1
|
Spinard E, Dinhobl M, Erdelyan CNG, O’Dwyer J, Fenster J, Birtley H, Tesler N, Calvelage S, Leijon M, Steinaa L, O’Donnell V, Blome S, Bastos A, Ramirez-Medina E, Lacasta A, Ståhl K, Qiu H, Nilubol D, Tennakoon C, Maesembe C, Faburay B, Ambagala A, Williams D, Ribeca P, Borca MV, Gladue DP. A Standardized Pipeline for Assembly and Annotation of African Swine Fever Virus Genome. Viruses 2024; 16:1293. [PMID: 39205267 PMCID: PMC11359534 DOI: 10.3390/v16081293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2024] [Revised: 08/02/2024] [Accepted: 08/06/2024] [Indexed: 09/04/2024] Open
Abstract
Obtaining a complete good-quality sequence and annotation for the long double-stranded DNA genome of the African swine fever virus (ASFV) from next-generation sequencing (NGS) technology has proven difficult, despite the increasing availability of reference genome sequences and the increasing affordability of NGS. A gap analysis conducted by the global African swine fever research alliance (GARA) partners identified that a standardized, automatic pipeline for NGS analysis was urgently needed, particularly for new outbreak strains. Whilst there are several diagnostic and research labs worldwide that collect isolates of the ASFV from outbreaks, many do not have the capability to analyze, annotate, and format NGS data from outbreaks for submission to NCBI, and some publicly available ASFV genomes have missing or incorrect annotations. We developed an automated, standardized pipeline for the analysis of NGS reads that directly provides users with assemblies and annotations formatted for their submission to NCBI. This pipeline is freely available on GitHub and has been tested through the GARA partners by examining two previously sequenced ASFV genomes; this study also aimed to assess the accuracy and limitations of two strategies present within the pipeline: reference-based (Illumina reads) and de novo assembly (Illumina and Nanopore reads) strategies.
Collapse
Affiliation(s)
- Edward Spinard
- U.S. Department of Agriculture, Agricultural Research Service, Foreign Animal Disease Research Unit, Plum Island Animal Disease Center (PIADC), P.O. Box 848, Greenport, NY 11944, USA; (E.S.); (M.D.)
- U.S. Department of Agriculture, Agricultural Research Service, Foreign Animal Disease Research Unit, National Bio and Agro-Defense Facility, Manhattan, KS 66502, USA
| | - Mark Dinhobl
- U.S. Department of Agriculture, Agricultural Research Service, Foreign Animal Disease Research Unit, Plum Island Animal Disease Center (PIADC), P.O. Box 848, Greenport, NY 11944, USA; (E.S.); (M.D.)
- U.S. Department of Agriculture, Agricultural Research Service, Foreign Animal Disease Research Unit, National Bio and Agro-Defense Facility, Manhattan, KS 66502, USA
| | | | - James O’Dwyer
- National Centre for Foreign Animal Disease, Canadian Food Inspection Agency, Winnipeg, MB R3E 3M4, Canada
| | - Jacob Fenster
- Oak Ridge Institute for Science and Education (ORISE), Oak Ridge, TN 37830, USA
| | - Hillary Birtley
- Oak Ridge Institute for Science and Education (ORISE), Oak Ridge, TN 37830, USA
| | - Nicolas Tesler
- Oak Ridge Institute for Science and Education (ORISE), Oak Ridge, TN 37830, USA
| | - Sten Calvelage
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Südufer 10, 17493 Greifswald-Insel Riems, Germany
| | - Mikael Leijon
- Department of Microbiology, Swedish Veterinary Agency, SE-751 89 Uppsala, Sweden
| | - Lucilla Steinaa
- Animal and Human Heath Program, International Livestock Research Institute, Nairobi 00100, Kenya
| | - Vivian O’Donnell
- U.S. Department of Agriculture, Animal and Plant Inspection Service, Plum Island Animal Disease Center, Greenport, NY 11944, USA
| | - Sandra Blome
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Südufer 10, 17493 Greifswald-Insel Riems, Germany
| | - Armanda Bastos
- Department of Veterinary Tropical Diseases, Faculty of Veterinary Science, University of Pretoria, Onderstepoort 0110, South Africa
| | - Elizabeth Ramirez-Medina
- U.S. Department of Agriculture, Agricultural Research Service, Foreign Animal Disease Research Unit, Plum Island Animal Disease Center (PIADC), P.O. Box 848, Greenport, NY 11944, USA; (E.S.); (M.D.)
- U.S. Department of Agriculture, Agricultural Research Service, Foreign Animal Disease Research Unit, National Bio and Agro-Defense Facility, Manhattan, KS 66502, USA
| | - Anna Lacasta
- Animal and Human Heath Program, International Livestock Research Institute, Nairobi 00100, Kenya
| | - Karl Ståhl
- Department of Epidemiology, Surveillance and Risk assessment, Swedish Veterinary Agency, SE-751 89 Uppsala, Sweden
| | - Huaji Qiu
- State Key Laboratory for Animal Disease Control and Prevention, National African Swine Fever Para-Reference Laboratory, National High Containment Facilities for Animal Diseases Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 100081, China
| | - Dachrit Nilubol
- Swine Viral Evolution and Vaccine Development Research Unit, Department of Veterinary Microbiology, Faculty of Veterinary Science, Chulalongkorn University, Henry Dunant Road, Pathumwan, Bangkok 10330, Thailand
| | | | - Charles Maesembe
- Department of Zoology, Entomology and Fisheries Sciences, School of Biosciences, College of Natural Sciences, Makerere University, Kampala P.O. Box 7062, Uganda
| | - Bonto Faburay
- U.S. Department of Agriculture, Animal and Plant Inspection Service, Plum Island Animal Disease Center, Greenport, NY 11944, USA
| | - Aruna Ambagala
- National Centre for Foreign Animal Disease, Canadian Food Inspection Agency, Winnipeg, MB R3E 3M4, Canada
| | - David Williams
- CSIRO, Australian Centre for Disease Preparedness, Geelong, VIC 3220, Australia
| | - Paolo Ribeca
- UK Health Security Agency, London E14 4PU, UK
- Biomathematics and Statistics Scotland, Edinburgh EH9 3FD, UK
| | - Manuel V. Borca
- U.S. Department of Agriculture, Agricultural Research Service, Foreign Animal Disease Research Unit, Plum Island Animal Disease Center (PIADC), P.O. Box 848, Greenport, NY 11944, USA; (E.S.); (M.D.)
- U.S. Department of Agriculture, Agricultural Research Service, Foreign Animal Disease Research Unit, National Bio and Agro-Defense Facility, Manhattan, KS 66502, USA
| | - Douglas P. Gladue
- U.S. Department of Agriculture, Agricultural Research Service, Foreign Animal Disease Research Unit, Plum Island Animal Disease Center (PIADC), P.O. Box 848, Greenport, NY 11944, USA; (E.S.); (M.D.)
- U.S. Department of Agriculture, Agricultural Research Service, Foreign Animal Disease Research Unit, National Bio and Agro-Defense Facility, Manhattan, KS 66502, USA
| |
Collapse
|
2
|
Chen S, Wang T, Luo R, Lu Z, Lan J, Sun Y, Fu Q, Qiu HJ. Genetic Variations of African Swine Fever Virus: Major Challenges and Prospects. Viruses 2024; 16:913. [PMID: 38932205 PMCID: PMC11209373 DOI: 10.3390/v16060913] [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: 05/06/2024] [Revised: 05/26/2024] [Accepted: 05/30/2024] [Indexed: 06/28/2024] Open
Abstract
African swine fever (ASF) is a contagious viral disease affecting pigs and wild boars. It typically presents as a hemorrhagic fever but can also manifest in various forms, ranging from acute to asymptomatic. ASF has spread extensively globally, significantly impacting the swine industry. The complex and highly variable character of the ASFV genome makes vaccine development and disease surveillance extremely difficult. The overall trend in ASFV evolution is towards decreased virulence and increased transmissibility. Factors such as gene mutation, viral recombination, and the strain-specificity of virulence-associated genes facilitate viral variations. This review deeply discusses the influence of these factors on viral immune evasion, pathogenicity, and the ensuing complexities encountered in vaccine development, disease detection, and surveillance. The ultimate goal of this review is to thoroughly explore the genetic evolution patterns and variation mechanisms of ASFV, providing a theoretical foundation for advancement in vaccine and diagnostic technologies.
Collapse
Affiliation(s)
- Shengmei Chen
- College of Life Science and Engineering, Foshan University, Foshan 528231, China
- State Key Laboratory for Animal Disease Control and Prevention, National African Swine Fever Para-Reference Laboratory, National High Containment Facilities for Animal Diseases Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150069, China
| | - Tao Wang
- State Key Laboratory for Animal Disease Control and Prevention, National African Swine Fever Para-Reference Laboratory, National High Containment Facilities for Animal Diseases Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150069, China
| | - Rui Luo
- State Key Laboratory for Animal Disease Control and Prevention, National African Swine Fever Para-Reference Laboratory, National High Containment Facilities for Animal Diseases Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150069, China
| | - Zhanhao Lu
- State Key Laboratory for Animal Disease Control and Prevention, National African Swine Fever Para-Reference Laboratory, National High Containment Facilities for Animal Diseases Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150069, China
| | - Jing Lan
- State Key Laboratory for Animal Disease Control and Prevention, National African Swine Fever Para-Reference Laboratory, National High Containment Facilities for Animal Diseases Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150069, China
- College of Animal Sciences, Yangtze University, Jingzhou 434023, China
| | - Yuan Sun
- State Key Laboratory for Animal Disease Control and Prevention, National African Swine Fever Para-Reference Laboratory, National High Containment Facilities for Animal Diseases Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150069, China
| | - Qiang Fu
- College of Life Science and Engineering, Foshan University, Foshan 528231, China
| | - Hua-Ji Qiu
- College of Life Science and Engineering, Foshan University, Foshan 528231, China
- State Key Laboratory for Animal Disease Control and Prevention, National African Swine Fever Para-Reference Laboratory, National High Containment Facilities for Animal Diseases Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150069, China
- College of Animal Sciences, Yangtze University, Jingzhou 434023, China
| |
Collapse
|
3
|
Ji CM, Feng XY, Huang YW, Chen RA. The Applications of Nanopore Sequencing Technology in Animal and Human Virus Research. Viruses 2024; 16:798. [PMID: 38793679 PMCID: PMC11125791 DOI: 10.3390/v16050798] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Revised: 05/07/2024] [Accepted: 05/13/2024] [Indexed: 05/26/2024] Open
Abstract
In recent years, an increasing number of viruses have triggered outbreaks that pose a severe threat to both human and animal life, as well as caused substantial economic losses. It is crucial to understand the genomic structure and epidemiology of these viruses to guide effective clinical prevention and treatment strategies. Nanopore sequencing, a third-generation sequencing technology, has been widely used in genomic research since 2014. This technology offers several advantages over traditional methods and next-generation sequencing (NGS), such as the ability to generate ultra-long reads, high efficiency, real-time monitoring and analysis, portability, and the ability to directly sequence RNA or DNA molecules. As a result, it exhibits excellent applicability and flexibility in virus research, including viral detection and surveillance, genome assembly, the discovery of new variants and novel viruses, and the identification of chemical modifications. In this paper, we provide a comprehensive review of the development, principles, advantages, and applications of nanopore sequencing technology in animal and human virus research, aiming to offer fresh perspectives for future studies in this field.
Collapse
Affiliation(s)
- Chun-Miao Ji
- Zhaoqing Branch Center of Guangdong Laboratory for Lingnan Modern Agricultural Science and Technology, Zhaoqing 526238, China; (C.-M.J.); (X.-Y.F.)
| | - Xiao-Yin Feng
- Zhaoqing Branch Center of Guangdong Laboratory for Lingnan Modern Agricultural Science and Technology, Zhaoqing 526238, China; (C.-M.J.); (X.-Y.F.)
| | - Yao-Wei Huang
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China;
- Department of Veterinary Medicine, Zhejiang University, Hangzhou 310058, China
| | - Rui-Ai Chen
- Zhaoqing Branch Center of Guangdong Laboratory for Lingnan Modern Agricultural Science and Technology, Zhaoqing 526238, China; (C.-M.J.); (X.-Y.F.)
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China;
| |
Collapse
|
4
|
Xin G, Kuang Q, Le S, Wu W, Gao Q, Gao H, Xu Z, Zheng Z, Lu G, Gong L, Wang H, Zhang G, Shi M, Sun Y. Origin, genomic diversity and evolution of African swine fever virus in East Asia. Virus Evol 2023; 9:vead060. [PMID: 37868933 PMCID: PMC10590196 DOI: 10.1093/ve/vead060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 08/29/2023] [Accepted: 10/05/2023] [Indexed: 10/24/2023] Open
Abstract
Since 2018, the outbreaks of genotype II African swine fever virus (ASFV) in China and several eastern Asian countries have caused a huge impact on the local swine industry, resulting in huge economic losses. However, little is known about the origin, genomic diversity, evolutionary features, and epidemiological history of the genotype II ASFV. Here, 14 high-quality complete genomes of ASFVs were generated via sequencing of samples collected from China over the course of 3 years, followed by phylogenetic and phylodynamic analyses. The strains identified were relatively homogeneous, with a total of 52 SNPs and 11 indels compared with the prototype strain HLJ/2018, among which there were four exceptionally large deletions (620-18,023 nt). Evolutionary analyses revealed that ASFV strains distributed in eastern Asia formed a monophyly and a 'star-like' structure centered around the prototype strain, suggesting a single origin. Additionally, phylogenetic network analysis and ancestral reconstruction of geographic state indicated that genotype II ASFV strains in eastern Asia likely originated from Western Europe. Overall, these results contribute to the understanding of the history and current status of genotype II ASFV strains in eastern Asian, which could be of considerable importance in disease control and prevention.
Collapse
Affiliation(s)
- Genyang Xin
- State Key Laboratory for Biocontrol, School of Medicine, Shenzhen campus of Sun Yat-sen University, Shenzhen 518107, China
| | - Qiyuan Kuang
- Guangdong Provincial Key Laboratory of Zoonosis Prevention and Control, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, PR China
- African Swine Fever Regional Laboratory of China (Guangzhou), South China Agricultural University, Guangzhou 510642, PR China
- Research Center for African Swine Fever Prevention and Control, South China Agricultural University, Guangzhou 510642, PR China
- Maoming Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong 510642, PR China
| | - Shijia Le
- State Key Laboratory for Biocontrol, School of Medicine, Shenzhen campus of Sun Yat-sen University, Shenzhen 518107, China
| | - Weichen Wu
- State Key Laboratory for Biocontrol, School of Medicine, Shenzhen campus of Sun Yat-sen University, Shenzhen 518107, China
| | - Qi Gao
- Guangdong Provincial Key Laboratory of Zoonosis Prevention and Control, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, PR China
- African Swine Fever Regional Laboratory of China (Guangzhou), South China Agricultural University, Guangzhou 510642, PR China
- Research Center for African Swine Fever Prevention and Control, South China Agricultural University, Guangzhou 510642, PR China
- Maoming Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong 510642, PR China
| | - Han Gao
- Guangdong Provincial Key Laboratory of Zoonosis Prevention and Control, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, PR China
- African Swine Fever Regional Laboratory of China (Guangzhou), South China Agricultural University, Guangzhou 510642, PR China
- Research Center for African Swine Fever Prevention and Control, South China Agricultural University, Guangzhou 510642, PR China
- Maoming Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong 510642, PR China
| | - Zhiying Xu
- Guangdong Provincial Key Laboratory of Zoonosis Prevention and Control, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, PR China
- African Swine Fever Regional Laboratory of China (Guangzhou), South China Agricultural University, Guangzhou 510642, PR China
- Research Center for African Swine Fever Prevention and Control, South China Agricultural University, Guangzhou 510642, PR China
- Maoming Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong 510642, PR China
| | - Zezhong Zheng
- Guangdong Provincial Key Laboratory of Zoonosis Prevention and Control, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, PR China
- African Swine Fever Regional Laboratory of China (Guangzhou), South China Agricultural University, Guangzhou 510642, PR China
- Research Center for African Swine Fever Prevention and Control, South China Agricultural University, Guangzhou 510642, PR China
- Maoming Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong 510642, PR China
| | - Gang Lu
- Guangdong Provincial Key Laboratory of Zoonosis Prevention and Control, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, PR China
- African Swine Fever Regional Laboratory of China (Guangzhou), South China Agricultural University, Guangzhou 510642, PR China
- Research Center for African Swine Fever Prevention and Control, South China Agricultural University, Guangzhou 510642, PR China
- Maoming Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong 510642, PR China
| | - Lang Gong
- Guangdong Provincial Key Laboratory of Zoonosis Prevention and Control, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, PR China
- African Swine Fever Regional Laboratory of China (Guangzhou), South China Agricultural University, Guangzhou 510642, PR China
- Research Center for African Swine Fever Prevention and Control, South China Agricultural University, Guangzhou 510642, PR China
- Maoming Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong 510642, PR China
| | - Heng Wang
- Guangdong Provincial Key Laboratory of Zoonosis Prevention and Control, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, PR China
- African Swine Fever Regional Laboratory of China (Guangzhou), South China Agricultural University, Guangzhou 510642, PR China
- Research Center for African Swine Fever Prevention and Control, South China Agricultural University, Guangzhou 510642, PR China
- Maoming Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong 510642, PR China
| | - Guihong Zhang
- Guangdong Provincial Key Laboratory of Zoonosis Prevention and Control, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, PR China
- African Swine Fever Regional Laboratory of China (Guangzhou), South China Agricultural University, Guangzhou 510642, PR China
- Research Center for African Swine Fever Prevention and Control, South China Agricultural University, Guangzhou 510642, PR China
- Maoming Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong 510642, PR China
- State Key Laboratory for Biocontrol, School of Medicine, Shenzhen campus of Sun Yat-sen University, Shenzhen 518107, China
| | - Mang Shi
- State Key Laboratory for Biocontrol, School of Medicine, Shenzhen campus of Sun Yat-sen University, Shenzhen 518107, China
| | - Yankuo Sun
- Guangdong Provincial Key Laboratory of Zoonosis Prevention and Control, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, PR China
- African Swine Fever Regional Laboratory of China (Guangzhou), South China Agricultural University, Guangzhou 510642, PR China
- Research Center for African Swine Fever Prevention and Control, South China Agricultural University, Guangzhou 510642, PR China
- Maoming Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong 510642, PR China
| |
Collapse
|
5
|
Zheng P, Zhou C, Ding Y, Liu B, Lu L, Zhu F, Duan S. Nanopore sequencing technology and its applications. MedComm (Beijing) 2023; 4:e316. [PMID: 37441463 PMCID: PMC10333861 DOI: 10.1002/mco2.316] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 05/29/2023] [Accepted: 05/31/2023] [Indexed: 07/15/2023] Open
Abstract
Since the development of Sanger sequencing in 1977, sequencing technology has played a pivotal role in molecular biology research by enabling the interpretation of biological genetic codes. Today, nanopore sequencing is one of the leading third-generation sequencing technologies. With its long reads, portability, and low cost, nanopore sequencing is widely used in various scientific fields including epidemic prevention and control, disease diagnosis, and animal and plant breeding. Despite initial concerns about high error rates, continuous innovation in sequencing platforms and algorithm analysis technology has effectively addressed its accuracy. During the coronavirus disease (COVID-19) pandemic, nanopore sequencing played a critical role in detecting the severe acute respiratory syndrome coronavirus-2 virus genome and containing the pandemic. However, a lack of understanding of this technology may limit its popularization and application. Nanopore sequencing is poised to become the mainstream choice for preventing and controlling COVID-19 and future epidemics while creating value in other fields such as oncology and botany. This work introduces the contributions of nanopore sequencing during the COVID-19 pandemic to promote public understanding and its use in emerging outbreaks worldwide. We discuss its application in microbial detection, cancer genomes, and plant genomes and summarize strategies to improve its accuracy.
Collapse
Affiliation(s)
- Peijie Zheng
- Department of Clinical MedicineSchool of MedicineZhejiang University City CollegeHangzhouChina
| | - Chuntao Zhou
- Department of Clinical MedicineSchool of MedicineZhejiang University City CollegeHangzhouChina
| | - Yuemin Ding
- Department of Clinical MedicineSchool of MedicineZhejiang University City CollegeHangzhouChina
- Institute of Translational Medicine, School of MedicineZhejiang University City CollegeHangzhouChina
- Key Laboratory of Novel Targets and Drug Study for Neural Repair of Zhejiang Province, School of MedicineZhejiang University City CollegeHangzhouChina
| | - Bin Liu
- Department of Clinical MedicineSchool of MedicineZhejiang University City CollegeHangzhouChina
| | - Liuyi Lu
- Department of Clinical MedicineSchool of MedicineZhejiang University City CollegeHangzhouChina
| | - Feng Zhu
- Department of Clinical MedicineSchool of MedicineZhejiang University City CollegeHangzhouChina
| | - Shiwei Duan
- Department of Clinical MedicineSchool of MedicineZhejiang University City CollegeHangzhouChina
- Institute of Translational Medicine, School of MedicineZhejiang University City CollegeHangzhouChina
- Key Laboratory of Novel Targets and Drug Study for Neural Repair of Zhejiang Province, School of MedicineZhejiang University City CollegeHangzhouChina
| |
Collapse
|
6
|
Kim G, Kim SJ, Kim WJ, Kim JH, Kim JC, Lee SG, Kim ES, Lee SH, Jheong WH. Emergence and Prevalence of an African Swine Fever Virus Variant in Wild Boar Populations in South Korea from 2019 to 2022. Viruses 2023; 15:1667. [PMID: 37632010 PMCID: PMC10459476 DOI: 10.3390/v15081667] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 07/26/2023] [Accepted: 07/27/2023] [Indexed: 08/27/2023] Open
Abstract
African swine fever (ASF), a viral disease caused by the African swine fever virus (ASFV), is associated with high mortality rates in domestic pigs and wild boars. ASF has been spreading since its discovery in wild boars in Korea in October 2019. Genomic analyses have provided insights into the genetic diversity of the ASFV isolated from various regions, enabling a better understanding of the virus origin and transmission patterns. We conducted a genome analysis to evaluate the diversity and mutations of ASFV spreading among wild boars in Korea during 2019-2022. We compared the genomes of ASFV strains isolated from Korean wild boars and publicly available ASFV genomes. Genomic analysis revealed several single-nucleotide polymorphisms within multigene families (MGFs) 360-1La and 360-4L in Korean ASFV. MGF 360-1La and 360-4L variations were not observed in other ASFV strains, including those of genotype II. Finally, we partially analyzed MGFs 360-1La and 360-4L in ASFV-positive samples between 2019 and 2022, confirming the geographical distribution of the variants. Our findings can help identify new genetic markers for epidemiological ASFV analysis and provide essential information for effective disease management.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | | | - Weon-Hwa Jheong
- Wildlife Disease Response Team, National Institute of Wildlife Disease Control and Prevention (NIWDC), 1 Songam-gil, Gwangsan-gu, Gwangju 62407, Republic of Korea; (G.K.); (S.-J.K.); (W.-J.K.); (J.-H.K.); (J.-C.K.); (S.-G.L.); (E.-S.K.); (S.-H.L.)
| |
Collapse
|
7
|
Zhang Y, Wang Q, Zhu Z, Wang S, Tu S, Zhang Y, Zou Y, Liu Y, Liu C, Ren W, Zheng D, Zhao Y, Hu Y, Li L, Shi C, Ge S, Lin P, Xu F, Ma J, Wu X, Ma H, Wang Z, Bao J. Tracing the Origin of Genotype II African Swine Fever Virus in China by Genomic Epidemiology Analysis. Transbound Emerg Dis 2023. [DOI: 10.1155/2023/4820809] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/03/2023]
Abstract
The pandemic spread of African swine fever (ASF) has caused serious effects on the global pig industry. Virus genome sequencing and genomic epidemiology analysis play an important role in tracking the outbreaks of the disease and tracing the transmission of the virus. Here we obtained the full-length genome sequence of African swine fever virus (ASFV) in the first outbreak of ASF in China on August 3rd, 2018 and compared it with other published genotype II ASFV genomes including 9 genomes collected in China from September 2018 to October 2020. Phylogenetic analysis on genomic sequences revealed that genotype II ASFV has evolved into different genetic clusters with temporal and spatial correlation since being introduced into Europe and then Asia. There was a strong support for the monophyletic grouping of all the ASFV genome sequences from China and other Asian countries, which shared a common ancestor with those from the Central or Eastern Europe. An evolutionary rate of 1.312 × 10−5 nucleotide substitutions per site per year was estimated for genotype II ASFV genomes. Eight single nucleotide variations which located in MGF110-1L, MGF110-7L, MGF360-10L, MGF505-5R, MGF505-9R, K145R, NP419L, and I267L were identified as anchor mutations that defined genetic clusters of genotype II ASFV in Europe and Asia. This study expanded our knowledge of the molecular epidemiology of ASFV and provided valuable information for effective control of the disease.
Collapse
|
8
|
Kim G, Park JE, Kim SJ, Kim Y, Kim W, Kim YK, Jheong W. Complete genome analysis of the African swine fever virus isolated from a wild boar responsible for the first viral outbreak in Korea, 2019. Front Vet Sci 2023; 9:1080397. [PMID: 36713858 PMCID: PMC9875005 DOI: 10.3389/fvets.2022.1080397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 12/19/2022] [Indexed: 01/12/2023] Open
Abstract
African swine fever (ASF), a highly contagious and severe hemorrhagic viral disease in swine, is emerging as a major threat not only in Korea but also worldwide. The first confirmed case of ASF in Korea was reported in 2019. Despite the occurrence of ASF in Korea, only a few studies have genetically characterized the causative ASF virus (ASFV). In this study, we aimed to genetically characterize the ASFV responsible for the 2019 outbreak in Korea. The genome of the ASFV isolated during the first outbreak in Korea was analyzed. The Korea/YC1/2019 strain has 188,950 base pairs, with a GC content of 38.4%. The complete genome sequence was compared with other ASFV genomes annotated in the NCBI database. The Korea/YC1/2019 strain shared the highest similarity with Georgia 2007, Belgium 2018/1, and ASFV-wbBS01 strains. This study expands our knowledge of the genetic diversity of ASFV, providing valuable information for epidemiology, diagnostics, therapies, and vaccine development.
Collapse
|
9
|
Zhang C, Cheng T, Li D, Yu X, Chen F, He Q. Low-host double MDA workflow for uncultured ASFV positive blood and serum sample sequencing. Front Vet Sci 2022; 9:936781. [PMID: 36204298 PMCID: PMC9531595 DOI: 10.3389/fvets.2022.936781] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 08/03/2022] [Indexed: 11/13/2022] Open
Abstract
African swine fever (ASF) is a highly lethal and contagious disease caused by African swine fever virus (ASFV). Whole-genome sequencing of ASFV is necessary to study its mutation, recombination, and trace its transmission. Uncultured samples have a considerable amount of background DNA, which causes waste of sequencing throughput, storage space, and computing resources. Sequencing methods attempted for uncultured samples have various drawbacks. In this study, we improved C18 spacer MDA (Multiple Displacement Amplification)-combined host DNA exhaustion strategy to remove background DNA and fit NGS and TGS sequencing. Using this workflow, we successfully sequenced two uncultured ASFV positive samples. The results show that this method can significantly reduce the percentage of background DNA. We also developed software that can perform real-time base call and analyses in set intervals of ASFV TGS sequencing reads on a cloud server.
Collapse
Affiliation(s)
- Chengjun Zhang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Tangyu Cheng
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Dongfan Li
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, China
| | - Xuexiang Yu
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, China
| | - Fangzhou Chen
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, China
- *Correspondence: Fangzhou Chen
| | - Qigai He
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, China
- Qigai He
| |
Collapse
|
10
|
Bao J, Zhang Y, Shi C, Wang Q, Wang S, Wu X, Cao S, Xu F, Wang Z. Genome-Wide Diversity Analysis of African Swine Fever Virus Based on a Curated Dataset. Animals (Basel) 2022; 12:ani12182446. [PMID: 36139306 PMCID: PMC9495133 DOI: 10.3390/ani12182446] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Revised: 09/11/2022] [Accepted: 09/12/2022] [Indexed: 11/29/2022] Open
Abstract
Simple Summary African swine fever (ASF) is one of the most important animal diseases affecting the domestic swine population globally. Whole-genome sequence analysis on the circulating African swine fever virus (ASFV) strains would provide valuable information in tracking the outbreaks of the disease. The aim of this study was to prepare a curated dataset of ASFV genome sequences and investigate genome-wide diversity of circulating ASFV strains. We prepared a curated dataset containing 123 high-quality ASFV genome sequences representing 10 genotypes collected from 28 countries between 1949 and 2020. Phylogenetic analysis based on whole-genome sequences provided high-resolution topology in genotyping ASFV isolates, which was supported by pairwise genome sequence similarity comparison. Wide distribution and high variation of tandem repeat sequences were found in ASFV genomes. Structural variation and highly variable poly G or poly C tracts were also identified. This study improved our understanding on the patterns of genetic variation of ASFV and facilitated future studies on ASFV molecular epidemiology. Abstract African swine fever (ASF) is a lethal contagious viral disease of domestic pigs and wild boars caused by the African swine fever virus (ASFV). The pandemic spread of ASF has had serious effects on the global pig industry. Virus genome sequencing and comparison play an important role in tracking the outbreaks of the disease and tracing the transmission of the virus. Although more than 140 ASFV genome sequences have been deposited in the public databases, the genome-wide diversity of ASFV remains unclear. Here we prepared a curated dataset of ASFV genome sequences by filtering genomes with sequencing errors as well as duplicated genomes. A total of 123 ASFV genome sequences were included in the dataset, representing 10 genotypes collected between 1949 and 2020. Phylogenetic analysis based on whole-genome sequences provided high-resolution topology in differentiating closely related ASFV isolates, and drew new clues in the classification of some ASFV isolates. Genome-wide diversity of ASFV genomes was explored by pairwise sequence similarity comparison and ORF distribution comparison. Tandem repeat sequences were found widely distributed and highly varied in ASFV genomes. Structural variation and highly variable poly G or poly C tracts also contributed to the genome diversity. This study expanded our knowledge on the patterns of genetic diversity and evolution of ASFV, and provided valuable information for diagnosis improvement and vaccine development.
Collapse
Affiliation(s)
- Jingyue Bao
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
- China Animal Health and Epidemiology Center, Qingdao 266032, China
| | - Yong Zhang
- China Animal Health and Epidemiology Center, Qingdao 266032, China
- Lars Bolund Institute of Regenerative Medicine, Qingdao-Europe Advanced Institute for Life Sciences, BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 518083, China
| | - Chuan Shi
- China Animal Health and Epidemiology Center, Qingdao 266032, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 518083, China
- BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China
| | - Qinghua Wang
- China Animal Health and Epidemiology Center, Qingdao 266032, China
| | - Shujuan Wang
- China Animal Health and Epidemiology Center, Qingdao 266032, China
| | - Xiaodong Wu
- China Animal Health and Epidemiology Center, Qingdao 266032, China
| | - Shengbo Cao
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
| | - Fengping Xu
- Lars Bolund Institute of Regenerative Medicine, Qingdao-Europe Advanced Institute for Life Sciences, BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 518083, China
- Correspondence: (F.X.); (Z.W.)
| | - Zhiliang Wang
- China Animal Health and Epidemiology Center, Qingdao 266032, China
- Correspondence: (F.X.); (Z.W.)
| |
Collapse
|
11
|
Vandenbogaert M, Kwasiborski A, Gonofio E, Descorps-Declère S, Selekon B, Nkili Meyong AA, Ouilibona RS, Gessain A, Manuguerra JC, Caro V, Nakoune E, Berthet N. Nanopore sequencing of a monkeypox virus strain isolated from a pustular lesion in the Central African Republic. Sci Rep 2022; 12:10768. [PMID: 35750759 PMCID: PMC9232561 DOI: 10.1038/s41598-022-15073-1] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Accepted: 06/17/2022] [Indexed: 12/16/2022] Open
Abstract
Monkeypox is an emerging and neglected zoonotic disease whose number of reported cases has been gradually increasing in Central Africa since 1980. This disease is caused by the monkeypox virus (MPXV), which belongs to the genus Orthopoxvirus in the family Poxviridae. Obtaining molecular data is particularly useful for establishing the relationships between the viral strains involved in outbreaks in countries affected by this disease. In this study, we evaluated the use of the MinION real-time sequencer as well as different polishing tools on MinION-sequenced genome for sequencing the MPXV genome originating from a pustular lesion in the context of an epidemic in a remote area of the Central African Republic. The reads corresponding to the MPXV genome were identified using two taxonomic classifiers, Kraken2 and Kaiju. Assembly of these reads led to a complete sequence of 196,956 bases, which is 6322 bases longer than the sequence previously obtained with Illumina sequencing from the same sample. The comparison of the two sequences showed mainly indels at the homopolymeric regions. However, the combined use of Canu with specific polishing tools such as Medaka and Homopolish was the best combination that reduced their numbers without adding mismatches. Although MinION sequencing is known to introduce a number of characteristic errors compared to Illumina sequencing, the new polishing tools allow a better-quality MinION-sequenced genome, thus to be used to help determine strain origin through phylogenetic analysis.
Collapse
Affiliation(s)
- Mathias Vandenbogaert
- Unité Environnement et Risque Infectieux, Cellule d'Intervention Biologique d'Urgence, Institut Pasteur, Paris, France
| | - Aurélia Kwasiborski
- Unité Environnement et Risque Infectieux, Cellule d'Intervention Biologique d'Urgence, Institut Pasteur, Paris, France
| | - Ella Gonofio
- Institut Pasteur de Bangui, Bangui, Central African Republic
| | - Stéphane Descorps-Declère
- Centre of Bioinformatics, Biostatistics and Integrative Biology (C3BI), Institut Pasteur, Paris, France
| | | | | | | | - Antoine Gessain
- Unité d'Epidémiologie et Physiopathologie des Virus Oncogènes, Département de Virologie, UMR3569, Institut Pasteur, Centre National de la Recherche Scientifique (CNRS, Paris, France
| | - Jean-Claude Manuguerra
- Unité Environnement et Risque Infectieux, Cellule d'Intervention Biologique d'Urgence, Institut Pasteur, Paris, France
| | - Valérie Caro
- Unité Environnement et Risque Infectieux, Cellule d'Intervention Biologique d'Urgence, Institut Pasteur, Paris, France
| | | | - Nicolas Berthet
- Unité Environnement et Risque Infectieux, Cellule d'Intervention Biologique d'Urgence, Institut Pasteur, Paris, France.
- The Center for Microbes, Development and Health, CAS Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai-Chinese Academy of Sciences, Discovery and Molecular Characterization of Pathogens, No. 320 Yueyang Road, XuHui District, Shanghai, 200031, China.
| |
Collapse
|
12
|
Wang Y, Wang B, Xu D, Zhang M, Zhang X, Wang D. Development of a ladder-shape melting temperature isothermal amplification (LMTIA) assay for detection of African swine fever virus (ASFV). J Vet Sci 2022; 23:e51. [PMID: 35698807 PMCID: PMC9346532 DOI: 10.4142/jvs.22001] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2022] [Revised: 03/31/2022] [Accepted: 04/12/2022] [Indexed: 12/05/2022] Open
Abstract
Background Due to the unavailability of an effective vaccine or antiviral drug against the African swine fever virus (ASFV), rapid diagnosis methods are needed to prevent highly contagious African swine fever. Objectives The objective of this study was to establish the ladder-shape melting temperature isothermal amplification (LMTIA) assay for the detection of ASFV. Methods LMTIA primers were designed with the p72 gene of ASFV as the target, and plasmid pUC57 was used to clone the gene. The LMTIA reaction system was optimized with the plasmid as the positive control, and the performance of the LMTIA assay was compared with that of the commercial real-time polymerase chain reaction (PCR) kit in terms of sensitivity and detection rate using 200 serum samples. Results Our results showed that the LMTIA assay could detect the 104 dilution of DNA extracted from the positive reference serum sample, which was the same as that of the commercial real-time PCR kit. The coincidence rate between the two assays was 100%. Conclusions The LMTIA assay had high sensitivity, good detection, and simple operation. Thus, it is suitable for facilitating preliminary and cost-effective surveillance for the prevention and control of ASFV.
Collapse
Affiliation(s)
- Yongzhen Wang
- Key Laboratory of Biomarker Based Rapid-Detection Technology for Food Safety of Henan Province, Xuchang University, Xuchang 461000, China
| | - Borui Wang
- School of Food and Biological Engineering, Henan University of Science and Technology, Luoyang 471000, China
| | - Dandan Xu
- School of Food and Biological Engineering, Henan University of Science and Technology, Luoyang 471000, China
| | - Meng Zhang
- School of Food and Biological Engineering, Henan University of Science and Technology, Luoyang 471000, China
| | - Xiaohua Zhang
- Key Laboratory of Biomarker Based Rapid-Detection Technology for Food Safety of Henan Province, Xuchang University, Xuchang 461000, China
| | - Deguo Wang
- Key Laboratory of Biomarker Based Rapid-Detection Technology for Food Safety of Henan Province, Xuchang University, Xuchang 461000, China
| |
Collapse
|
13
|
Ji C, Jiang J, Wei Y, Wang Z, Chen Y, Mai Z, Cai M, Qin C, Cai Y, Yi H, Liang G, Lu G, Gong L, Zhang G, Wang H. A Method for the Analysis of African Swine Fever by Viral Metagenomic Sequencing. Front Vet Sci 2021; 8:766533. [PMID: 34888376 PMCID: PMC8649765 DOI: 10.3389/fvets.2021.766533] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Accepted: 10/28/2021] [Indexed: 12/14/2022] Open
Abstract
In 2018, there was an outbreak of African swine fever (ASF) in China, which spread to other provinces in the following 3 years and severely damaged China's pig industry. ASF is caused by the African swine fever virus (ASFV). Given that the genome of the African swine fever virus is very complex and whole genome information is currently inadequate, it is important to efficiently obtain virus genome sequences for genomic and epidemiological studies. The prevalent ASFV strains have low genetic variability; therefore, whole genome sequencing analysis provides a basis for the study of ASFV. We provide a method for the efficient sequencing of whole genomes, which requires only a small number of tissues. The database construction method was selected according to the genomic types of ASFV, and the whole ASFV genome was obtained through data filtering, host sequence removal, virus classification, data assembly, virus sequence identification, statistical analysis, gene prediction, and functional analysis. Our proposed method will facilitate ASFV genome sequencing and novel virus discovery.
Collapse
Affiliation(s)
- ChiHai Ji
- Guangdong Provincial Key Laboratory of Prevention and Control for Severe Clinical Animal Diseases, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China.,Shenzhen Kingkey Smart Agriculture Times Co., Ltd., Shenzhen, China.,Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, Guangzhou, China.,Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China.,National Engineering Research Center for Breeding Swine Industry, Guangzhou, China
| | - JingZhe Jiang
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
| | - YingFang Wei
- Guangdong Provincial Key Laboratory of Prevention and Control for Severe Clinical Animal Diseases, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China.,Shenzhen Kingkey Smart Agriculture Times Co., Ltd., Shenzhen, China.,Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, Guangzhou, China.,Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China.,National Engineering Research Center for Breeding Swine Industry, Guangzhou, China
| | - ZhiYuan Wang
- Guangdong Provincial Key Laboratory of Prevention and Control for Severe Clinical Animal Diseases, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China.,Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, Guangzhou, China.,Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China.,National Engineering Research Center for Breeding Swine Industry, Guangzhou, China
| | - YongJie Chen
- Guangdong Provincial Key Laboratory of Prevention and Control for Severe Clinical Animal Diseases, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China.,Shenzhen Kingkey Smart Agriculture Times Co., Ltd., Shenzhen, China.,Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, Guangzhou, China.,Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China.,National Engineering Research Center for Breeding Swine Industry, Guangzhou, China
| | - ZhanZhuo Mai
- Guangdong Provincial Key Laboratory of Prevention and Control for Severe Clinical Animal Diseases, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China.,Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, Guangzhou, China.,Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China.,National Engineering Research Center for Breeding Swine Industry, Guangzhou, China
| | - MengKai Cai
- Guangdong Provincial Key Laboratory of Prevention and Control for Severe Clinical Animal Diseases, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China.,Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, Guangzhou, China.,Guangdong Meizhou Vocational and Technical College, Meizhou, China
| | - ChenXiao Qin
- Guangdong Provincial Key Laboratory of Prevention and Control for Severe Clinical Animal Diseases, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China.,Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, Guangzhou, China.,Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China.,National Engineering Research Center for Breeding Swine Industry, Guangzhou, China
| | - Yu Cai
- Guangdong Provincial Key Laboratory of Prevention and Control for Severe Clinical Animal Diseases, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China.,Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, Guangzhou, China.,Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China.,National Engineering Research Center for Breeding Swine Industry, Guangzhou, China
| | - HeYou Yi
- Guangdong Provincial Key Laboratory of Prevention and Control for Severe Clinical Animal Diseases, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China.,Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, Guangzhou, China.,Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China.,National Engineering Research Center for Breeding Swine Industry, Guangzhou, China
| | - Guan Liang
- Guangdong Provincial Key Laboratory of Prevention and Control for Severe Clinical Animal Diseases, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China.,Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, Guangzhou, China.,Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China.,National Engineering Research Center for Breeding Swine Industry, Guangzhou, China
| | - Gang Lu
- Guangdong Provincial Key Laboratory of Prevention and Control for Severe Clinical Animal Diseases, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China.,Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, Guangzhou, China
| | - Lang Gong
- Guangdong Provincial Key Laboratory of Prevention and Control for Severe Clinical Animal Diseases, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China.,Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, Guangzhou, China.,Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China.,National Engineering Research Center for Breeding Swine Industry, Guangzhou, China
| | - GuiHong Zhang
- Guangdong Provincial Key Laboratory of Prevention and Control for Severe Clinical Animal Diseases, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China.,Shenzhen Kingkey Smart Agriculture Times Co., Ltd., Shenzhen, China.,Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, Guangzhou, China.,Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China.,National Engineering Research Center for Breeding Swine Industry, Guangzhou, China
| | - Heng Wang
- Guangdong Provincial Key Laboratory of Prevention and Control for Severe Clinical Animal Diseases, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China.,Shenzhen Kingkey Smart Agriculture Times Co., Ltd., Shenzhen, China.,Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, Guangzhou, China.,Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China.,National Engineering Research Center for Breeding Swine Industry, Guangzhou, China
| |
Collapse
|
14
|
Yan Y, Wu K, Chen J, Liu H, Huang Y, Zhang Y, Xiong J, Quan W, Wu X, Liang Y, He K, Jia Z, Wang D, Liu D, Wei H, Chen J. Rapid Acquisition of High-Quality SARS-CoV-2 Genome via Amplicon-Oxford Nanopore Sequencing. Virol Sin 2021; 36:901-912. [PMID: 33851337 PMCID: PMC8043101 DOI: 10.1007/s12250-021-00378-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Accepted: 02/18/2021] [Indexed: 02/07/2023] Open
Abstract
Genome sequencing has shown strong capabilities in the initial stages of the COVID-19 pandemic such as pathogen identification and virus preliminary tracing. While the rapid acquisition of SARS-CoV-2 genome from clinical specimens is limited by their low nucleic acid load and the complexity of the nucleic acid background. To address this issue, we modified and evaluated an approach by utilizing SARS-CoV-2-specific amplicon amplification and Oxford Nanopore PromethION platform. This workflow started with the throat swab of the COVID-19 patient, combined reverse transcript PCR, and multi-amplification in one-step to shorten the experiment time, then can quickly and steadily obtain high-quality SARS-CoV-2 genome within 24 h. A comprehensive evaluation of the method was conducted in 42 samples: the sequencing quality of the method was correlated well with the viral load of the samples; high-quality SARS-CoV-2 genome could be obtained stably in the samples with Ct value up to 39.14; data yielding for different Ct values were assessed and the recommended sequencing time was 8 h for samples with Ct value of less than 20; variation analysis indicated that the method can detect the existing and emerging genomic mutations as well; Illumina sequencing verified that ultra-deep sequencing can greatly improve the single read error rate of Nanopore sequencing, making it as low as 0.4/10,000 bp. In summary, high-quality SARS-CoV-2 genome can be acquired by utilizing the amplicon amplification and it is an effective method in accelerating the acquisition of genetic resources and tracking the genome diversity of SARS-CoV-2.
Collapse
Affiliation(s)
- Yi Yan
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, China
- National Virus Resource Center, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China
- Computational Virology Group, Center for Bacteria and Viruses Resources and Bioinformation, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China
- University of Chinese Academy of Sciences, Beijing, 101409, China
| | - Ke Wu
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, China
- National Virus Resource Center, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China
- Computational Virology Group, Center for Bacteria and Viruses Resources and Bioinformation, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China
- University of Chinese Academy of Sciences, Beijing, 101409, China
| | - Jun Chen
- Wuhan Pulmonary Hospital, Wuhan Tuberculosis Prevention and Treatment Institute, Wuhan, 430030, China
| | - Haizhou Liu
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, China
- National Virus Resource Center, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China
- Computational Virology Group, Center for Bacteria and Viruses Resources and Bioinformation, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Yi Huang
- National Biosafety Laboratory, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Yong Zhang
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Jin Xiong
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, China
| | | | - Xin Wu
- GrandOmics Biosciences, Beijing, 102200, China
| | - Yu Liang
- GrandOmics Diagnostics, Wuhan, 430000, China
| | - Kunlun He
- Key Laboratory of Biomedical Engineering and Translational Medicine, Ministry of Industry and Information Technology, Chinese PLA General Hospital, Beijing, 100039, China
- Beijing Key Laboratory for Precision Medicine of Chronic Heart Failure, Chinese PLA General Hospital, Beijing, 100039, China
| | - Zhilong Jia
- Key Laboratory of Biomedical Engineering and Translational Medicine, Ministry of Industry and Information Technology, Chinese PLA General Hospital, Beijing, 100039, China
- Beijing Key Laboratory for Precision Medicine of Chronic Heart Failure, Chinese PLA General Hospital, Beijing, 100039, China
| | - Depeng Wang
- GrandOmics Biosciences, Beijing, 102200, China
| | - Di Liu
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, China.
- National Virus Resource Center, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China.
- Computational Virology Group, Center for Bacteria and Viruses Resources and Bioinformation, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China.
- University of Chinese Academy of Sciences, Beijing, 101409, China.
- First Affiliated Hospital of Xinjiang Medical University, Urumqi, 830054, China.
| | - Hongping Wei
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, China.
| | - Jianjun Chen
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, China.
- National Virus Resource Center, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China.
| |
Collapse
|
15
|
Huo W, Ling W, Wang Z, Li Y, Zhou M, Ren M, Li X, Li J, Xia Z, Liu X, Huang X. Miniaturized DNA Sequencers for Personal Use: Unreachable Dreams or Achievable Goals. FRONTIERS IN NANOTECHNOLOGY 2021. [DOI: 10.3389/fnano.2021.628861] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
The appearance of next generation sequencing technology that features short read length with high measurement throughput and low cost has revolutionized the field of life science, medicine, and even computer science. The subsequent development of the third-generation sequencing technologies represented by nanopore and zero-mode waveguide techniques offers even higher speed and long read length with promising applications in portable and rapid genomic tests in field. Especially under the current circumstances, issues such as public health emergencies and global pandemics impose soaring demand on quick identification of origins and species of analytes through DNA sequences. In addition, future development of disease diagnosis, treatment, and tracking techniques may also require frequent DNA testing. As a result, DNA sequencers with miniaturized size and highly integrated components for personal and portable use to tackle increasing needs for disease prevention, personal medicine, and biohazard protection may become future trends. Just like many other biological and medical analytical systems that were originally bulky in sizes, collaborative work from various subjects in engineering and science eventually leads to the miniaturization of these systems. DNA sequencers that involve nanoprobes, detectors, microfluidics, microelectronics, and circuits as well as complex functional materials and structures are extremely complicated but may be miniaturized with technical advancement. This paper reviews the state-of-the-art technology in developing essential components in DNA sequencers and analyzes the feasibility to achieve miniaturized DNA sequencers for personal use. Future perspectives on the opportunities and associated challenges for compact DNA sequencers are also identified.
Collapse
|
16
|
Bisimwa PN, Ongus JR, Steinaa L, Bisimwa EB, Bochere E, Machuka EM, Entfellner JBD, Okoth E, Pelle R. The first complete genome sequence of the African swine fever virus genotype X and serogroup 7 isolated in domestic pigs from the Democratic Republic of Congo. Virol J 2021; 18:23. [PMID: 33478547 PMCID: PMC7819171 DOI: 10.1186/s12985-021-01497-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Accepted: 01/12/2021] [Indexed: 11/25/2022] Open
Abstract
Background African swine fever (ASF), a highly contagious hemorrhagic disease, affects domestic pigs in the Democratic Republic of Congo (DRC) where regular outbreaks are reported leading to high mortality rates approaching 100% in the affected regions. No study on the characteristics of the complete genome of strains responsible for ASF outbreaks in the South Kivu province of DRC is available, limited a better understanding of molecular evolution and spread of this virus within the country. The present study aimed at determining the complete genome sequence of ASFV strains genotype X involved in 2018–2019 ASF disease outbreaks in South Kivu province of DRC. Materials and methods Genomic DNA of a spleen sample from an ASFV genotype X-positive domestic pig in Uvira, during the 2018–2019 outbreaks in South Kivu, was sequenced using the Illumina HiSeq X platform. Obtained trimmed reads using Geneious Prime 2020.0.4 were blasted against a pig reference genome then contigs were generated from the unmapped reads enriched in ASFV DNA using Spades implemented in Geneious 2020.0.4. The assembly of the complete genome sequence of ASFV was achieved from the longest overlapping contigs. The new genome was annotated with the genome annotation transfer utility (GATU) software and the CLC Genomics Workbench 8 software was further used to search for any ORFs that failed to be identified by GATU. Subsequent analyses of the newly determined Uvira ASFV genotype X genome were done using BLAST for databases search, CLUSTAL W for multiple sequences alignments and MEGA X for phylogeny. Results 42 Gbp paired-end reads of 150 bp long were obtained containing about 0.1% of ASFV DNA. The assembled Uvira ASFV genome, termed Uvira B53, was 180,916 bp long that could be assembled in 2 contigs. The Uvira B53genome had a GC content of 38.5%, encoded 168 open reading frames (ORFs) and had 98.8% nucleotide identity with the reference ASFV genotype X Kenya 1950. The phylogenetic relationship with selected representative genomes clustered the Uvira B53 strain together with ASFV genotype X reported to date (Kenya 1950 and Ken05/Tk1). Multiple genome sequences comparison with the two reference ASFV genotype X strains showed that 130 of the 168 ORFs were fully conserved in the Uvira B53. The other 38 ORFs were divergent mainly due to SNPs and indels (deletions and insertions). Most of 46 multigene family (MGF) genes identified were affected by various genetic variations. However, 8 MGF ORFs present in Kenya 1950 and Ken05/Tk1 were absent from the Uvira B53 genome including three members of MGF 360, four of MGF 110 and one of MGF 100 while one MGF ORF (MGF 360-1L) at the left end of the genome was truncated in Uvira B53. Moreover, ORFs DP96R and p285L were also absent in the Uvira B53 genome. In contrast, the ORF MGF 110-5L present in Uvira B53 and Ken05/Tk1 was missing in Kenya 1950. The analysis of the intergenic region between the I73R and I329L genes also revealed sequence variations between the three genotype X strains mainly characterized by a deletion of 69 bp in Uvira B53 and 36 bp in Kenya 1950, compared to Ken05/Tk1. Assessment of the CD2v (EP402R) antigen unveiled the presence of SNPs and indels particularly in the PPPKPY tandem repeat region between selected variants representing the eight serogroups reported to date. Uvira B53 had identical CD2v variable region to the Uganda (KM609361) strain, the only other ASFV serogroup 7 reported to date. Conclusion We report the first complete genome sequence of an African swine fever virus (ASFV) p72 genotype X and CD2v serogroup 7, termed Uvira B53. This study provides additional insights on genetic characteristics and evolution of ASFV useful for tracing the geographical spread of ASF and essential for improved design of control and management strategies against ASF.
Collapse
Affiliation(s)
- Patrick N Bisimwa
- Institute of Basic Sciences, Technology and Innovation, Department of Molecular Biology and Biotechnology, Pan African University, Nairobi, Kenya. .,Department of Animal Science and Production, Université Evangélique en Afrique, P.O. Box 3323, Bukavu, Democratic Republic of Congo.
| | - Juliette R Ongus
- Institute of Basic Sciences, Technology and Innovation, Department of Molecular Biology and Biotechnology, Pan African University, Nairobi, Kenya.,Department of Medical Laboratory Sciences, Jomo Kenyatta University of Agriculture and Technology, Juja, Kenya
| | - Lucilla Steinaa
- International Livestock Research Institute, Animal and Human Health, Nairobi, Kenya
| | - Espoir B Bisimwa
- Department of Animal Science and Production, Université Evangélique en Afrique, P.O. Box 3323, Bukavu, Democratic Republic of Congo
| | - Edwina Bochere
- Biosciences Eastern and Central Africa-International Livestock Research Institute (BecA-ILRI) Hub, Naivasha Road, P.O. Box 30709, Nairobi, 00100, Kenya
| | - Eunice M Machuka
- Biosciences Eastern and Central Africa-International Livestock Research Institute (BecA-ILRI) Hub, Naivasha Road, P.O. Box 30709, Nairobi, 00100, Kenya
| | - Jean-Baka Domelevo Entfellner
- Biosciences Eastern and Central Africa-International Livestock Research Institute (BecA-ILRI) Hub, Naivasha Road, P.O. Box 30709, Nairobi, 00100, Kenya
| | - Edward Okoth
- Biosciences Eastern and Central Africa-International Livestock Research Institute (BecA-ILRI) Hub, Naivasha Road, P.O. Box 30709, Nairobi, 00100, Kenya
| | - Roger Pelle
- Biosciences Eastern and Central Africa-International Livestock Research Institute (BecA-ILRI) Hub, Naivasha Road, P.O. Box 30709, Nairobi, 00100, Kenya.
| |
Collapse
|
17
|
The Spillover of African Swine Fever in Western Poland Revealed Its Estimated Origin on the Basis of O174L, K145R, MGF 505-5R and IGR I73R/I329L Genomic Sequences. Viruses 2020; 12:v12101094. [PMID: 32992547 PMCID: PMC7601147 DOI: 10.3390/v12101094] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Revised: 09/23/2020] [Accepted: 09/23/2020] [Indexed: 02/07/2023] Open
Abstract
The African swine fever epidemic occurred in Poland at the beginning of 2014 and, up to date, the disease has been spreading mainly in the eastern part of the country. Unexpectedly, in November 2019 an infected wild boar case was confirmed in Lubuskie voivodship in western Poland. During the following weeks, several dozen African swine fever virus (ASFV)-positive animals were notified in the neighboring area, causing severe concern regarding further spread of the disease to the mostly pig-dense region in Poland, namely, Wielkopolskie voivodship. Moreover, almost a year after, several infected wild boar cases were confirmed for the first time in Germany, just beyond the Polish border, sending out a shock wave through the global pig market. The whole genome sequence of ASFV, isolated from the first case of ASF in western Poland, and three selected viruses from other affected areas, revealed the tandem repeat and single nucleotide polymorphism (SNP) variations in reference to the Georgia 2007/1 strain. These data, supported by the conventional sequencing of selected genomic regions from a total of 154 virus samples isolated between 2017 and 2020 in Poland, shed a new light on pathogen epidemiology. The sequence variations within the O174L gene detected in this study showed that cases identified in western Poland might be originating from the so-called southern Warsaw cluster. Moreover, the viruses originating from the northern Warsaw cluster do not possess single nucleotide polymorphism (SNP) mutations within the K145R and MGF 505-5R genes, which are specific to all of the other Polish ASFV strains. These results led to a conclusion of their distinct origin. Supporting these results, the nucleotide sequencing of I73R/I329L intergenic region revealed its new, previously undescribed variant, called IGR IV, with an additional three tandem repeats of 10 nucleotides in comparison to the reference sequence of the Georgia 2007/1 strain.
Collapse
|
18
|
Jia L, Chen J, Liu H, Fan W, Wang D, Li J, Liu D. Potential m6A and m5C Methylations within the Genome of A Chinese African Swine Fever Virus Strain. Virol Sin 2020; 36:321-324. [PMID: 32270427 DOI: 10.1007/s12250-020-00217-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2020] [Accepted: 03/07/2020] [Indexed: 01/26/2023] Open
Affiliation(s)
- Lijia Jia
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China.,Computational Virology Group, Center for Bacteria and Viruses Resources and Bioinformation, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jianjun Chen
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China.,Computational Virology Group, Center for Bacteria and Viruses Resources and Bioinformation, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China.,African Swine Fever Regional Laboratory of China, Wuhan, 430071, China.,Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Haizhou Liu
- Computational Virology Group, Center for Bacteria and Viruses Resources and Bioinformation, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Wenhui Fan
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | | | - Jing Li
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China. .,University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Di Liu
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China. .,Computational Virology Group, Center for Bacteria and Viruses Resources and Bioinformation, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China. .,African Swine Fever Regional Laboratory of China, Wuhan, 430071, China. .,Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, China. .,University of Chinese Academy of Sciences, Beijing, 100049, China.
| |
Collapse
|