamanesh
- Zanjan Metabolic Diseases Research CenterZanjan University of Medical SciencesZanjanIran
| | - Abdolreza Esmaeilzadeh
- Department of ImmunologyZanjan University of Medical ScienceZanjanIran
- Cancer Gene Therapy Research CenterZanjan University of Medical ScienceZanjanIran
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15
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Updated insight into COVID-19 disease and health management to combat the pandemic. ENVIRONMENTAL AND HEALTH MANAGEMENT OF NOVEL CORONAVIRUS DISEASE (COVID-19 ) 2021. [PMCID: PMC8237642 DOI: 10.1016/b978-0-323-85780-2.00017-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causes COVID-19 disease in humans and is the responsible viral agent for the currently ongoing pandemic. Early cases of COVID-19 were reported from Wuhan, Hubei province of China, the likely birthplace of this outbreak. Currently, over 92 million people in the globe are actively battling this virus, and over 2 million individuals have already succumbed to the disease. The high human-to-human transmission capacity of the virus is among the primary causes for such a rapid global spread of COVID-19. In humans, it causes acute to severe respiratory distress in the form of pneumonia. The presentation of clinical features of the disease ranges from mild in healthy adults to severe among individuals with weakened or immunocompromised immune systems and the elderly. Thus, increasing patient cases of COVID-19 warrants a growing demand for medical attention that is eventually overburdening our health care systems. Rapid detection of COVID-19 in suspected individuals and isolation are among the crucial intervention norms in health management strategies to control the COVID-19 pandemic, in addition to strict observance of public hygienic practices such as reduced public gathering, use of facial masks, and practicing of social distancing. This chapter provides an overview of the epidemiology of COVID-19 and the current classical health management strategies and issues to tackle this pandemic. It particularly highlights the role of standard as well as novel biomolecular diagnostic techniques as a tool for successful implementation of such public safety measures issued by medical policy makers and the governing bodies.
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16
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Wille M, Holmes EC. Wild birds as reservoirs for diverse and abundant gamma- and deltacoronaviruses. FEMS Microbiol Rev 2020; 44:631-644. [PMID: 32672814 PMCID: PMC7454673 DOI: 10.1093/femsre/fuaa026] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Accepted: 06/30/2020] [Indexed: 12/17/2022] Open
Abstract
Wild birds interconnect all parts of the globe through annual cycles of migration with little respect for country or continental borders. Although wild birds are reservoir hosts for a high diversity of gamma- and deltacoronaviruses, we have little understanding of the ecology or evolution of any of these viruses. In this review, we use genome sequence and ecological data to disentangle the evolution of coronaviruses in wild birds. Specifically, we explore host range at the levels of viral genus and species, and reveal the multi-host nature of many viral species, albeit with biases to certain types of avian host. We conclude that it is currently challenging to infer viral ecology due to major sampling and technical limitations, and suggest that improved assay performance across the breadth of gamma- and deltacoronaviruses, assay standardization, as well as better sequencing approaches, will improve both the repeatability and interpretation of results. Finally, we discuss cross-species virus transmission across both the wild bird - poultry interface as well as from birds to mammals. Clarifying the ecology and diversity in the wild bird reservoir has important ramifications for our ability to respond to the likely future emergence of coronaviruses in socioeconomically important animal species or human populations.
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Affiliation(s)
- Michelle Wille
- WHO Collaborating Centre for Reference and Research on Influenza, at The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Edward C Holmes
- Marie Bashir Institute for Infectious Diseases and Biosecurity, School of Life and Environmental Sciences and School of Medical Sciences, The University of Sydney, Sydney, New South Wales, Australia
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17
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Zhuang Q, Liu S, Zhang X, Jiang W, Wang K, Wang S, Peng C, Hou G, Li J, Yu X, Yuan L, Wang J, Li Y, Liu H, Chen J. Surveillance and taxonomic analysis of the coronavirus dominant in pigeons in China. Transbound Emerg Dis 2020; 67:1981-1990. [PMID: 32163661 PMCID: PMC7228218 DOI: 10.1111/tbed.13541] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Revised: 03/04/2020] [Accepted: 03/04/2020] [Indexed: 11/30/2022]
Abstract
Coronaviruses (CoVs) are found in humans and a wide variety of wild and domestic animals, and of substantial impact on human and animal health. In poultry, the genetic diversity, evolution, distribution and taxonomy of CoVs dominant in birds other than chickens remain enigmatic. In our previous study, we proposed that the CoVs dominant (i.e. mainly circulating) in ducks (DdCoVs) should represent a novel species, which was different from the one represented by the CoVs dominant in chickens (CdCoVs). In this study, we conducted a large-scale surveillance of CoVs in chickens, ducks, geese, pigeons and other birds (quails, sparrows and partridges) using a conserved RT-PCR assay. The surveillance demonstrated that CdCoVs, DdCoVs and the CoVs dominant in pigeons (PdCoVs) belong to different lineages, and they are all prevalent in live poultry markets and the backyard flocks in some regions of China. We further sequenced seven Coronaviridae-wide conserved domains in their replicase polyprotein pp1ab of seven PdCoVs and found that the genetic distances in these domains between PdCoVs and DdCoVs or CdCoVs are large enough to separate PdCoVs into a novel species, which were different from the ones represented by DdCoVs or CdCoVs within the genus Gammacoronavirus, per the species demarcation criterion of International Committee on Taxonomy of Viruses. This report shed novel insight into the genetic diversity, distribution, evolution and taxonomy of avian CoVs.
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Affiliation(s)
- Qingye Zhuang
- China Animal Health and Epidemiology CenterQingdaoChina
| | - Shuo Liu
- China Animal Health and Epidemiology CenterQingdaoChina
| | | | - Wenming Jiang
- China Animal Health and Epidemiology CenterQingdaoChina
| | - Kaicheng Wang
- China Animal Health and Epidemiology CenterQingdaoChina
| | - Suchun Wang
- China Animal Health and Epidemiology CenterQingdaoChina
| | - Cheng Peng
- China Animal Health and Epidemiology CenterQingdaoChina
| | - Guangyu Hou
- China Animal Health and Epidemiology CenterQingdaoChina
| | - Jinping Li
- China Animal Health and Epidemiology CenterQingdaoChina
| | - Xiaohui Yu
- China Animal Health and Epidemiology CenterQingdaoChina
| | - Liping Yuan
- China Animal Health and Epidemiology CenterQingdaoChina
| | - Jingjing Wang
- China Animal Health and Epidemiology CenterQingdaoChina
| | - Yang Li
- China Animal Health and Epidemiology CenterQingdaoChina
| | - Hualei Liu
- China Animal Health and Epidemiology CenterQingdaoChina
| | - Jiming Chen
- China Animal Health and Epidemiology CenterQingdaoChina
- College of Veterinary MedicineQingdao Agricultural UniversityQingdaoChina
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18
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On the Coronaviruses and Their Associations with the Aquatic Environment and Wastewater. WATER 2020. [DOI: 10.3390/w12061598] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The outbreak of Coronavirus Disease 2019 (COVID-19), a severe respiratory disease caused by betacoronavirus SARS-CoV-2, in 2019 that further developed into a pandemic has received an unprecedented response from the scientific community and sparked a general research interest into the biology and ecology of Coronaviridae, a family of positive-sense single-stranded RNA viruses. Aquatic environments, lakes, rivers and ponds, are important habitats for bats and birds, which are hosts for various coronavirus species and strains and which shed viral particles in their feces. It is therefore of high interest to fully explore the role that aquatic environments may play in coronavirus spread, including cross-species transmissions. Besides the respiratory tract, coronaviruses pathogenic to humans can also infect the digestive system and be subsequently defecated. Considering this, it is pivotal to understand whether wastewater can play a role in their dissemination, particularly in areas with poor sanitation. This review provides an overview of the taxonomy, molecular biology, natural reservoirs and pathogenicity of coronaviruses; outlines their potential to survive in aquatic environments and wastewater; and demonstrates their association with aquatic biota, mainly waterfowl. It also calls for further, interdisciplinary research in the field of aquatic virology to explore the potential hotspots of coronaviruses in the aquatic environment and the routes through which they may enter it.
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19
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Decaro N, Lorusso A. Novel human coronavirus (SARS-CoV-2): A lesson from animal coronaviruses. Vet Microbiol 2020; 244:108693. [PMID: 32402329 PMCID: PMC7195271 DOI: 10.1016/j.vetmic.2020.108693] [Citation(s) in RCA: 231] [Impact Index Per Article: 57.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Revised: 04/10/2020] [Accepted: 04/10/2020] [Indexed: 12/16/2022]
Abstract
The recent pandemic caused by the novel human coronavirus, referrred to as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), not only is having a great impact on the health care systems and economies in all continents but it is also causing radical changes of common habits and life styles. The novel coronavirus (CoV) recognises, with high probability, a zoonotic origin but the role of animals in the SARS-CoV-2 epidemiology is still largely unknown. However, CoVs have been known in animals since several decades, so that veterinary coronavirologists have a great expertise on how to face CoV infections in animals, which could represent a model for SARS-CoV-2 infection in humans. In the present paper, we provide an up-to-date review of the literature currently available on animal CoVs, focusing on the molecular mechanisms that are responsible for the emergence of novel CoV strains with different antigenic, biologic and/or pathogenetic features. A full comprehension of the mechanisms driving the evolution of animal CoVs will help better understand the emergence, spreading, and evolution of SARS-CoV-2.
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Affiliation(s)
- Nicola Decaro
- Department of Veterinary Medicine, University of Bari, Valenzano, Bari, Italy.
| | - Alessio Lorusso
- Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise 'G. Caporale', Teramo, Italy
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20
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Virus Metagenomics in Farm Animals: A Systematic Review. Viruses 2020; 12:v12010107. [PMID: 31963174 PMCID: PMC7019290 DOI: 10.3390/v12010107] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2019] [Revised: 01/12/2020] [Accepted: 01/14/2020] [Indexed: 02/07/2023] Open
Abstract
A majority of emerging infectious diseases are of zoonotic origin. Metagenomic Next-Generation Sequencing (mNGS) has been employed to identify uncommon and novel infectious etiologies and characterize virus diversity in human, animal, and environmental samples. Here, we systematically reviewed studies that performed viral mNGS in common livestock (cattle, small ruminants, poultry, and pigs). We identified 2481 records and 120 records were ultimately included after a first and second screening. Pigs were the most frequently studied livestock and the virus diversity found in samples from poultry was the highest. Known animal viruses, zoonotic viruses, and novel viruses were reported in available literature, demonstrating the capacity of mNGS to identify both known and novel viruses. However, the coverage of metagenomic studies was patchy, with few data on the virome of small ruminants and respiratory virome of studied livestock. Essential metadata such as age of livestock and farm types were rarely mentioned in available literature, and only 10.8% of the datasets were publicly available. Developing a deeper understanding of livestock virome is crucial for detection of potential zoonotic and animal pathogens and One Health preparedness. Metagenomic studies can provide this background but only when combined with essential metadata and following the “FAIR” (Findable, Accessible, Interoperable, and Reusable) data principles.
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21
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Kaszab E, Doszpoly A, Lanave G, Verma A, Bányai K, Malik YS, Marton S. Metagenomics revealing new virus species in farm and pet animals and aquaculture. GENOMICS AND BIOTECHNOLOGICAL ADVANCES IN VETERINARY, POULTRY, AND FISHERIES 2020. [PMCID: PMC7149329 DOI: 10.1016/b978-0-12-816352-8.00002-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
Abstract
Viral metagenomics is slowly taking over the traditional and widely used molecular techniques for the investigation of pathogenic viruses responsible for illness and inflicting great economic burden on the farm animal industry. Owing to the continued improvements in sequencing technologies and the dramatic reduction of per base costs of sequencing the use of next generation sequencing have been key factors in this progress. Discoveries linked to viral metagenomics are expected to be beneficial to the field of veterinary medicine starting from the development of better diagnostic assays to the design of new subunit vaccines with minimal investments. With these achievements the research has taken a giant leap even toward the better healthcare of animals and, as a result, the animal sector could be growing at an unprecedented pace.
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22
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Ma X, Bi S, Wang Y, Chi X, Hu S. Combined adjuvant effect of ginseng stem-leaf saponins and selenium on immune responses to a live bivalent vaccine of Newcastle disease virus and infectious bronchitis virus in chickens. Poult Sci 2019; 98:3548-3556. [PMID: 31220864 PMCID: PMC7107245 DOI: 10.3382/ps/pez207] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Accepted: 03/24/2019] [Indexed: 12/12/2022] Open
Abstract
Vaccination with a live bivalent vaccine of Newcastle disease virus (NDV) and infectious bronchitis virus (IBV) is a routine practice in poultry industry in China. This study was designed to evaluate ginseng stem-leaf saponins (GSLS) in combination with selenium (Se) for their adjuvant effect on the immune response to vaccination against NDV and IBV in chickens. A live bivalent vaccine of NDV and IBV was diluted in saline solution containing GSLS or Se or both and used to immunize chickens via a intraocular-and-intranasal route. Results showed that GSLS promoted significantly higher NDV- and IBV-specific antibody responses with the highest antibody response detected in GSLS-Se group. The increased antibody was capable of neutralizing NDV and IBV. In addition, GSLS-Se enhanced lymphocyte proliferation and production of IFN-γ and IL-4. More importantly GSLS-Se was found to promote early production and prolong the duration of the antibody responses. In order to improve the efficacy of vaccination in chicken flocks, the diluent containing GSLS-Se deserves further studies to evaluate its effect on other chicken vaccines.
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Affiliation(s)
- X Ma
- Department of Veterinary Medicine, College of Animal Sci., Zhejiang University, Hangzhou, Zhejiang 310058, P. R. China
| | - S Bi
- Department of Veterinary Medicine, College of Animal Sci., Zhejiang University, Hangzhou, Zhejiang 310058, P. R. China
| | - Y Wang
- Department of Veterinary Medicine, College of Animal Sci., Zhejiang University, Hangzhou, Zhejiang 310058, P. R. China
| | - X Chi
- Department of Veterinary Medicine, College of Animal Sci., Zhejiang University, Hangzhou, Zhejiang 310058, P. R. China
| | - S Hu
- Department of Veterinary Medicine, College of Animal Sci., Zhejiang University, Hangzhou, Zhejiang 310058, P. R. China
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Canuti M, Kroyer ANK, Ojkic D, Whitney HG, Robertson GJ, Lang AS. Discovery and Characterization of Novel RNA Viruses in Aquatic North American Wild Birds. Viruses 2019; 11:E768. [PMID: 31438486 PMCID: PMC6784231 DOI: 10.3390/v11090768] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Revised: 08/16/2019] [Accepted: 08/18/2019] [Indexed: 12/25/2022] Open
Abstract
Wild birds are recognized viral reservoirs but our understanding about avian viral diversity is limited. We describe here three novel RNA viruses that we identified in oropharyngeal/cloacal swabs collected from wild birds. The complete genome of a novel gull metapneumovirus (GuMPV B29) was determined. Phylogenetic analyses indicated that this virus could represent a novel avian metapneumovirus (AMPV) sub-group, intermediate between AMPV-C and the subgroup of the other AMPVs. This virus was detected in an American herring (1/24, 4.2%) and great black-backed (4/26, 15.4%) gulls. A novel gull coronavirus (GuCoV B29) was detected in great black-backed (3/26, 11.5%) and American herring (2/24, 8.3%) gulls. Phylogenetic analyses of GuCoV B29 suggested that this virus could represent a novel species within the genus Gammacoronavirus, close to other recently identified potential novel avian coronaviral species. One GuMPV-GuCoV co-infection was detected. A novel duck calicivirus (DuCV-2 B6) was identified in mallards (2/5, 40%) and American black ducks (7/26, 26.9%). This virus, of which we identified two different types, was fully sequenced and was genetically closest to other caliciviruses identified in Anatidae, but more distant to other caliciviruses from birds in the genus Anas. These discoveries increase our knowledge about avian virus diversity and host distributions.
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Affiliation(s)
- Marta Canuti
- Department of Biology, Memorial University of Newfoundland, 232 Elizabeth Ave., St. John's, NL A1B 3X9, Canada.
| | - Ashley N K Kroyer
- Department of Biology, Memorial University of Newfoundland, 232 Elizabeth Ave., St. John's, NL A1B 3X9, Canada
| | - Davor Ojkic
- Animal Health Laboratory, Laboratory Services Division, University of Guelph, 419 Gordon St., Guelph, ON N1H 6R8, Canada
| | - Hugh G Whitney
- Department of Biology, Memorial University of Newfoundland, 232 Elizabeth Ave., St. John's, NL A1B 3X9, Canada
| | - Gregory J Robertson
- Wildlife Research Division, Environment and Climate Change Canada, 6 Bruce Street, Mount Pearl, NL A1N 4T3, Canada
| | - Andrew S Lang
- Department of Biology, Memorial University of Newfoundland, 232 Elizabeth Ave., St. John's, NL A1B 3X9, Canada.
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Pauly M, Snoeck CJ, Phoutana V, Keosengthong A, Sausy A, Khenkha L, Nouanthong P, Samountry B, Jutavijittum P, Vilivong K, Hübschen JM, Black AP, Pommasichan S, Muller CP. Cross-species transmission of poultry pathogens in backyard farms: ducks as carriers of chicken viruses. Avian Pathol 2019; 48:503-511. [PMID: 31199168 DOI: 10.1080/03079457.2019.1628919] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
In backyard farms of Lao People's Democratic Republic, mixed-species rearing of poultry is a breeding-ground for cross-species transmission. Here, the epidemiology of viruses circulating among backyard poultry in Vientiane Province was assessed to guide future control strategies. Oral/tracheal and cloacal swabs, collected from 605 poultry (308 ducks, 297 chickens) between 2011 and 2015, were screened by PCR for Newcastle disease virus (NDV), coronavirus (CoV) and chicken anaemia virus (CAV). Chicken sera were screened for anti-NDV antibodies by ELISA. Statistical and phylogenetic analyses revealed transmission patterns and relationships. Closely related strains co-circulated in chickens and ducks. While CoV RNA was detected in oral/tracheal swabs of 9.3% of the chickens and 2.4% of the ducks, rates were higher in faecal swabs of both species (27.3% and 48.2%). RNA of infectious bronchitis virus (IBV) and duck CoV was found in faecal swabs of chickens (19.7% and 7.1%) and ducks (4.1% and 44.1%). Moreover, DNA of the generally chicken-specific CAV was detected in oral/tracheal swabs of chickens (18.1%) and, sporadically, of ducks (2.4%). Despite serological evidence of NDV circulation or vaccination (86.9%), NDV RNA was not detected. We found a high prevalence and indication for cross-species transmission of different CoV strains in backyard poultry. Interestingly, ducks served as biological, or at least mechanical, carriers of viral strains closely related not only to IBV, but also to CAV. Bird containment and poultry species separation could be first steps to avoid cross-species transmission and emergence of novel strains with broad host range and enhanced pathogenicity. RESEARCH HIGHLIGHTS High rates of avian viruses were detected by PCR in backyard poultry from Lao PDR. Diverse coronavirus and chicken anemia virus strains co-circulated. Phylogenetic analyses suggested virus transmission between chickens and ducks. Serological evidence of Newcastle disease was found, but viral RNA was not detected.
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Affiliation(s)
- Maude Pauly
- Department of Infection and Immunity, Luxembourg Institute of Health , Esch-sur-Alzette , Luxembourg
| | - Chantal J Snoeck
- Department of Infection and Immunity, Luxembourg Institute of Health , Esch-sur-Alzette , Luxembourg
| | - Vannaphone Phoutana
- The Faculty of Agriculture, National University of Laos - Nabong Campus , Vientiane , Lao People's Democratic Republic
| | - Amphone Keosengthong
- The Faculty of Agriculture, National University of Laos - Nabong Campus , Vientiane , Lao People's Democratic Republic
| | - Aurélie Sausy
- Department of Infection and Immunity, Luxembourg Institute of Health , Esch-sur-Alzette , Luxembourg
| | - Latdavone Khenkha
- Lao-Lux-Laboratory, Institute Pasteur du Laos , Vientiane , Lao People's Democratic Republic
| | | | - Bounthome Samountry
- Department of Pathology, Faculty of Basic Sciences, Ministry of Public Health, University of Health Sciences , Vientiane , Lao People's Democratic Republic
| | - Prapan Jutavijittum
- Department of Pathology, Faculty of Medicine, Chiang Mai University , Chiang Mai , Thailand
| | - Keooudomphone Vilivong
- National Centre for Laboratory and Epidemiology, Lao Ministry of Health , Vientiane , Lao People's Democratic Republic
| | - Judith M Hübschen
- Department of Infection and Immunity, Luxembourg Institute of Health , Esch-sur-Alzette , Luxembourg
| | - Antony P Black
- Lao-Lux-Laboratory, Institute Pasteur du Laos , Vientiane , Lao People's Democratic Republic
| | - Sisavath Pommasichan
- The Faculty of Agriculture, National University of Laos - Nabong Campus , Vientiane , Lao People's Democratic Republic
| | - Claude P Muller
- Department of Infection and Immunity, Luxembourg Institute of Health , Esch-sur-Alzette , Luxembourg.,Lao-Lux-Laboratory, Institute Pasteur du Laos , Vientiane , Lao People's Democratic Republic.,Laboratoire National de Santé , Dudelange , Luxembourg
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25
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MOLECULAR IDENTIFICATION OF AVIAN VIRUSES IN NEOTROPIC CORMORANTS ( PHALACROCORAX BRASILIANUS) IN CHILE. J Wildl Dis 2018; 55:105-112. [PMID: 30216128 DOI: 10.7589/2017-10-256] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
We identified two RNA (paramyxovirus and coronavirus) and two DNA (adenovirus and herpesvirus) viruses in a common aquatic bird, the Neotropic Cormorant ( Phalacrocorax brasilianus), and determined their phylogenetic relationships to other global circulating variants. We analyzed 104 cloacal swabs from individuals collected at locations in Central Chile. Sequences were obtained from amplicons using consensus primers targeting conserved genes of the virus families Paramyxoviridae, Coronaviridae, Adenoviridae, and Herpesviridae. A total of 20.2% of the samples was positive for coronavirus, 8.7% for adenovirus, and 3.8% for herpesvirus. No paramyxoviruses were detected. All coronaviruses were identified as viruses of the Gammacoronavirus genus, closely related to the infectious bronchitis virus clade (bootstrap clade support=75%). All adenovirus samples were identified as Aviadenovirus, related to a gull and falcon adenovirus (Bayesian posterior probability=0.86). The herpesviruses identified were related to the infectious laryngotracheitis virus ( Gallid herpesvirus 1) of the genus Iltovirus (bootstrap clade support=99%). We provide information about the diversity of viruses circulating among apparently healthy Neotropic Cormorants.
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26
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Miłek J, Blicharz-Domańska K. Coronaviruses in Avian Species - Review with Focus on Epidemiology and Diagnosis in Wild Birds. J Vet Res 2018; 62:249-255. [PMID: 30584600 PMCID: PMC6296008 DOI: 10.2478/jvetres-2018-0035] [Citation(s) in RCA: 77] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Accepted: 09/19/2018] [Indexed: 12/12/2022] Open
Abstract
Coronaviruses (CoVs) are a large group of enveloped viruses with a single-strand RNA genome, which continuously circulate in mammals and birds and pose a threat to livestock, companion animals, and humans. CoVs harboured by avian species are classified to the genera gamma- and deltacoronaviruses. Within the gamma-CoVs the main representative is avian coronavirus, a taxonomic name which includes the highly contagious infectious bronchitis viruses (IBVs) in chickens and similar viruses infecting other domestic birds such as turkeys, guinea fowls, or quails. Additionally, IBVs have been detected in healthy wild birds, demonstrating that they may act as the vector between domestic and free-living birds. Moreover, CoVs other than IBVs, are identified in wild birds, which suggests that wild birds play a key role in the epidemiology of other gammaCoVs and deltaCoVs. Development of molecular techniques has significantly improved knowledge of the prevalence of CoVs in avian species. The methods adopted in monitoring studies of CoVs in different avian species are mainly based on detection of conservative regions within the viral replicase, nucleocapsid genes, and 3'UTR or 5'UTR. The purpose of this review is to summarise recent discoveries in the areas of epidemiology and diagnosis of CoVs in avian species and to understand the role of wild birds in the virus distribution.
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Affiliation(s)
- Justyna Miłek
- Department of Poultry Diseases, National Veterinary Research Institute, 24-100Puławy, Poland
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27
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Next-generation sequencing library preparation method for identification of RNA viruses on the Ion Torrent Sequencing Platform. Virus Genes 2018; 54:536-542. [PMID: 29744712 PMCID: PMC7088580 DOI: 10.1007/s11262-018-1568-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Accepted: 05/04/2018] [Indexed: 12/19/2022]
Abstract
Next generation sequencing (NGS) is a powerful tool for the characterization, discovery, and molecular identification of RNA viruses. There were multiple NGS library preparation methods published for strand-specific RNA-seq, but some methods are not suitable for identifying and characterizing RNA viruses. In this study, we report a NGS library preparation method to identify RNA viruses using the Ion Torrent PGM platform. The NGS sequencing adapters were directly inserted into the sequencing library through reverse transcription and polymerase chain reaction, without fragmentation and ligation of nucleic acids. The results show that this method is simple to perform, able to identify multiple species of RNA viruses in clinical samples.
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28
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Zhao L, Niu Y, Lu T, Yin H, Zhang Y, Xu L, Wang Y, Chen H. Metagenomic Analysis of the Jinding Duck Fecal Virome. Curr Microbiol 2018; 75:658-665. [PMID: 29368024 PMCID: PMC7080049 DOI: 10.1007/s00284-018-1430-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Accepted: 01/03/2018] [Indexed: 01/01/2023]
Abstract
Ducks play an important role in transmitting and maintaining mammalian viruses in nature, and are a reservoir host of many animal viruses. We analyzed the fecal virome of four strains (A, B, C, and D) of ducks living in isolation by using metagenomic analysis. The feces of the ducks tested contained 18 animal virus families. The percentage values of RNA virus reads, compared to the total animal virus reads in each of the four strains were 96.96% (A), 97.30% (B), 98.01 (C), and 67.49% (D), and were mainly from Orthomyxoviridae, Mimiviridae, Bunyaviridae, Picobirnaviridae, and Reoviridae. Meanwhile, the minority of DNA virus reads were related to Herpesviridae, Adenoviridae, Iridoviridae, and other, low abundance viral families. The percentage values of Orthomyxoviridae, Mimiviridae, Bunyaviridae, Picobirnaviridae, and Herpesviridae reads were not significantly different among strains A, B, and C; however, there were marked differences in the abundance of these reads in strain D. In summary, this study provides an unbiased examination of the viral diversity in the feces of four strains of ducks in specific-pathogen-free periods, and highlights the variation in the percentage of viral families present. These results can be used as a reference for detecting duck viral pathogens and predicting zoonotic potential.
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Affiliation(s)
- Lili Zhao
- State Key Laboratory of Veterinary Biotechnology, Heilongjiang Provincial Key Laboratory of Laboratory Animal and Comparative Medicine, Harbin Veterinary Research Institute, The Chinese Academy of Agriculture Sciences, 678 Haping Road, Harbin, 150069, People's Republic of China
| | - Yinjie Niu
- State Key Laboratory of Veterinary Biotechnology, Heilongjiang Provincial Key Laboratory of Laboratory Animal and Comparative Medicine, Harbin Veterinary Research Institute, The Chinese Academy of Agriculture Sciences, 678 Haping Road, Harbin, 150069, People's Republic of China
| | - Taofeng Lu
- State Key Laboratory of Veterinary Biotechnology, Heilongjiang Provincial Key Laboratory of Laboratory Animal and Comparative Medicine, Harbin Veterinary Research Institute, The Chinese Academy of Agriculture Sciences, 678 Haping Road, Harbin, 150069, People's Republic of China
| | - Haichang Yin
- State Key Laboratory of Veterinary Biotechnology, Heilongjiang Provincial Key Laboratory of Laboratory Animal and Comparative Medicine, Harbin Veterinary Research Institute, The Chinese Academy of Agriculture Sciences, 678 Haping Road, Harbin, 150069, People's Republic of China
| | - Yuanyuan Zhang
- State Key Laboratory of Veterinary Biotechnology, Heilongjiang Provincial Key Laboratory of Laboratory Animal and Comparative Medicine, Harbin Veterinary Research Institute, The Chinese Academy of Agriculture Sciences, 678 Haping Road, Harbin, 150069, People's Republic of China
| | - Lijing Xu
- State Key Laboratory of Veterinary Biotechnology, Heilongjiang Provincial Key Laboratory of Laboratory Animal and Comparative Medicine, Harbin Veterinary Research Institute, The Chinese Academy of Agriculture Sciences, 678 Haping Road, Harbin, 150069, People's Republic of China
| | - Yiping Wang
- State Key Laboratory of Veterinary Biotechnology, Heilongjiang Provincial Key Laboratory of Laboratory Animal and Comparative Medicine, Harbin Veterinary Research Institute, The Chinese Academy of Agriculture Sciences, 678 Haping Road, Harbin, 150069, People's Republic of China
| | - Hongyan Chen
- State Key Laboratory of Veterinary Biotechnology, Heilongjiang Provincial Key Laboratory of Laboratory Animal and Comparative Medicine, Harbin Veterinary Research Institute, The Chinese Academy of Agriculture Sciences, 678 Haping Road, Harbin, 150069, People's Republic of China.
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29
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Bande F, Arshad SS, Omar AR, Hair-Bejo M, Mahmuda A, Nair V. Global distributions and strain diversity of avian infectious bronchitis virus: a review. Anim Health Res Rev 2017; 18:70-83. [PMID: 28776490 DOI: 10.1017/s1466252317000044] [Citation(s) in RCA: 94] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The poultry industry faces challenge amidst global food security crisis. Infectious bronchitis is one of the most important viral infections that cause huge economic loss to the poultry industry worldwide. The causative agent, infectious bronchitis virus (IBV) is an RNA virus with great ability for mutation and recombination; thus, capable of generating new virus strains that are difficult to control. There are many IBV strains found worldwide, including the Massachusetts, 4/91, D274, and QX-like strains that can be grouped under the classic or variant serotypes. Currently, information on the epidemiology, strain diversity, and global distribution of IBV has not been comprehensively reported. This review is an update of current knowledge on the distribution, genetic relationship, and diversity of the IBV strains found worldwide.
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Affiliation(s)
- Faruku Bande
- Department of Veterinary Pathology and Microbiology,Faculty of Veterinary Medicine,Universiti Putra Malaysia,43400 UPM Serdang,Selangor Darul Ehsan,Malaysia
| | - Siti Suri Arshad
- Department of Veterinary Pathology and Microbiology,Faculty of Veterinary Medicine,Universiti Putra Malaysia,43400 UPM Serdang,Selangor Darul Ehsan,Malaysia
| | - Abdul Rahman Omar
- Department of Veterinary Pathology and Microbiology,Faculty of Veterinary Medicine,Universiti Putra Malaysia,43400 UPM Serdang,Selangor Darul Ehsan,Malaysia
| | - Mohd Hair-Bejo
- Department of Veterinary Pathology and Microbiology,Faculty of Veterinary Medicine,Universiti Putra Malaysia,43400 UPM Serdang,Selangor Darul Ehsan,Malaysia
| | - Aliyu Mahmuda
- Department of Microbiology and Parasitology,Faculty of Medicine and Health Sciences,Universiti Putra Malaysia,43400 UPM Serdang,Selangor Darul Ehsan,Malaysia
| | - Venugopal Nair
- Avian Oncogenic Virus Group,The Pirbright Institute,Working,Guildford,Surrey,GU24 0NF,UK
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30
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Jordan I, John K, Höwing K, Lohr V, Penzes Z, Gubucz-Sombor E, Fu Y, Gao P, Harder T, Zádori Z, Sandig V. Continuous cell lines from the Muscovy duck as potential replacement for primary cells in the production of avian vaccines. Avian Pathol 2017; 45:137-55. [PMID: 26814192 DOI: 10.1080/03079457.2016.1138280] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Veterinary vaccines contribute to food security, interrupt zoonotic transmissions, and help to maintain overall health in livestock. Although vaccines are usually cost-effective, their adoption depends on a multitude of factors. Because poultry vaccines are usually given to birds with a short life span, very low production cost per dose is one important challenge. Other hurdles are to ensure a consistent and reliable supply of very large number of doses, and to have flexible production processes to accommodate a range of different pathogens and dosage requirements. Most poultry vaccines are currently being produced on primary avian cells derived from chicken or waterfowl embryos. This production system is associated with high costs, logistic complexities, rigid intervals between harvest and production, and supply limitations. We investigated whether the continuous cell lines Cairina retina and CR.pIX may provide a substrate independent of primary cell cultures or embryonated eggs. Viruses examined for replication in these cell lines are strains associated with, or contained in vaccines against egg drop syndrome, Marek's disease, Newcastle disease, avian influenza, infectious bursal disease and Derzsy's disease. Each of the tested viruses required the development of unique conditions for replication that are described here and can be used to generate material for in vivo efficacy studies and to accelerate transfer of the processes to larger production volumes.
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Affiliation(s)
| | | | | | | | - Zoltán Penzes
- b Ceva-Phylaxia Veterinary Biologicals Co. Ltd. , Budapest , Hungary
| | | | - Yan Fu
- c Ningbo Tech-Bank Co Ltd , Shanghai , People's Republic of China
| | - Peng Gao
- c Ningbo Tech-Bank Co Ltd , Shanghai , People's Republic of China
| | - Timm Harder
- d Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health , Greifswald-Insel Riems , Germany
| | - Zoltán Zádori
- e Veterinary Medical Research, Centre for Agricultural Research, Hungarian Academy of Sciences , Budapest , Hungary
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31
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Fawaz M, Vijayakumar P, Mishra A, Gandhale PN, Dutta R, Kamble NM, Sudhakar SB, Roychoudhary P, Kumar H, Kulkarni DD, Raut AA. Duck gut viral metagenome analysis captures snapshot of viral diversity. Gut Pathog 2016; 8:30. [PMID: 27284287 PMCID: PMC4899906 DOI: 10.1186/s13099-016-0113-5] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/05/2016] [Accepted: 05/30/2016] [Indexed: 11/18/2022] Open
Abstract
Background Ducks (Anas platyrhynchos) an economically important waterfowl for meat, eggs and feathers; is also a natural reservoir for influenza A viruses. The emergence of novel viruses is attributed to the status of co-existence of multiple types and subtypes of viruses in the reservoir hosts. For effective prediction of future viral epidemic or pandemic an in-depth understanding of the virome status in the key reservoir species is highly essential. Methods To obtain an unbiased measure of viral diversity in the enteric tract of ducks by viral metagenomic approach, we deep sequenced the viral nucleic acid extracted from cloacal swabs collected from the flock of 23 ducks which shared the water bodies with wild migratory birds. Result In total 7,455,180 reads with average length of 146 bases were generated of which 7,354,300 reads were de novo assembled into 24,945 contigs with an average length of 220 bases and the remaining 100,880 reads were singletons. The duck virome were identified by sequence similarity comparisons of contigs and singletons (BLASTx E score, <10−3) against viral reference database. Numerous duck virome sequences were homologous to the animal virus of the Papillomaviridae family; and phages of the Caudovirales, Inoviridae, Tectiviridae, Microviridae families and unclassified phages. Further, several duck virome sequences had homologous with the insect viruses of the Poxviridae, Alphatetraviridae, Baculoviridae, Densovirinae, Iflaviridae and Dicistroviridae families; and plant viruses of the Secoviridae, Virgaviridae, Tombusviridae and Partitiviridae families, which reflects the diet and habitation of ducks. Conclusion This study increases our understanding of the viral diversity and expands the knowledge about the spectrum of viruses harboured in the enteric tract of ducks.
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Affiliation(s)
- Mohammed Fawaz
- OIE Reference Laboratory for Avian Influenza, ICAR-National Institute of High Security Animal Diseases, Bhopal, Madhya Pradesh India
| | - Periyasamy Vijayakumar
- OIE Reference Laboratory for Avian Influenza, ICAR-National Institute of High Security Animal Diseases, Bhopal, Madhya Pradesh India
| | - Anamika Mishra
- OIE Reference Laboratory for Avian Influenza, ICAR-National Institute of High Security Animal Diseases, Bhopal, Madhya Pradesh India
| | - Pradeep N Gandhale
- OIE Reference Laboratory for Avian Influenza, ICAR-National Institute of High Security Animal Diseases, Bhopal, Madhya Pradesh India
| | - Rupam Dutta
- OIE Reference Laboratory for Avian Influenza, ICAR-National Institute of High Security Animal Diseases, Bhopal, Madhya Pradesh India
| | - Nitin M Kamble
- OIE Reference Laboratory for Avian Influenza, ICAR-National Institute of High Security Animal Diseases, Bhopal, Madhya Pradesh India
| | - Shashi B Sudhakar
- OIE Reference Laboratory for Avian Influenza, ICAR-National Institute of High Security Animal Diseases, Bhopal, Madhya Pradesh India
| | - Parimal Roychoudhary
- College of Veterinary Sciences and Animal Husbandry, Central Agricultural University, Aizawl, Mizoram India
| | - Himanshu Kumar
- Laboratory of Immunology, Department of Biological Sciences, Indian Institute of Science Education and Research, Bhopal, Madhya Pradesh India
| | - Diwakar D Kulkarni
- OIE Reference Laboratory for Avian Influenza, ICAR-National Institute of High Security Animal Diseases, Bhopal, Madhya Pradesh India
| | - Ashwin Ashok Raut
- OIE Reference Laboratory for Avian Influenza, ICAR-National Institute of High Security Animal Diseases, Bhopal, Madhya Pradesh India
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32
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Yao S, Ou C, Liu X, Wang X, Yao Z, Liu J. Isolation of a novel serotype strain of infectious bronchitis virus ZZ2004 from ducks in China. Virus Genes 2016; 52:660-70. [PMID: 27164844 PMCID: PMC7089278 DOI: 10.1007/s11262-016-1352-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Accepted: 05/03/2016] [Indexed: 01/03/2023]
Abstract
In chickens, the infectious bronchitis virus (IBV) often causes respiratory distress, a decrease in egg production, poor egg quality, and occasional nephritis. However, ZZ2004, a Chinese isolate of IBV, was obtained from ducks with clinical growth suppression and mild respiratory symptoms that had been reared with chickens in the central region of China. Virus isolation, virus neutralization testing, and RT-PCR were employed to identify the causative pathogen, while sequence alignment was used to analyze gene variations of the S1 subunit and M genes. The results showed that the ducks were infected with IBV due to the emergence of a dwarfing phenotype and the death of embryos between 48 and 144 h post-inoculation. RT-PCR also confirmed the presence of the expected fragment sizes of the S1 subunit and M genes by RT-PCR. Meanwhile, the results of the virus neutralization test indicated that the strains of JX/99/01, GD, SAIBK, LDT3 showed cross-reactivity with the ZZ2004 isolate, and hardly any cross-neutralization of IBV ZZ2004 was observed with the strains of M41, H120, Gray, Holte, or Aust-T. Phylogenetic analysis suggested that there were large differences between ZZ2004 and other IBV reference strains on the S1 subunit. Meanwhile, homologies in the nucleotide and amino acid sequences of the M gene of IBV ZZ2004 were 86.9–92.0 % and 91.1–93.9 %, respectively, compared with 35 other IBV reference strains derived from different regions. This result revealed that there were conspicuous variations among the selected strains. Furthermore, the results showed that the prevalent strains of IBV in ducks had no antigen homology with the vaccine strains widely used in China except the LDT3-strain, making it urgent to explore and develop new IBV vaccines.
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Affiliation(s)
- Sixin Yao
- College of Animal Science, Henan Institute of Science and Technology, Hualan Street, Xinxiang, 453003, Henan, PR China
| | - Changbo Ou
- College of Animal Science, Henan Institute of Science and Technology, Hualan Street, Xinxiang, 453003, Henan, PR China
| | - Xingyou Liu
- College of Animal Science, Henan Institute of Science and Technology, Hualan Street, Xinxiang, 453003, Henan, PR China. .,School of Life Science and Technology, Xinxiang University, Xinxiang, 453003, PR China.
| | - Xianwen Wang
- College of Animal Science, Henan Institute of Science and Technology, Hualan Street, Xinxiang, 453003, Henan, PR China
| | - Zonghui Yao
- College of Animal Science, Henan Institute of Science and Technology, Hualan Street, Xinxiang, 453003, Henan, PR China
| | - Jinjing Liu
- Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, PR China
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Zhuang QY, Wang KC, Liu S, Hou GY, Jiang WM, Wang SC, Li JP, Yu JM, Chen JM. Genomic Analysis and Surveillance of the Coronavirus Dominant in Ducks in China. PLoS One 2015; 10:e0129256. [PMID: 26053682 PMCID: PMC4459809 DOI: 10.1371/journal.pone.0129256] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2014] [Accepted: 05/06/2015] [Indexed: 01/09/2023] Open
Abstract
The genetic diversity, evolution, distribution, and taxonomy of some coronaviruses dominant in birds other than chickens remain enigmatic. In this study we sequenced the genome of a newly identified coronavirus dominant in ducks (DdCoV), and performed a large-scale surveillance of coronaviruses in chickens and ducks using a conserved RT-PCR assay. The viral genome harbors a tandem repeat which is rare in vertebrate RNA viruses. The repeat is homologous to some proteins of various cellular organisms, but its origin remains unknown. Many substitutions, insertions, deletions, and some frameshifts and recombination events have occurred in the genome of the DdCoV, as compared with the coronavirus dominant in chickens (CdCoV). The distances between DdCoV and CdCoV are large enough to separate them into different species within the genus Gammacoronavirus. Our surveillance demonstrated that DdCoVs and CdCoVs belong to different lineages and occupy different ecological niches, further supporting that they should be classified into different species. Our surveillance also demonstrated that DdCoVs and CdCoVs are prevalent in live poultry markets in some regions of China. In conclusion, this study shed novel insight into the genetic diversity, evolution, distribution, and taxonomy of the coronaviruses circulating in chickens and ducks.
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Affiliation(s)
- Qing-Ye Zhuang
- China Animal Health and Epidemiology Center, Qingdao, 266032, China
| | - Kai-Cheng Wang
- China Animal Health and Epidemiology Center, Qingdao, 266032, China
| | - Shuo Liu
- China Animal Health and Epidemiology Center, Qingdao, 266032, China
| | - Guang-Yu Hou
- China Animal Health and Epidemiology Center, Qingdao, 266032, China
| | - Wen-Ming Jiang
- China Animal Health and Epidemiology Center, Qingdao, 266032, China
| | - Su-Chun Wang
- China Animal Health and Epidemiology Center, Qingdao, 266032, China
| | - Jin-Ping Li
- China Animal Health and Epidemiology Center, Qingdao, 266032, China
| | - Jian-Min Yu
- China Animal Health and Epidemiology Center, Qingdao, 266032, China
| | - Ji-Ming Chen
- China Animal Health and Epidemiology Center, Qingdao, 266032, China
- * E-mail:
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Host tissue and glycan binding specificities of avian viral attachment proteins using novel avian tissue microarrays. PLoS One 2015; 10:e0128893. [PMID: 26035584 PMCID: PMC4452732 DOI: 10.1371/journal.pone.0128893] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2015] [Accepted: 05/03/2015] [Indexed: 01/06/2023] Open
Abstract
The initial interaction between viral attachment proteins and the host cell is a critical determinant for the susceptibility of a host for a particular virus. To increase our understanding of avian pathogens and the susceptibility of poultry species, we developed novel avian tissue microarrays (TMAs). Tissue binding profiles of avian viral attachment proteins were studied by performing histochemistry on multi-species TMA, comprising of selected tissues from ten avian species, and single-species TMAs, grouping organ systems of each species together. The attachment pattern of the hemagglutinin protein was in line with the reported tropism of influenza virus H5N1, confirming the validity of TMAs in profiling the initial virus-host interaction. The previously believed chicken-specific coronavirus (CoV) M41 spike (S1) protein displayed a broad attachment pattern to respiratory tissues of various avian species, albeit with lower affinity than hemagglutinin, suggesting that other avian species might be susceptible for chicken CoV. When comparing tissue-specific binding patterns of various avian coronaviral S1 proteins on the single-species TMAs, chicken and partridge CoV S1 had predominant affinity for the trachea, while pigeon CoV S1 showed marked preference for lung of their respective hosts. Binding of all coronaviral S1 proteins was dependent on sialic acids; however, while chicken CoV S1 preferred sialic acids type I lactosamine (Gal(1-3)GlcNAc) over type II (Gal(1-4)GlcNAc), the fine glycan specificities of pigeon and partridge CoVs were different, as chicken CoV S1-specific sialylglycopolymers could not block their binding to tissues. Taken together, TMAs provide a novel platform in the field of infectious diseases to allow identification of binding specificities of viral attachment proteins and are helpful to gain insight into the susceptibility of host and organ for avian pathogens.
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Rossi LMG, Escobar-Gutierrez A, Rahal P. Advanced molecular surveillance of hepatitis C virus. Viruses 2015; 7:1153-88. [PMID: 25781918 PMCID: PMC4379565 DOI: 10.3390/v7031153] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2014] [Revised: 02/05/2015] [Accepted: 02/20/2015] [Indexed: 12/12/2022] Open
Abstract
Hepatitis C virus (HCV) infection is an important public health problem worldwide. HCV exploits complex molecular mechanisms, which result in a high degree of intrahost genetic heterogeneity. This high degree of variability represents a challenge for the accurate establishment of genetic relatedness between cases and complicates the identification of sources of infection. Tracking HCV infections is crucial for the elucidation of routes of transmission in a variety of settings. Therefore, implementation of HCV advanced molecular surveillance (AMS) is essential for disease control. Accounting for virulence is also important for HCV AMS and both viral and host factors contribute to the disease outcome. Therefore, HCV AMS requires the incorporation of host factors as an integral component of the algorithms used to monitor disease occurrence. Importantly, implementation of comprehensive global databases and data mining are also needed for the proper study of the mechanisms responsible for HCV transmission. Here, we review molecular aspects associated with HCV transmission, as well as the most recent technological advances used for virus and host characterization. Additionally, the cornerstone discoveries that have defined the pathway for viral characterization are presented and the importance of implementing advanced HCV molecular surveillance is highlighted.
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Affiliation(s)
- Livia Maria Gonçalves Rossi
- Department of Biology, Institute of Bioscience, Language and Exact Science, Sao Paulo State University, Sao Jose do Rio Preto, SP 15054-000, Brazil.
| | | | - Paula Rahal
- Department of Biology, Institute of Bioscience, Language and Exact Science, Sao Paulo State University, Sao Jose do Rio Preto, SP 15054-000, Brazil.
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Chan JFW, To KKW, Chen H, Yuen KY. Cross-species transmission and emergence of novel viruses from birds. Curr Opin Virol 2015; 10:63-9. [PMID: 25644327 PMCID: PMC7102742 DOI: 10.1016/j.coviro.2015.01.006] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2014] [Revised: 12/29/2014] [Accepted: 01/09/2015] [Indexed: 12/29/2022]
Abstract
The role of birds in cross-species transmission and emergence of novel viruses such as avian influenza A viruses are discussed. The novel avian viruses identified between 2012 and 2014 are summarized. The concept of ‘pathogen augmentation’ is introduced.
Birds, the only living member of the Dinosauria clade, are flying warm-blooded vertebrates displaying high species biodiversity, roosting and migratory behavior, and a unique adaptive immune system. Birds provide the natural reservoir for numerous viral species and therefore gene source for evolution, emergence and dissemination of novel viruses. The intrusions of human into natural habitats of wild birds, the domestication of wild birds as pets or racing birds, and the increasing poultry consumption by human have facilitated avian viruses to cross species barriers to cause zoonosis. Recently, a novel adenovirus was exclusively found in birds causing an outbreak of Chlamydophila psittaci infection among birds and humans. Instead of being the primary cause of an outbreak by jumping directly from bird to human, a novel avian virus can be an augmenter of another zoonotic agent causing the outbreak. A comprehensive avian virome will improve our understanding of birds’ evolutionary dynamics.
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Affiliation(s)
- Jasper Fuk-Woo Chan
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, and Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong Special Administrative Region
| | - Kelvin Kai-Wang To
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, and Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong Special Administrative Region
| | - Honglin Chen
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, and Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong Special Administrative Region
| | - Kwok-Yung Yuen
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, and Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong Special Administrative Region.
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Domanska-Blicharz K, Jacukowicz A, Lisowska A, Wyrostek K, Minta Z. Detection and molecular characterization of infectious bronchitis-like viruses in wild bird populations. Avian Pathol 2014; 43:406-13. [PMID: 25133705 DOI: 10.1080/03079457.2014.949619] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
We examined 884 wild birds mainly from the Anseriformes, Charadriiformes and Galliformes orders for infectious bronchitis (IBV)-like coronavirus in Poland between 2008 and 2011. Coronavirus was detected in 31 (3.5%) of the tested birds, with detection rates of 3.5% in Anseriformes and 2.3% in Charadriiformes and as high as 17.6% in Galliformes. From the 31 positive samples, only 10 gave positive results in molecular tests aimed at various IBV genome fragments: five samples were positive for the RdRp gene, four for gene 3, eight for gene N and eight for the 3'-untranslated region fragment. All analysed genome fragments of the coronavirus strains shared different evolutionary branches, resulting in a different phylogenetic tree topology. Most detected fragment genes seem to be IBV-like genes of the most frequently detected lineages of IBV in this geographical region (i.e. Massachusetts, 793B and QX). Two waves of coronavirus infections were identified: one in spring (April and May) and another in late autumn (October to December). To our knowledge this is the first report of the detection of different fragment IBV-like genes in wild bird populations.
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Zhuang QY, Wang SC, Li JP, Liu D, Liu S, Jiang WM, Chen JM. A clinical survey of common avian infectious diseases in China. Avian Dis 2014; 58:297-302. [PMID: 25055636 DOI: 10.1637/10709-110113-resnote.1] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Multiple common avian infectious diseases (CAIDs), namely, avian infectious diseases excluding highly pathogenic avian influenza and Newcastle disease, such as avian salmonellosis and coccidiosis, cause huge economic loss in poultry production and are of great significance in public health. However, they are usually not covered in the systems for reporting of animal diseases. Consequently, the distribution of CAIDs is not clear in many countries. Here, we report a clinical survey of CAIDs in China based on clinical diagnosis of eight veterinary clinics in 2011 and 2012. This survey provided the distribution data of viral, bacterial, and parasitic CAIDs in different types of avian flocks, seasons, and regions, data that are of great value in the research, prevention, and control of poultry diseases. This survey suggested that avian colibacillosis, infectious serositis in ducks caused by Riemerella anatipestifer, avian salmonellosis, fowl cholera, avian mycoplasmosis, avian aspergillosis, coccidiosis, low pathogenic avian influenza, infectious bronchitis, infectious bursal disease, and infectious laryngotracheitis are likely to be prevalent in the poultry in China.
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Cunha MV, Inácio J, Freimanis G, Fusaro A, Granberg F, Höper D, King DP, Monne I, Orton R, Rosseel T. Next-generation sequencing in veterinary medicine: how can the massive amount of information arising from high-throughput technologies improve diagnosis, control, and management of infectious diseases? Methods Mol Biol 2014; 1247:415-36. [PMID: 25399113 PMCID: PMC7123048 DOI: 10.1007/978-1-4939-2004-4_30] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The development of high-throughput molecular technologies and associated bioinformatics has dramatically changed the capacities of scientists to produce, handle, and analyze large amounts of genomic, transcriptomic, and proteomic data. A clear example of this step-change is represented by the amount of DNA sequence data that can be now produced using next-generation sequencing (NGS) platforms. Similarly, recent improvements in protein and peptide separation efficiencies and highly accurate mass spectrometry have promoted the identification and quantification of proteins in a given sample. These advancements in biotechnology have increasingly been applied to the study of animal infectious diseases and are beginning to revolutionize the way that biological and evolutionary processes can be studied at the molecular level. Studies have demonstrated the value of NGS technologies for molecular characterization, ranging from metagenomic characterization of unknown pathogens or microbial communities to molecular epidemiology and evolution of viral quasispecies. Moreover, high-throughput technologies now allow detailed studies of host-pathogen interactions at the level of their genomes (genomics), transcriptomes (transcriptomics), or proteomes (proteomics). Ultimately, the interaction between pathogen and host biological networks can be questioned by analytically integrating these levels (integrative OMICS and systems biology). The application of high-throughput biotechnology platforms in these fields and their typical low-cost per information content has revolutionized the resolution with which these processes can now be studied. The aim of this chapter is to provide a current and prospective view on the opportunities and challenges associated with the application of massive parallel sequencing technologies to veterinary medicine, with particular focus on applications that have a potential impact on disease control and management.
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Affiliation(s)
- Mónica V. Cunha
- Instituto Nacional de Investigação Agrária e Veterinária, IP and Centro de Biologia Ambiental, Faculdade de Ciências, Universidade de Lisboa, Lisbon, Portugal
| | - João Inácio
- Instituto Nacional de Investigação Agrária e Veterinária, IP, Lisboa, Portugal and School of Pharmacy and Biomolecular Sciences, University of Brighton, Brighton, United Kingdom
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Abstract
We examined the role of wild birds in the epidemiology of avian coronaviruses by studying oropharyngeal swabs from 32 wild bird species. The 14 avian coronaviruses detected belonged to the gamma-coronaviruses and shared high nucleotide sequence identity with some previously identified strains in wild waterfowl, but not with infectious bronchitis viruses.
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