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Bankamp B, Kim G, Hart D, Beck A, Ben Mamou M, Penedos A, Zhang Y, Evans R, Rota PA. Global Update on Measles Molecular Epidemiology. Vaccines (Basel) 2024; 12:810. [PMID: 39066448 PMCID: PMC11281501 DOI: 10.3390/vaccines12070810] [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: 05/29/2024] [Revised: 06/25/2024] [Accepted: 07/15/2024] [Indexed: 07/28/2024] Open
Abstract
Molecular surveillance of circulating measles variants serves as a line of evidence for the absence of endemic circulation and provides a means to track chains of transmission. Molecular surveillance for measles (genotyping) is based on the sequence of 450 nucleotides at the end of the nucleoprotein coding region (N450) of the measles genome. Genotyping was established in 1998 and, with over 50,000 sequence submissions to the Measles Nucleotide Surveillance database, has proven to be an effective resource for countries attempting to trace pathways of transmission. This review summarizes the tools used for the molecular surveillance of measles and describes the challenge posed by the decreased number of circulating measles genotypes. The Global Measles and Rubella Laboratory Network addressed this challenge through the development of new tools such as named strains and distinct sequence identifiers that analyze the diversity within the currently circulating genotypes. The advantages and limitations of these approaches are discussed, together with the need to generate additional sequence data including whole genome sequences to ensure the continued utility of strain surveillance for measles.
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Affiliation(s)
- Bettina Bankamp
- Centers for Disease Control and Prevention, 1600 Clifton Road NE, Atlanta, GA 30329, USA; (G.K.); (A.B.)
| | - Gimin Kim
- Centers for Disease Control and Prevention, 1600 Clifton Road NE, Atlanta, GA 30329, USA; (G.K.); (A.B.)
| | | | - Andrew Beck
- Centers for Disease Control and Prevention, 1600 Clifton Road NE, Atlanta, GA 30329, USA; (G.K.); (A.B.)
| | - Myriam Ben Mamou
- World Health Organization Regional Office for Europe, 2100 Copenhagen, Denmark;
| | - Ana Penedos
- United Kingdom Health Security Agency, London NW9 5EQ, UK;
| | - Yan Zhang
- WHO Western Pacific Regional Measles/Rubella Reference Laboratory, National Institute for Viral Disease Control and Prevention, Beijing 100013, China;
| | - Roger Evans
- World Health Organization Western Pacific Regional Office, Manila 1000, Philippines;
| | - Paul A. Rota
- Centers for Disease Control and Prevention, 1600 Clifton Road NE, Atlanta, GA 30329, USA; (G.K.); (A.B.)
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Li T, Zhao C, Guo Y, Dong J, Du F, Zhou Y, Shu S, Liu Y, Cheng Y, Cao Z, Cao Q, Shi S, Huang Y, Pu J, Liu L. Genetic and Biological Characteristics of Duck-Origin H4N6 Avian Influenza Virus Isolated in China in 2022. Viruses 2024; 16:207. [PMID: 38399984 PMCID: PMC10892581 DOI: 10.3390/v16020207] [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: 12/05/2023] [Revised: 01/23/2024] [Accepted: 01/25/2024] [Indexed: 02/25/2024] Open
Abstract
The interaction between migratory birds and domestic waterfowl facilitates viral co-infections, leading to viral reassortment and the emergence of novel viruses. In 2022, samples were collected from duck farms around Poyang Lake in Jiangxi Province, China, which is located within the East Asia-Australasia flyway. Three strains of H4N6 avian influenza virus (AIV) were isolated. Genetic and phylogenetic analyses showed that the isolated H4N6 avian influenza viruses (AIVs) belonged to new genotypes, G23 and G24. All isolated strains demonstrated dual receptor binding properties. Additionally, the isolated strains were able to replicate efficiently not only in avian cells but also in mammalian cells. Furthermore, the H4N6 AIV isolates could infect chickens, with viral replication detected in the lungs and extrapulmonary organs, and could transmit within chicken flocks through contact, with viral shedding detected only in oropharyngeal swabs from chickens in the contact group. Notably, the H4N6 AIV could infect mice without prior adaptation and replicate in the lungs with high viral titers, suggesting that it is a potential threat to humans. In conclusion, this study provides valuable insight into the characteristics of H4N6 strains currently circulating in China.
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Affiliation(s)
- Tian Li
- Key Laboratory for Prevention and Control of Avian Influenza and Other Major Poultry Diseases, Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China; (T.L.); (C.Z.); (Y.G.); (J.D.); (F.D.); (Y.Z.); (S.S.); (J.P.)
| | - Chuankuo Zhao
- Key Laboratory for Prevention and Control of Avian Influenza and Other Major Poultry Diseases, Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China; (T.L.); (C.Z.); (Y.G.); (J.D.); (F.D.); (Y.Z.); (S.S.); (J.P.)
| | - Yuxin Guo
- Key Laboratory for Prevention and Control of Avian Influenza and Other Major Poultry Diseases, Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China; (T.L.); (C.Z.); (Y.G.); (J.D.); (F.D.); (Y.Z.); (S.S.); (J.P.)
| | - Jinze Dong
- Key Laboratory for Prevention and Control of Avian Influenza and Other Major Poultry Diseases, Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China; (T.L.); (C.Z.); (Y.G.); (J.D.); (F.D.); (Y.Z.); (S.S.); (J.P.)
| | - Fanshu Du
- Key Laboratory for Prevention and Control of Avian Influenza and Other Major Poultry Diseases, Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China; (T.L.); (C.Z.); (Y.G.); (J.D.); (F.D.); (Y.Z.); (S.S.); (J.P.)
| | - Yong Zhou
- Key Laboratory for Prevention and Control of Avian Influenza and Other Major Poultry Diseases, Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China; (T.L.); (C.Z.); (Y.G.); (J.D.); (F.D.); (Y.Z.); (S.S.); (J.P.)
| | - Sicheng Shu
- Key Laboratory for Prevention and Control of Avian Influenza and Other Major Poultry Diseases, Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China; (T.L.); (C.Z.); (Y.G.); (J.D.); (F.D.); (Y.Z.); (S.S.); (J.P.)
| | - Yang Liu
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-Sen University, Guangzhou 510275, China; (Y.L.); (Y.C.)
| | - Yachang Cheng
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-Sen University, Guangzhou 510275, China; (Y.L.); (Y.C.)
| | - Zhiyong Cao
- Duchang County Aquaculture and Animal Husbandry Industry Development Center, Jiujiang 332600, China;
| | - Qi Cao
- Duchang County Yangfeng Township Government, Jiujiang 332600, China;
| | - Shuiping Shi
- Duchang County Migratory Bird Nature Reserve Administration, Jiujiang 332600, China;
| | - Yinhua Huang
- State Key Laboratory for Agrobiotechnology, College of Biology Sciences, China Agricultural University, Beijing 100193, China;
| | - Juan Pu
- Key Laboratory for Prevention and Control of Avian Influenza and Other Major Poultry Diseases, Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China; (T.L.); (C.Z.); (Y.G.); (J.D.); (F.D.); (Y.Z.); (S.S.); (J.P.)
| | - Litao Liu
- Key Laboratory for Prevention and Control of Avian Influenza and Other Major Poultry Diseases, Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China; (T.L.); (C.Z.); (Y.G.); (J.D.); (F.D.); (Y.Z.); (S.S.); (J.P.)
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3
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Wang X, Kim KW, Walker G, Stelzer‐Braid S, Scotch M, Rawlinson WD. Genome characterization of influenza A and B viruses in New South Wales, Australia, in 2019: A retrospective study using high-throughput whole genome sequencing. Influenza Other Respir Viruses 2024; 18:e13252. [PMID: 38288510 PMCID: PMC10824601 DOI: 10.1111/irv.13252] [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: 07/12/2023] [Revised: 12/22/2023] [Accepted: 12/23/2023] [Indexed: 02/01/2024] Open
Abstract
BACKGROUND During the 2019 severe influenza season, New South Wales (NSW) experienced the highest number of cases in Australia. This study retrospectively investigated the genetic characteristics of influenza viruses circulating in NSW in 2019 and identified genetic markers related to antiviral resistance and potential virulence. METHODS The complete genomes of influenza A and B viruses were amplified using reverse transcription-polymerase chain reaction (PCR) and sequenced with an Illumina MiSeq platform. RESULTS When comparing the sequencing data with the vaccine strains and reference sequences, the phylogenetic analysis revealed that most NSW A/H3N2 viruses (n = 68; 94%) belonged to 3C.2a1b and a minority (n = 4; 6%) belonged to 3C.3a. These viruses all diverged from the vaccine strain A/Switzerland/8060/2017. All A/H1N1pdm09 viruses (n = 20) showed genetic dissimilarity from vaccine strain A/Michigan/45/2015, with subclades 6B.1A.5 and 6B.1A.2 identified. All B/Victoria-lineage viruses (n = 21) aligned with clade V1A.3, presenting triple amino acid deletions at positions 162-164 in the hemagglutinin protein, significantly diverging from the vaccine strain B/Colorado/06/2017. Multiple amino acid substitutions were also found in the internal proteins of influenza viruses, some of which have been previously reported in hospitalized influenza patients in Thailand. Notably, the oseltamivir-resistant marker H275Y was present in one immunocompromised patient infected with A/H1N1pdm09 and the resistance-related mutation I222V was detected in another A/H3N2-infected patient. CONCLUSIONS Considering antigenic drift and the constant evolution of circulating A and B strains, we believe continuous monitoring of influenza viruses in NSW via the high-throughput sequencing approach provides timely and pivotal information for both public health surveillance and clinical treatment.
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Affiliation(s)
- Xinye Wang
- School of Biomedical Sciences, Faculty of Medicine and HealthUniversity of New South WalesSydneyNew South WalesAustralia
- Virology Research Laboratory, Serology and Virology Division (SAViD), NSW Health PathologyPrince of Wales HospitalSydneyNew South WalesAustralia
| | - Ki Wook Kim
- Virology Research Laboratory, Serology and Virology Division (SAViD), NSW Health PathologyPrince of Wales HospitalSydneyNew South WalesAustralia
- Discipline of Paediatrics and Child Health, School of Clinical Medicine, Faculty of Medicine and HealthUniversity of New South WalesSydneyNew South WalesAustralia
| | - Gregory Walker
- School of Biomedical Sciences, Faculty of Medicine and HealthUniversity of New South WalesSydneyNew South WalesAustralia
- Virology Research Laboratory, Serology and Virology Division (SAViD), NSW Health PathologyPrince of Wales HospitalSydneyNew South WalesAustralia
| | - Sacha Stelzer‐Braid
- School of Biomedical Sciences, Faculty of Medicine and HealthUniversity of New South WalesSydneyNew South WalesAustralia
- Virology Research Laboratory, Serology and Virology Division (SAViD), NSW Health PathologyPrince of Wales HospitalSydneyNew South WalesAustralia
| | - Matthew Scotch
- Biodesign Center for Environmental Health Engineering, Biodesign InstituteArizona State UniversityPhoenixArizonaUSA
- College of Health SolutionsArizona State UniversityPhoenixArizonaUSA
- Kirby InstituteUniversity of New South WalesSydneyNew South WalesAustralia
| | - William D. Rawlinson
- School of Biomedical Sciences, Faculty of Medicine and HealthUniversity of New South WalesSydneyNew South WalesAustralia
- Virology Research Laboratory, Serology and Virology Division (SAViD), NSW Health PathologyPrince of Wales HospitalSydneyNew South WalesAustralia
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4
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Sun H, Wang Y, Liu H, Pang Z, Cui X, Zhao R, Liu Y, Qu X, Huang M, Ke C, Liao M. The genetic diversity, replication, and transmission of 2009 pandemic H1N1 viruses in China. Front Microbiol 2023; 14:1110100. [PMID: 36876101 PMCID: PMC9982095 DOI: 10.3389/fmicb.2023.1110100] [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: 11/28/2022] [Accepted: 01/30/2023] [Indexed: 02/19/2023] Open
Abstract
Background The 2009 pandemic H1N1 influenza A virus (pdm09) continue to evolve, and few studies have systemically analyzed the evolution, replication, and transmission of pmd09 viruses in China. Methods To better understand the evolution and pathogenicity of pdm09 viruses, we systematically analyzed viruses that were confirmed in 2009-2020 in China and characterized their replication and transmission ability. We extensively analyzed the evolution characteristics of pdm/09 in China over the past decades. The replication ability of 6B.1 and 6B.2 lineages on Madin-Darby canine kidney (MDCK) and human lung adenocarcinoma epithelial (A549) cells and their pathogenicity and transmission in guinea pigs were also compared. Results In total, 3,038 pdm09 viruses belonged to clade 6B.1 (62% of all pdm09 viruses) and clade 6B.2 (4%). Clade 6B.1 pdm09 viruses are the predominant clade, with proportions of 54.1%, 78.9%, 57.2%, 58.6%, 61.7%, 76.3%, and 66.6% in the North, Northeast, East, Central, South, Southwest, and Northeast regions in China, respectively. The isolation proportion of clade 6B.1 pdm/09 viruses was 57.1%, 74.3%, 96.1%, 98.2%, 86.7%, and 78.5% in 2015-2020, respectively. A clear differentiation time point appeared in 2015 before which the evolution trend of pdm09 viruses in China was similar to that in North America but then showed a different trend after that point. To characterize pdm09 viruses in China after 2015, we further analyzed 33 pdm09 viruses isolated in Guangdong in 2016-2017, among which A/ Guangdong/33/2016 and A/Guangdong/184/2016 (184/2016) belonged to clade 6B.2, and the other 31 strains belonged to clade 6B.1. A/Guangdong/887/2017 (887/2017) and A/Guangdong/752/2017 (752/2017) (clade 6B.1), 184/2016 (clade 6B.2) and A/California/04/2009 (CA04) replicated efficiently in MDCK cells and A549 cells, as well as the turbinates of guinea pigs. 184/2016 and CA04 could transmit among guinea pigs through physical contact. Conclusion Our findings provide novel insights into the evolution, pathogenicity, and transmission of pdm09 virus. The results show that enhancing surveillance of pdm09 viruses and timely evaluation of their virulence are essential.
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Affiliation(s)
- Hailiang Sun
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China.,National and Regional Joint Engineering Laboratory for Medicament of Zoonosis Prevention and Control, South China Agricultural University, Guangzhou, China.,Key Laboratory of Zoonosis Control and Prevention of Guangdong Province, South China Agricultural University, Guangzhou, China
| | - Yongcui Wang
- The Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
| | - Hanlin Liu
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China.,National and Regional Joint Engineering Laboratory for Medicament of Zoonosis Prevention and Control, South China Agricultural University, Guangzhou, China.,Key Laboratory of Zoonosis Control and Prevention of Guangdong Province, South China Agricultural University, Guangzhou, China
| | - Zifeng Pang
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China.,National and Regional Joint Engineering Laboratory for Medicament of Zoonosis Prevention and Control, South China Agricultural University, Guangzhou, China.,Key Laboratory of Zoonosis Control and Prevention of Guangdong Province, South China Agricultural University, Guangzhou, China
| | - Xinxin Cui
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China.,National and Regional Joint Engineering Laboratory for Medicament of Zoonosis Prevention and Control, South China Agricultural University, Guangzhou, China.,Key Laboratory of Zoonosis Control and Prevention of Guangdong Province, South China Agricultural University, Guangzhou, China
| | - Rui Zhao
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China.,National and Regional Joint Engineering Laboratory for Medicament of Zoonosis Prevention and Control, South China Agricultural University, Guangzhou, China.,Key Laboratory of Zoonosis Control and Prevention of Guangdong Province, South China Agricultural University, Guangzhou, China
| | - Yanwei Liu
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China.,National and Regional Joint Engineering Laboratory for Medicament of Zoonosis Prevention and Control, South China Agricultural University, Guangzhou, China.,Key Laboratory of Zoonosis Control and Prevention of Guangdong Province, South China Agricultural University, Guangzhou, China
| | - Xiaoyun Qu
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China.,National and Regional Joint Engineering Laboratory for Medicament of Zoonosis Prevention and Control, South China Agricultural University, Guangzhou, China.,Key Laboratory of Zoonosis Control and Prevention of Guangdong Province, South China Agricultural University, Guangzhou, China
| | - Mian Huang
- Guangzhou Zoo, The People's Government of Guangzhou Municipality, Guangzhou, China
| | - Changwen Ke
- Guangdong Provincial Center for Disease Control and Prevention, The People's Government of Guangzhou Municipality, Guangzhou, China
| | - Ming Liao
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China.,National and Regional Joint Engineering Laboratory for Medicament of Zoonosis Prevention and Control, South China Agricultural University, Guangzhou, China.,Key Laboratory of Zoonosis Control and Prevention of Guangdong Province, South China Agricultural University, Guangzhou, China
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5
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Zhang M, Chen Z, Zhou J, Zhao X, Chen Y, Sun Y, Liu Z, Gu W, Luo C, Fu X, Zhao X. An imported human case with the SARS-CoV-2 Omicron subvariant BA.2.75 in Yunnan Province, China. BIOSAFETY AND HEALTH 2022; 4:406-409. [PMID: 36320663 PMCID: PMC9613801 DOI: 10.1016/j.bsheal.2022.10.003] [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: 08/10/2022] [Revised: 10/17/2022] [Accepted: 10/24/2022] [Indexed: 11/06/2022] Open
Abstract
The Omicron variants spread rapidly worldwide after being initially detected in South Africa in November 2021. It showed increased transmissibility and immune evasion with far more amino acid mutations in the spike (S) protein than the previously circulating variants of concern (VOCs). Notably, on 15 July 2022, we monitored the first VOC / Omicron subvariant BA.2.75 in China from an imported case. Moreover, nowadays, this subvariant still is predominant in India. It has nine additional mutations in the S protein compared to BA.2, three of which (W152R, G446S, and R493Q reversion) might contribute to higher transmissibility and immune escape. This subvariant could cause wider spread and pose a threat to the global situation. Our timely reporting and continuous genomic analysis are essential to fully elucidate the characteristics of the subvariant BA.2.75 in the future.
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Affiliation(s)
- Meiling Zhang
- Yunnan Center for Disease Control and Prevention, Kunming 650022, China,Corresponding authors: Yunnan Center for Disease Control and Prevention, Kunming 650022, China (M. Zhang and X. Fu); National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China (X. Zhao)
| | - Zhixiao Chen
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Jienan Zhou
- Yunnan Center for Disease Control and Prevention, Kunming 650022, China
| | - Xiaonan Zhao
- Yunnan Center for Disease Control and Prevention, Kunming 650022, China
| | - Yaoyao Chen
- Yunnan Center for Disease Control and Prevention, Kunming 650022, China
| | - Yanhong Sun
- Yunnan Center for Disease Control and Prevention, Kunming 650022, China
| | - Zhaosheng Liu
- Yunnan Center for Disease Control and Prevention, Kunming 650022, China
| | - Wenpeng Gu
- Yunnan Center for Disease Control and Prevention, Kunming 650022, China
| | - Chunrui Luo
- Yunnan Center for Disease Control and Prevention, Kunming 650022, China
| | - Xiaoqing Fu
- Yunnan Center for Disease Control and Prevention, Kunming 650022, China,Corresponding authors: Yunnan Center for Disease Control and Prevention, Kunming 650022, China (M. Zhang and X. Fu); National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China (X. Zhao)
| | - Xiang Zhao
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China,Corresponding authors: Yunnan Center for Disease Control and Prevention, Kunming 650022, China (M. Zhang and X. Fu); National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China (X. Zhao)
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6
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Rattanaburi S, Sawaswong V, Nimsamer P, Mayuramart O, Sivapornnukul P, Khamwut A, Chanchaem P, Kongnomnan K, Suntronwong N, Poovorawan Y, Payungporn S. Genome characterization and mutation analysis of human influenza A virus in Thailand. Genomics Inform 2022; 20:e21. [PMID: 35794701 PMCID: PMC9299564 DOI: 10.5808/gi.21077] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 04/05/2022] [Indexed: 11/20/2022] Open
Abstract
The influenza A viruses have high mutation rates and cause a serious health problem worldwide. Therefore, this study focused on genome characterization of the viruses isolated from Thai patients based on the next-generation sequencing technology. The nasal swabs were collected from patients with influenza-like illness in Thailand during 2017-2018. Then, the influenza A viruses were detected by reverse transcription-quantitative polymerase chain reaction and isolated by MDCK cells. The viral genomes were amplified and sequenced by Illumina MiSeq platform. Whole genome sequences were used for characterization, phylogenetic construction, mutation analysis and nucleotide diversity of the viruses. The result revealed that 90 samples were positive for the viruses including 44 of A/H1N1 and 46 of A/H3N2. Among these, 43 samples were successfully isolated and then the viral genomes of 25 samples were completely amplified. Finally, 17 whole genomes of the viruses (A/H1N1, n=12 and A/H3N2, n=5) were successfully sequenced with an average of 232,578 mapped reads and 1,720 genome coverage per sample. Phylogenetic analysis demonstrated that the A/H1N1 viruses were distinguishable from the recommended vaccine strains. However, the A/H3N2 viruses from this study were closely related to the recommended vaccine strains. The nonsynonymous mutations were found in all genes of both viruses, especially in HA and NA genes. The nucleotide diversity analysis revealed negative selection in the PB1, PA, hemagglutinin (HA) and neuraminidase (NA) genes of the A/H1N1 viruses. High-throughput data in this study allow for genetic characterization of circulating influenza viruses which would be crucial for preparation against pandemic and epidemic outbreaks in the future.
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Affiliation(s)
- Somruthai Rattanaburi
- Interdisciplinary Program of Biomedical Sciences, Graduate School, Chulalongkorn University, Bangkok 10330, Thailand.,Research Unit of Systems Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
| | - Vorthon Sawaswong
- Research Unit of Systems Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
| | - Pattaraporn Nimsamer
- Research Unit of Systems Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
| | - Oraphan Mayuramart
- Research Unit of Systems Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
| | - Pavaret Sivapornnukul
- Research Unit of Systems Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand.,Department of Biochemistry, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
| | - Ariya Khamwut
- Research Unit of Systems Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
| | - Prangwalai Chanchaem
- Research Unit of Systems Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
| | - Kritsada Kongnomnan
- Research Unit of Systems Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
| | - Nungruthai Suntronwong
- Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
| | - Yong Poovorawan
- Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
| | - Sunchai Payungporn
- Research Unit of Systems Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand.,Department of Biochemistry, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
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7
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Hasan A, Sasaki T, Phadungsombat J, Koketsu R, Rahim R, Ara N, Biswas SM, Yonezawa R, Nakayama EE, Rahman M, Shioda T. Genetic Analysis of Influenza A/H1N1pdm Strains Isolated in Bangladesh in Early 2020. Trop Med Infect Dis 2022; 7:tropicalmed7030038. [PMID: 35324585 PMCID: PMC8949303 DOI: 10.3390/tropicalmed7030038] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 02/24/2022] [Accepted: 02/26/2022] [Indexed: 12/10/2022] Open
Abstract
Influenza is one of the most common respiratory virus infections. We analyzed hemagglutinin (HA) and neuraminidase (NA) gene segments of viruses isolated from influenza patients who visited Evercare Hospital Dhaka, Bangladesh, in early 2020 immediately before the coronavirus disease 2019 (COVID-19) pandemic. All of them were influenza virus type A (IAV) H1N1pdm. Sequence analysis of the HA segments of the virus strains isolated from the clinical specimens and the subsequent phylogenic analyses of the obtained sequences revealed that all of the H1N1pdm recent subclades 6B.1A5A + 187V/A, 6B.1A5A + 156K, and 6B.1A5A + 156K with K209M were already present in Bangladesh in January 2020. Molecular clock analysis results suggested that the subclade 6B.1A5A + 156K emerged in Denmark, Australia, or the United States in July 2019, while subclades 6B.1A5A + 187V/A and 6B.1A5A + 156K with K209M emerged in East Asia in April and September 2019, respectively. On the other hand, sequence analysis of NA segments showed that the viruses lacked the H275Y mutation that confers oseltamivir resistance. Since the number of influenza cases in Bangladesh is usually small between November and January, these results indicated that the IAV H1N1pdm had spread extremely rapidly without acquiring oseltamivir resistance during a time of active international flow of people before the COVID-19 pandemic.
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Affiliation(s)
- Abu Hasan
- Evercare Hospital Dhaka (Ex Apollo Hospitals Dhaka), Dhaka 1229, Bangladesh; (A.H.); (R.R.); (N.A.); (S.M.B.)
| | - Tadahiro Sasaki
- Research Institute of Microbial Diseases, Osaka University, Suita 565-0781, Japan; (T.S.); (J.P.); (R.K.); (R.Y.); (E.E.N.)
- Center for Infectious Disease Education and Research, Osaka University, Suita 565-0781, Japan
| | - Juthamas Phadungsombat
- Research Institute of Microbial Diseases, Osaka University, Suita 565-0781, Japan; (T.S.); (J.P.); (R.K.); (R.Y.); (E.E.N.)
- Center for Infectious Disease Education and Research, Osaka University, Suita 565-0781, Japan
- Mahidol-Osaka Center for Infectious Diseases (MOCID), Faculty of Tropical Medicine, Mahidol University, Bangkok 10400, Thailand
| | - Ritsuko Koketsu
- Research Institute of Microbial Diseases, Osaka University, Suita 565-0781, Japan; (T.S.); (J.P.); (R.K.); (R.Y.); (E.E.N.)
- Center for Infectious Disease Education and Research, Osaka University, Suita 565-0781, Japan
| | - Rummana Rahim
- Evercare Hospital Dhaka (Ex Apollo Hospitals Dhaka), Dhaka 1229, Bangladesh; (A.H.); (R.R.); (N.A.); (S.M.B.)
| | - Nikhat Ara
- Evercare Hospital Dhaka (Ex Apollo Hospitals Dhaka), Dhaka 1229, Bangladesh; (A.H.); (R.R.); (N.A.); (S.M.B.)
| | - Suma Mita Biswas
- Evercare Hospital Dhaka (Ex Apollo Hospitals Dhaka), Dhaka 1229, Bangladesh; (A.H.); (R.R.); (N.A.); (S.M.B.)
| | - Riku Yonezawa
- Research Institute of Microbial Diseases, Osaka University, Suita 565-0781, Japan; (T.S.); (J.P.); (R.K.); (R.Y.); (E.E.N.)
- Center for Infectious Disease Education and Research, Osaka University, Suita 565-0781, Japan
| | - Emi E. Nakayama
- Research Institute of Microbial Diseases, Osaka University, Suita 565-0781, Japan; (T.S.); (J.P.); (R.K.); (R.Y.); (E.E.N.)
- Center for Infectious Disease Education and Research, Osaka University, Suita 565-0781, Japan
| | - Mizanur Rahman
- Evercare Hospital Dhaka (Ex Apollo Hospitals Dhaka), Dhaka 1229, Bangladesh; (A.H.); (R.R.); (N.A.); (S.M.B.)
- Correspondence: (M.R.); (T.S.)
| | - Tatsuo Shioda
- Research Institute of Microbial Diseases, Osaka University, Suita 565-0781, Japan; (T.S.); (J.P.); (R.K.); (R.Y.); (E.E.N.)
- Center for Infectious Disease Education and Research, Osaka University, Suita 565-0781, Japan
- Mahidol-Osaka Center for Infectious Diseases (MOCID), Faculty of Tropical Medicine, Mahidol University, Bangkok 10400, Thailand
- Correspondence: (M.R.); (T.S.)
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Abstract
Introduction: As the pathogen that caused the first influenza virus pandemic in this century, the swine-origin A(H1N1) pdm09 influenza virus has caused continuous harm to human public health. The evolution of hemagglutinin protein glycosylation sites, including the increase in number and positional changes, is an important way for influenza viruses to escape host immune pressure. Based on the traditional influenza virus molecular monitoring, special attention should be paid to the influence of glycosylation evolution on the biological characteristics of virus antigenicity, transmission and pathogenicity. The epidemiological significance of glycosylation mutants should be analyzed as a predictive tool for early warning of new outbreaks and pandemics, as well as the design of vaccines and drug targets.Areas covered: We review on the evolutionary characteristics of glycosylation on the HA protein of the A(H1N1)pdm09 influenza virus in the last ten years.Expert opinion: We discuss the crucial impact of evolutionary glycosylation on the biological characteristics of the virus and the host immune responses, summarize studies revealing different roles of glycosylation play during host adaptation. Although these studies show the significance of glycosylation evolution in host-virus interaction, much remains to be discovered about the mechanism.
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Affiliation(s)
- Pan Ge
- Center for Vaccines and Immunology, University of Georgia, Athens, GA, USA
| | - Ted M Ross
- Center for Vaccines and Immunology, University of Georgia, Athens, GA, USA.,Department of Infectious Diseases, University of Georgia, Athens, GA USA
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