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Du Y, Xia J, Wang Z, Xu J, Ji Y, Jin Y, Pu L, Xu S. Evolution of H6N6 viruses in China between 2014 and 2019 involves multiple reassortment events. Emerg Microbes Infect 2024; 13:2341142. [PMID: 38581279 DOI: 10.1080/22221751.2024.2341142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 04/04/2024] [Indexed: 04/08/2024]
Abstract
H6N6 avian influenza viruses (AIVs) have been widely detected in wild birds, poultry, and even mammals. Recently, H6N6 viruses were reported to be involved in the generation of H5 and H7 subtype viruses. To investigate the emergence, evolutionary pattern, and potential for an epidemic of H6N6 viruses, the complete genomes of 198 H6N6 viruses were analyzed, including 168 H6N6 viruses deposited in the NCBI and GISAID databases from inception to January 2019 and 30 isolates collected from China between November 2014 and January 2019. Using phylogenetic analysis, the 198 strains of H6N6 viruses were identified as 98 genotypes. Molecular clock analysis indicated that the evolution of H6N6 viruses in China was constant and not interrupted by selective pressure. Notably, the laboratory isolates reassorted with six subtype viruses: H6N2, H5N6, H7N9, H5N2, H4N2, and H6N8, resulting in nine novel H6N6 reassortment events. These results suggested that H6N6 viruses can act as an intermediary in the evolution of H5N6, H6N6, and H7N9 viruses. Animal experiments demonstrated that the 10 representative H6N6 viruses showed low pathogenicity in chickens and were capable of infecting mice without prior adaptation. Our findings suggest that H6N6 viruses play an important role in the evolution of AIVs, and it is necessary to continuously monitor and evaluate the potential epidemic of the H6N6 subtype viruses.
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Affiliation(s)
- Yingying Du
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, People's Republic of China
| | - Jun Xia
- Institute of Veterinary Medicine, Xinjiang Academy of Animal Sciences, Urumqi, People's Republic of China
| | - Zhengxiang Wang
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, People's Republic of China
| | - Jie Xu
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, People's Republic of China
| | - Yanhong Ji
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, People's Republic of China
| | - Yinghong Jin
- Institute of Veterinary Medicine, Xinjiang Academy of Animal Sciences, Urumqi, People's Republic of China
| | - Ling Pu
- Guizhou Institute of Animal Husbandry and Veterinary Science, Guizhou, People's Republic of China
| | - Shuai Xu
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, People's Republic of China
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Feoktistova S, Sayganova M, Trutneva K, Glazova O, Blagodatski AS, Shevkova L, Navoikova A, Anisimov Y, Albert E, Mityaeva O, Volchkov P, Deviatkin A. Abundant Intra-Subtype Reassortment Revealed in H13N8 Influenza Viruses. Viruses 2024; 16:568. [PMID: 38675910 PMCID: PMC11054967 DOI: 10.3390/v16040568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Revised: 03/29/2024] [Accepted: 04/05/2024] [Indexed: 04/28/2024] Open
Abstract
Influenza A viruses (IAVs) pose a serious threat to global health. On the one hand, these viruses cause seasonal flu outbreaks in humans. On the other hand, they are a zoonotic infection that has the potential to cause a pandemic. The most important natural reservoir of IAVs are waterfowl. In this study, we investigated the occurrence of IAV in birds in the Republic of Buryatia (region in Russia). In 2020, a total of 3018 fecal samples were collected from wild migratory birds near Lake Baikal. Of these samples, 11 were found to be positive for the H13N8 subtype and whole-genome sequencing was performed on them. All samples contained the same virus with the designation A/Unknown/Buryatia/Arangatui-1/2020. To our knowledge, virus A/Unknown/Buryatia/Arangatui-1/2020 is the first representative of the H13N8 subtype collected on the territory of Russia, the sequence of which is available in the GenBank database. An analysis of reassortments based on the genome sequences of other known viruses has shown that A/Unknown/Buryatia/Arangatui-1/2020 arose as a result of reassortment. In addition, a reassortment most likely occurred several decades ago between the ancestors of the viruses recently collected in China, the Netherlands, the United States and Chile. The presence of such reassortment emphasizes the ongoing evolution of the H13N8 viruses distributed in Europe, North and East Asia, North and South America and Australia. This study underscores the importance of the continued surveillance and research of less-studied influenza subtypes.
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Affiliation(s)
- Sofia Feoktistova
- Federal Research Center for Innovator and Emerging Biomedical and Pharmaceutical Technologies, 125315 Moscow, Russia; (M.S.); (K.T.); (O.G.); (L.S.); (A.N.); (E.A.); (O.M.); (P.V.)
| | - Marya Sayganova
- Federal Research Center for Innovator and Emerging Biomedical and Pharmaceutical Technologies, 125315 Moscow, Russia; (M.S.); (K.T.); (O.G.); (L.S.); (A.N.); (E.A.); (O.M.); (P.V.)
| | - Kseniya Trutneva
- Federal Research Center for Innovator and Emerging Biomedical and Pharmaceutical Technologies, 125315 Moscow, Russia; (M.S.); (K.T.); (O.G.); (L.S.); (A.N.); (E.A.); (O.M.); (P.V.)
| | - Olga Glazova
- Federal Research Center for Innovator and Emerging Biomedical and Pharmaceutical Technologies, 125315 Moscow, Russia; (M.S.); (K.T.); (O.G.); (L.S.); (A.N.); (E.A.); (O.M.); (P.V.)
| | - Artem S. Blagodatski
- Federal State Budget Institution of Science Institute of Theoretical and Experimental Biophysics, 142290 Pushchino, Russia;
| | - Liudmila Shevkova
- Federal Research Center for Innovator and Emerging Biomedical and Pharmaceutical Technologies, 125315 Moscow, Russia; (M.S.); (K.T.); (O.G.); (L.S.); (A.N.); (E.A.); (O.M.); (P.V.)
| | - Anna Navoikova
- Federal Research Center for Innovator and Emerging Biomedical and Pharmaceutical Technologies, 125315 Moscow, Russia; (M.S.); (K.T.); (O.G.); (L.S.); (A.N.); (E.A.); (O.M.); (P.V.)
| | - Yuriy Anisimov
- Baikalsky State Nature Biosphere Reserve, 671220 Tankhoi, Russia;
| | - Eugene Albert
- Federal Research Center for Innovator and Emerging Biomedical and Pharmaceutical Technologies, 125315 Moscow, Russia; (M.S.); (K.T.); (O.G.); (L.S.); (A.N.); (E.A.); (O.M.); (P.V.)
| | - Olga Mityaeva
- Federal Research Center for Innovator and Emerging Biomedical and Pharmaceutical Technologies, 125315 Moscow, Russia; (M.S.); (K.T.); (O.G.); (L.S.); (A.N.); (E.A.); (O.M.); (P.V.)
- Department of Fundamental Medicine, Lomonosov Moscow State University, 119992 Moscow, Russia
| | - Pavel Volchkov
- Federal Research Center for Innovator and Emerging Biomedical and Pharmaceutical Technologies, 125315 Moscow, Russia; (M.S.); (K.T.); (O.G.); (L.S.); (A.N.); (E.A.); (O.M.); (P.V.)
- Department of Fundamental Medicine, Lomonosov Moscow State University, 119992 Moscow, Russia
- The Moscow Clinical Scientific Center (MCSC) Named after A.S. Loginov, 111123 Moscow, Russia
| | - Andrey Deviatkin
- Federal Research Center for Innovator and Emerging Biomedical and Pharmaceutical Technologies, 125315 Moscow, Russia; (M.S.); (K.T.); (O.G.); (L.S.); (A.N.); (E.A.); (O.M.); (P.V.)
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, 119992 Moscow, Russia
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Cui X, Ma J, Pang Z, Chi L, Mai C, Liu H, Liao M, Sun H. The evolution, pathogenicity and transmissibility of quadruple reassortant H1N2 swine influenza virus in China: A potential threat to public health. Virol Sin 2024; 39:205-217. [PMID: 38346538 DOI: 10.1016/j.virs.2024.02.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Accepted: 02/06/2024] [Indexed: 04/30/2024] Open
Abstract
Swine are regarded as "intermediate hosts" or "mixing vessels" of influenza viruses, capable of generating strains with pandemic potential. From 2020 to 2021, we conducted surveillance on swine H1N2 influenza (swH1N2) viruses in swine farms located in Guangdong, Yunnan, and Guizhou provinces in southern China, as well as Henan and Shandong provinces in northern China. We systematically analyzed the evolution and pathogenicity of swH1N2 isolates, and characterized their replication and transmission abilities. The isolated viruses are quadruple reassortant H1N2 viruses containing genes from pdm/09 H1N1 (PB2, PB1, PA and NP genes), triple-reassortant swine (NS gene), Eurasian Avian-like (HA and M genes), and recent human H3N2 (NA gene) lineages. The NA, PB2, and NP of SW/188/20 and SW/198/20 show high gene similarities to A/Guangdong/Yue Fang277/2017 (H3N2). The HA gene of swH1N2 exhibits a high evolutionary rate. The five swH1N2 isolates replicate efficiently in human, canine, and swine cells, as well as in the turbinate, trachea, and lungs of mice. A/swine/Shandong/198/2020 strain efficiently replicates in the respiratory tract of pigs and effectively transmitted among them. Collectively, these current swH1N2 viruses possess zoonotic potential, highlighting the need for strengthened surveillance of swH1N2 viruses.
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MESH Headings
- Animals
- Swine
- Reassortant Viruses/genetics
- Reassortant Viruses/pathogenicity
- Reassortant Viruses/isolation & purification
- China/epidemiology
- Orthomyxoviridae Infections/virology
- Orthomyxoviridae Infections/transmission
- Orthomyxoviridae Infections/veterinary
- Swine Diseases/virology
- Swine Diseases/transmission
- Influenza A Virus, H1N2 Subtype/genetics
- Influenza A Virus, H1N2 Subtype/pathogenicity
- Influenza A Virus, H1N2 Subtype/isolation & purification
- Humans
- Mice
- Dogs
- Evolution, Molecular
- Phylogeny
- Virus Replication
- Public Health
- Influenza A Virus, H1N1 Subtype/genetics
- Influenza A Virus, H1N1 Subtype/pathogenicity
- Influenza A Virus, H1N1 Subtype/isolation & purification
- Influenza, Human/virology
- Influenza, Human/transmission
- Mice, Inbred BALB C
- Influenza A Virus, H3N2 Subtype/genetics
- Influenza A Virus, H3N2 Subtype/pathogenicity
- Influenza A Virus, H3N2 Subtype/isolation & purification
- Virulence
- Female
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Affiliation(s)
- Xinxin Cui
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, China; Key Laboratory of Zoonosis Control and Prevention of Guangdong Province, South China Agricultural University, Guangzhou, 510642, China; National and Regional Joint Engineering Laboratory for Medicament of Zoonosis Prevention and Control, South China Agricultural University, Guangzhou, 510642, China
| | - Jinhuan Ma
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, China; Key Laboratory of Zoonosis Control and Prevention of Guangdong Province, South China Agricultural University, Guangzhou, 510642, China; National and Regional Joint Engineering Laboratory for Medicament of Zoonosis Prevention and Control, South China Agricultural University, Guangzhou, 510642, China
| | - Zifeng Pang
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, China; Key Laboratory of Zoonosis Control and Prevention of Guangdong Province, South China Agricultural University, Guangzhou, 510642, China; National and Regional Joint Engineering Laboratory for Medicament of Zoonosis Prevention and Control, South China Agricultural University, Guangzhou, 510642, China
| | - Lingzhi Chi
- Shandong Vocational Animal Science and Veterinary College, Weifang, 261061, China
| | - Cuishan Mai
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, China; Key Laboratory of Zoonosis Control and Prevention of Guangdong Province, South China Agricultural University, Guangzhou, 510642, China; National and Regional Joint Engineering Laboratory for Medicament of Zoonosis Prevention and Control, South China Agricultural University, Guangzhou, 510642, China
| | - Hanlin Liu
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, China; Key Laboratory of Zoonosis Control and Prevention of Guangdong Province, South China Agricultural University, Guangzhou, 510642, China; National and Regional Joint Engineering Laboratory for Medicament of Zoonosis Prevention and Control, South China Agricultural University, Guangzhou, 510642, China
| | - Ming Liao
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, China; Key Laboratory of Zoonosis Control and Prevention of Guangdong Province, South China Agricultural University, Guangzhou, 510642, China; National and Regional Joint Engineering Laboratory for Medicament of Zoonosis Prevention and Control, South China Agricultural University, Guangzhou, 510642, China; Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China.
| | - Hailiang Sun
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, China; Key Laboratory of Zoonosis Control and Prevention of Guangdong Province, South China Agricultural University, Guangzhou, 510642, China; National and Regional Joint Engineering Laboratory for Medicament of Zoonosis Prevention and Control, South China Agricultural University, Guangzhou, 510642, China.
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Gu G, Liu C, Lee SH, Chun Choi LS, Wilson MT, Pfeiffer DU, Go YY. Detection of a reassortant swine H1N2 influenza A virus from pigs in Hong Kong. Virol Sin 2024; 39:343-346. [PMID: 38309471 DOI: 10.1016/j.virs.2024.01.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 01/26/2024] [Indexed: 02/05/2024] Open
Affiliation(s)
- Guoqian Gu
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Hong Kong SAR, China
| | - Congnuan Liu
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Hong Kong SAR, China
| | - Song Hao Lee
- Center for Applied One Health Research and Policy Advice, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Hong Kong SAR, China
| | - Lewis Sze Chun Choi
- Center for Applied One Health Research and Policy Advice, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Hong Kong SAR, China
| | - Michael T Wilson
- Center for Applied One Health Research and Policy Advice, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Hong Kong SAR, China
| | - Dirk U Pfeiffer
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Hong Kong SAR, China; Center for Applied One Health Research and Policy Advice, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Hong Kong SAR, China
| | - Yun Young Go
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Hong Kong SAR, China; College of Veterinary Medicine, Konkuk University, Seoul, 143-701, Republic of Korea.
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Sashina TA, Velikzhanina EI, Morozova OV, Epifanova NV, Novikova NA. Detection and full-genotype determination of rare and reassortant rotavirus A strains in Nizhny Novgorod in the European part of Russia. Arch Virol 2023; 168:215. [PMID: 37524885 DOI: 10.1007/s00705-023-05838-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 06/13/2023] [Indexed: 08/02/2023]
Abstract
Reassortant DS-1-like rotavirus A strains have been shown to circulate widely in many countries around the world. In Russia, the prevalence of such strains remains unclear due to the preferred use of the traditional binary classification system. In this work, we obtained partial sequence data from all 11 genome segments and determined the full-genotype constellations of rare and reassortant rotaviruses circulating in Nizhny Novgorod in 2016-2019. DS-1-like G3P[8] and G8P[8] strains were found, reflecting the global trend. Most likely, these strains were introduced into the territory of Russia from other countries but subsequently underwent further evolutionary changes locally. G3P[8], G9P[8], and G12P[8] Wa-like strains of subgenotypic lineages that are unusual for the territory of Russia were also identified. Reassortant G2P[8], G4P[4], and G9P[4] strains with one Wa-like gene (VP4 or VP7) on a DS-1-like backbone were found, and these apparently had a local origin. Feline-like G3P[9] and G6P[9] strains were found to be phylogenetically close to BA222 isolated from a cat in Italy but carried some traces of reassortment with human strains from Russia and other countries. Thus, full-genotype determination of rotavirus A strains in Nizhny Novgorod has clarified some questions related to their origin and evolution.
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Affiliation(s)
- Tatiana A Sashina
- Laboratory of molecular epidemiology of viral infections, I.N. Blokhina Nizhny Novgorod Research Institute of Epidemiology and Microbiology, Nizhny Novgorod, Russian Federation.
| | - E I Velikzhanina
- Laboratory of molecular epidemiology of viral infections, I.N. Blokhina Nizhny Novgorod Research Institute of Epidemiology and Microbiology, Nizhny Novgorod, Russian Federation
| | - O V Morozova
- Laboratory of molecular epidemiology of viral infections, I.N. Blokhina Nizhny Novgorod Research Institute of Epidemiology and Microbiology, Nizhny Novgorod, Russian Federation
| | - N V Epifanova
- Laboratory of molecular epidemiology of viral infections, I.N. Blokhina Nizhny Novgorod Research Institute of Epidemiology and Microbiology, Nizhny Novgorod, Russian Federation
| | - N A Novikova
- Laboratory of molecular epidemiology of viral infections, I.N. Blokhina Nizhny Novgorod Research Institute of Epidemiology and Microbiology, Nizhny Novgorod, Russian Federation
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Mabasa VV, van Zyl WB, Ismail A, Allam M, Taylor MB, Mans J. Multiple Novel Human Norovirus Recombinants Identified in Wastewater in Pretoria, South Africa by Next-Generation Sequencing. Viruses 2022; 14:v14122732. [PMID: 36560736 PMCID: PMC9788511 DOI: 10.3390/v14122732] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 11/25/2022] [Accepted: 12/02/2022] [Indexed: 12/12/2022] Open
Abstract
The genogroup II genotype 4 (GII.4) noroviruses are a major cause of viral gastroenteritis. Since the emergence of the Sydney_2012 variant, no novel norovirus GII.4 variants have been reported. The high diversity of noroviruses and periodic emergence of novel strains necessitates continuous global surveillance. The aim of this study was to assess the diversity of noroviruses in selected wastewater samples from Pretoria, South Africa (SA) using amplicon-based next-generation sequencing (NGS). Between June 2018 and August 2020, 200 raw sewage and final effluent samples were collected fortnightly from two wastewater treatment plants in Pretoria. Viruses were recovered using skimmed milk flocculation and glass wool adsorption-elution virus recovery methods and screened for noroviruses using a one-step real-time reverse-transcription PCR (RT-PCR). The norovirus BC genotyping region (570-579 bp) was amplified from detected norovirus strains and subjected to Illumina MiSeq NGS. Noroviruses were detected in 81% (162/200) of samples. The majority (89%, 89/100) of raw sewage samples were positive for at least one norovirus, compared with 73% (73/100) of final effluent samples. Overall, a total of 89 different GI and GII RdRp-capsid combinations were identified, including 51 putative novel recombinants, 34 previously reported RdRp-capsid combinations, one emerging novel recombinant and three Sanger-sequencing confirmed novel recombinants.
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Affiliation(s)
- Victor Vusi Mabasa
- Department of Medical Virology, Faculty of Health Sciences, University of Pretoria, Private Bag X323, Gezina, Pretoria 0031, South Africa
| | - Walda Brenda van Zyl
- Department of Medical Virology, Faculty of Health Sciences, University of Pretoria, Private Bag X323, Gezina, Pretoria 0031, South Africa
- National Health Laboratory Service, Tshwane Academic Division, Pretoria 0002, South Africa
| | - Arshad Ismail
- Sequencing Core Facility, National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg 2192, South Africa
- Department of Biochemistry and Microbiology, Faculty of Science, Engineering and Agriculture, University of Venda, Thohoyandou 0950, South Africa
| | - Mushal Allam
- Sequencing Core Facility, National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg 2192, South Africa
- Department of Genetics and Genomics, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain 15551, United Arab Emirates
| | - Maureen Beatrice Taylor
- Department of Medical Virology, Faculty of Health Sciences, University of Pretoria, Private Bag X323, Gezina, Pretoria 0031, South Africa
| | - Janet Mans
- Department of Medical Virology, Faculty of Health Sciences, University of Pretoria, Private Bag X323, Gezina, Pretoria 0031, South Africa
- Correspondence: ; Tel.: +27-12-319-2660
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Duong BT, Bal J, Sung HW, Yeo SJ, Park H. Molecular Analysis of the Avian H7 Influenza Viruses Circulating in South Korea during 2018-2019: Evolutionary Significance and Associated Zoonotic Threats. Viruses 2021; 13:v13112260. [PMID: 34835066 PMCID: PMC8623559 DOI: 10.3390/v13112260] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2021] [Revised: 11/04/2021] [Accepted: 11/08/2021] [Indexed: 12/18/2022] Open
Abstract
Avian influenza virus (AIV) subtypes H5 and H7, possessing the ability to mutate spontaneously from low pathogenic (LP) to highly pathogenic (HP) variants, are major concerns for enormous socio-economic losses in the poultry industry, as well as for fatal human infections. Through antigenic drift and shift, genetic reassortments of the genotypes pose serious threats of increased virulence and pathogenicity leading to potential pandemics. In this study, we isolated the H7-subtype AIVs circulating in the Republic of Korea during 2018–2019, and perform detailed molecular analysis to study their circulation, evolution, and possible emergence as a zoonotic threat. Phylogenetic and nucleotide sequence analyses of these isolates revealed their distribution into two distinct clusters, with the HA gene sharing the highest nucleotide identity with either the A/common teal/Shanghai/CM1216/2017, isolated from wild birds in Shanghai, China, or the A/duck/Shimane/2014, isolated from Japan. Mutations were found in HA (S138A (H3 numbering)), M1 (N30D and T215A), NS1 (P42S), PB2 (L89V), and PA (H266R and F277S) proteins—the mutations had previously been reported to be related to mammalian adaptation and changes in the virulence of AIVs. Taken together, the results firmly put forth the demand for routine surveillance of AIVs in wild birds to prevent possible pandemics arising from reassortant AIVs.
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Affiliation(s)
- Bao Tuan Duong
- Zoonosis Research Center, Department of Infection Biology, School of Medicine, Wonkwang University, Iksan 54538, Korea; (B.T.D.); (J.B.)
| | - Jyotiranjan Bal
- Zoonosis Research Center, Department of Infection Biology, School of Medicine, Wonkwang University, Iksan 54538, Korea; (B.T.D.); (J.B.)
| | - Haan Woo Sung
- College of Veterinary Medicine, Kangwon National University, Chuncheon-si 24341, Korea
- Correspondence: (H.W.S.); (S.-J.Y.); (H.P.)
| | - Seon-Ju Yeo
- Department of Tropical Medicine and Parasitology, Seoul National University College of Medicine, Seoul 03080, Korea
- Correspondence: (H.W.S.); (S.-J.Y.); (H.P.)
| | - Hyun Park
- Zoonosis Research Center, Department of Infection Biology, School of Medicine, Wonkwang University, Iksan 54538, Korea; (B.T.D.); (J.B.)
- Correspondence: (H.W.S.); (S.-J.Y.); (H.P.)
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8
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Nguyen ATV, Hoang VT, Sung HW, Yeo SJ, Park H. Genetic Characterization and Pathogenesis of Three Novel Reassortant H5N2 Viruses in South Korea, 2018. Viruses 2021; 13:v13112192. [PMID: 34834997 PMCID: PMC8619638 DOI: 10.3390/v13112192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 10/26/2021] [Accepted: 10/26/2021] [Indexed: 12/03/2022] Open
Abstract
The outbreaks of H5N2 avian influenza viruses have occasionally caused the death of thousands of birds in poultry farms. Surveillance during the 2018 winter season in South Korea revealed three H5N2 isolates in feces samples collected from wild birds (KNU18-28: A/Wild duck/South Korea/KNU18-28/2018, KNU18-86: A/Bean Goose/South Korea/KNU18-86/2018, and KNU18-93: A/Wild duck/South Korea/KNU18-93/2018). Phylogenetic tree analysis revealed that these viruses arose from reassortment events among various virus subtypes circulating in South Korea and other countries in the East Asia–Australasian Flyway. The NS gene of the KNU18-28 and KNU18-86 isolates was closely related to that of China’s H10N3 strain, whereas the KNU18-93 strain originated from the H12N2 strain in Japan, showing two different reassortment events and different from a low pathogenic H5N3 (KNU18-91) virus which was isolated at the same day and same place with KNU18-86 and KNU18-93. These H5N2 isolates were characterized as low pathogenic avian influenza viruses. However, many amino acid changes in eight gene segments were identified to enhance polymerase activity and increase adaptation and virulence in mice and mammals. Experiments reveal that viral replication in MDCK cells was quite high after 12 hpi, showing the ability to replicate in mouse lungs. The hematoxylin and eosin-stained (H&E) lung sections indicated different degrees of pathogenicity of the three H5N2 isolates in mice compared with that of the control H1N1 strain. The continuing circulation of these H5N2 viruses may represent a potential threat to mammals and humans. Our findings highlight the need for intensive surveillance of avian influenza virus circulation in South Korea to prevent the risks posed by these reassortment viruses to animal and public health.
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Affiliation(s)
- Anh Thi Viet Nguyen
- Zoonosis Research Center, Department of Infection Biology, School of Medicine, Wonkwang University, Iksan 54538, Korea; (A.T.V.N.); (V.T.H.)
| | - Vui Thi Hoang
- Zoonosis Research Center, Department of Infection Biology, School of Medicine, Wonkwang University, Iksan 54538, Korea; (A.T.V.N.); (V.T.H.)
| | - Haan Woo Sung
- College of Veterinary Medicine, Kangwon National University, Chuncheon 24341, Korea;
| | - Seon-Ju Yeo
- Department of Tropical Medicine and Parasitology, College of Medicine, Seoul National University, Seoul 03080, Korea
- Correspondence: (S.-J.Y.); (H.P.)
| | - Hyun Park
- Zoonosis Research Center, Department of Infection Biology, School of Medicine, Wonkwang University, Iksan 54538, Korea; (A.T.V.N.); (V.T.H.)
- Correspondence: (S.-J.Y.); (H.P.)
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9
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Hoxie I, Dennehy JJ. Rotavirus A Genome Segments Show Distinct Segregation and Codon Usage Patterns. Viruses 2021; 13:v13081460. [PMID: 34452326 PMCID: PMC8402926 DOI: 10.3390/v13081460] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 07/05/2021] [Accepted: 07/07/2021] [Indexed: 12/29/2022] Open
Abstract
Reassortment of the Rotavirus A (RVA) 11-segment dsRNA genome may generate new genome constellations that allow RVA to expand its host range or evade immune responses. Reassortment may also produce phylogenetic incongruities and weakly linked evolutionary histories across the 11 segments, obscuring reassortment-specific epistasis and changes in substitution rates. To determine the co-segregation patterns of RVA segments, we generated time-scaled phylogenetic trees for each of the 11 segments of 789 complete RVA genomes isolated from mammalian hosts and compared the segments’ geodesic distances. We found that segments 4 (VP4) and 9 (VP7) occupied significantly different tree spaces from each other and from the rest of the genome. By contrast, segments 10 and 11 (NSP4 and NSP5/6) occupied nearly indistinguishable tree spaces, suggesting strong co-segregation. Host-species barriers appeared to vary by segment, with segment 9 (VP7) presenting the weakest association with host species. Bayesian Skyride plots were generated for each segment to compare relative genetic diversity among segments over time. All segments showed a dramatic decrease in diversity around 2007 coinciding with the introduction of RVA vaccines. To assess selection pressures, codon adaptation indices and relative codon deoptimization indices were calculated with respect to different host genomes. Codon usage varied by segment with segment 11 (NSP5) exhibiting significantly higher adaptation to host genomes. Furthermore, RVA codon usage patterns appeared optimized for expression in humans and birds relative to the other hosts examined, suggesting that translational efficiency is not a barrier in RVA zoonosis.
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Affiliation(s)
- Irene Hoxie
- Biology Department, The Graduate Center, The City University of New York, New York, NY 10016, USA;
- Biology Department, Queens College, The City University of New York, Flushing, New York, NY 11367, USA
- Correspondence:
| | - John J. Dennehy
- Biology Department, The Graduate Center, The City University of New York, New York, NY 10016, USA;
- Biology Department, Queens College, The City University of New York, Flushing, New York, NY 11367, USA
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10
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Tamim S, Heylen E, Zeller M, Ranst MV, Matthijnssens J, Salman M, Aamir UB, Sharif S, Ikram A, Hasan F. Phylogenetic analysis of open reading frame of 11 gene segments of novel human-bovine reassortant RVA G6P[1] strain in Pakistan. J Med Virol 2020; 92:3179-3186. [PMID: 31696948 DOI: 10.1002/jmv.25625] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Accepted: 10/30/2019] [Indexed: 11/05/2022]
Abstract
Multiple Rotavirus A (RVA) strains are linked with gastrointestinal infections in children that fall in age bracket of 0 to 60 months. However, the problem is augmented with emergence of unique strains that reassort with RVA strains of animal origin. The study describes the sequence analysis of a rare G6P[1] rotavirus strain isolated from a less than 1 year old child, during rotavirus surveillance in Rawalpindi district, Pakistan in 2010. Extracted RNA from fecal specimen was subjected to high throughput RT-PCR for structural and nonstructural gene segments. The complete rotavirus genome of one isolate RVA/Human-wt/PAK/PAK99/2010/G6P[1] was sequenced for phylogenetic analysis to elucidate the evolutionary linkages and origin. Full genome examination of novel strain RVA/Human-wt/PAK/PAK99/2010/G6P[1] revealed the unique genotype assemblage: G6-P[1]-I2-R2-C2-M2-A3-N2-T6-E2-H1. The evolutionary analyses of VP7, VP4, NSP1 and NSP3 gene segments revealed that PAK99 clustered with bovine, or cattle-like rotavirus strains from other closely related species, in the genotypes G6, P[1], A3 and T6 respectively. Gene segments VP6, VP1, VP2, VP3, NSP2 and NSP4 all possessed the DS-1-like bovine genotype 2 and bovine (-like) RVA strains instead of RVA strains having human origin. However, the NSP5 gene was found to cluster closely with contemporary human Wa-like rotavirus strains of H1 genotype. This is the first report on bovine-human (Wa-like reassortant) genotype constellation of G6P[1] strain from a human case in Pakistan (and the second description worldwide). Our results emphasize the significance of incessant monitoring of circulating RVA strains in humans and animals for better understanding of RV evolution.
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Affiliation(s)
- Sana Tamim
- Public Health Laboratories, Department of Virology/Immunology, National Institute of Health, Islamabad, Pakistan
| | - Elisabeth Heylen
- Laboratory of Virology and Chemotherapy, KU Leuven Department of Microbiology and Immunology, Rega Institute for Medical Research, Leuven, Belgium
| | - Mark Zeller
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, California
| | - Marc Van Ranst
- Laboratory for Clinical and Epidemiological Virology, Department of Microbiology and Immunology, Rega Institute for Medical Research, KU Leuven-University of Leuven, Leuven, Belgium
| | | | - Muhammad Salman
- Public Health Laboratories, Department of Virology/Immunology, National Institute of Health, Islamabad, Pakistan
| | - Uzma Bashir Aamir
- IHP unit Health Emergencies, WHO Country Office, Islamabad, Pakistan
| | - Salman Sharif
- Public Health Laboratories, Department of Virology/Immunology, National Institute of Health, Islamabad, Pakistan
| | - Aamer Ikram
- Public Health Laboratories, Department of Virology/Immunology, National Institute of Health, Islamabad, Pakistan
| | - Fariha Hasan
- Department of Microbiology, Quaid-i-Azam University, Islamabad, Pakistan
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11
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Zhang T, Fan K, Zhang X, Xu Y, Xu J, Xu B, Li R. Diversity of avian influenza A(H5N6) viruses in wild birds in southern China. J Gen Virol 2020; 101:902-909. [PMID: 32519938 PMCID: PMC7654745 DOI: 10.1099/jgv.0.001449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Accepted: 05/22/2020] [Indexed: 11/18/2022] Open
Abstract
The predominance of H5N6 in ducks and continuous human cases have heightened its potential threat to public health in China. Therefore, the detection of emerging variants of H5N6 avian influenza viruses has become a priority for pandemic preparedness. Questions remain as to its origin and circulation within the wild bird reservoir and interactions at the wild-domestic interface. Samples were collected from migratory birds in Poyang Lake, Jiangxi Province, PR China during the routine bird ring survey in 2014-16. Phylogenetic and coalescent analyses were conducted to uncover the evolutionary relationship among viruses circulating in wild birds. Here, we report the potential origin and phylogenetic diversity of H5N6 viruses isolated from wild birds in Poyang Lake. Sequence analyses indicated that Jiangxi H5N6 viruses most likely evolved from Eurasian-derived H5Nx and H6N6 viruses through multiple reassortment events. Crucially, the diversity of the HA gene implies that these Jiangxi H5N6 viruses have diverged into two primary clades - clade 2.3.4.4 and clade 2.3.2.1 c. Phylogenetic analysis revealed two independent pathways of reassortment during 2014-16 that might have facilitated the generation of emerging variants within wild bird populations as well as inter-species infections. Our findings contribute to our understanding of the genetic diversification of H5N6 viruses in the wild bird population. These results highlight the necessity of large-scale surveillance of wild birds in the Poyang Lake area to address the threat of regional epizootic epidemics and attendant pandemics.
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Affiliation(s)
- Tao Zhang
- Ministry of Education Key Laboratory for Earth System Modelling, Department of Earth System Science, Tsinghua University, Beijing, PR China
- Centre for Healthy Cities, Institute for China Sustainable Urbanization, Tsinghua University, Beijing, PR China
| | - Kai Fan
- College of Veterinary Medicine, China Agricultural University, Beijing, PR China
| | - Xue Zhang
- College of Veterinary Medicine, China Agricultural University, Beijing, PR China
| | - Yujuan Xu
- College of Veterinary Medicine, China Agricultural University, Beijing, PR China
| | - Jian Xu
- School of Geography and Environmental Science, Ministry of Education’s Key Laboratory of Poyang Lake Wetland and Watershed Research, Jiangxi Normal University, Nanchang, Jiangxi, PR China
| | - Bing Xu
- Ministry of Education Key Laboratory for Earth System Modelling, Department of Earth System Science, Tsinghua University, Beijing, PR China
- Centre for Healthy Cities, Institute for China Sustainable Urbanization, Tsinghua University, Beijing, PR China
| | - Ruiyun Li
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, School of Public Health, Faculty of Medicine, Imperial College London, London, UK
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12
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Ye D, Ji Z, Shi H, Chen J, Shi D, Cao L, Liu J, Li M, Dong H, Jing Z, Wang X, Liu Q, Fan Q, Cong G, Zhang J, Han Y, Zhou J, Gu J, Zhang X, Feng L. Molecular characterization of an emerging reassortant mammalian orthoreovirus in China. Arch Virol 2020; 165:2367-2372. [PMID: 32757058 DOI: 10.1007/s00705-020-04712-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Accepted: 05/22/2020] [Indexed: 12/14/2022]
Abstract
Mammalian orthoreoviruses (MRVs) infect almost all mammals, and there are some reports on MRVs in China. In this study, a novel strain was identified, which was designated as HLJYC2017. The results of genetic analysis showed that MRV HLJYC2017 is a reassortant strain. According to biological information analysis, different serotypes of MRV contain specific amino acid insertions and deletions in the σ1 protein. Neutralizing antibody epitope analysis revealed partial cross-protection among MRV1, MRV2, and MRV3 isolates from China. L3 gene recombination in MRV was identified for the first time in this study. The results of this study provide valuable information on MRV reassortment and evolution.
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Affiliation(s)
- Dandan Ye
- Division of Swine Infectious Diseases, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, No. 427 Maduan Street, Nangang District, Harbin, 150001, China
| | - Zhaoyang Ji
- Division of Swine Infectious Diseases, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, No. 427 Maduan Street, Nangang District, Harbin, 150001, China
| | - Hongyan Shi
- Division of Swine Infectious Diseases, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, No. 427 Maduan Street, Nangang District, Harbin, 150001, China
| | - Jianfei Chen
- Division of Swine Infectious Diseases, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, No. 427 Maduan Street, Nangang District, Harbin, 150001, China
| | - Da Shi
- Division of Swine Infectious Diseases, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, No. 427 Maduan Street, Nangang District, Harbin, 150001, China
| | - Liyan Cao
- Division of Swine Infectious Diseases, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, No. 427 Maduan Street, Nangang District, Harbin, 150001, China
| | - Jianbo Liu
- Division of Swine Infectious Diseases, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, No. 427 Maduan Street, Nangang District, Harbin, 150001, China
| | - Mingwei Li
- Division of Swine Infectious Diseases, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, No. 427 Maduan Street, Nangang District, Harbin, 150001, China
| | - Hui Dong
- Division of Swine Infectious Diseases, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, No. 427 Maduan Street, Nangang District, Harbin, 150001, China
| | - Zhaoyang Jing
- Division of Swine Infectious Diseases, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, No. 427 Maduan Street, Nangang District, Harbin, 150001, China
| | - Xiaobo Wang
- Division of Swine Infectious Diseases, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, No. 427 Maduan Street, Nangang District, Harbin, 150001, China
| | - Qiuge Liu
- Division of Swine Infectious Diseases, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, No. 427 Maduan Street, Nangang District, Harbin, 150001, China
| | - Qianjin Fan
- Division of Swine Infectious Diseases, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, No. 427 Maduan Street, Nangang District, Harbin, 150001, China
| | - Guangyi Cong
- Division of Swine Infectious Diseases, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, No. 427 Maduan Street, Nangang District, Harbin, 150001, China
| | - Jiyu Zhang
- Division of Swine Infectious Diseases, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, No. 427 Maduan Street, Nangang District, Harbin, 150001, China
| | - Yuru Han
- Division of Swine Infectious Diseases, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, No. 427 Maduan Street, Nangang District, Harbin, 150001, China
| | - Jiyong Zhou
- Key Laboratory of Animal Virology of Ministry of Agriculture, Department of Veterinary Medicine, Zhejiang University, Hangzhou, China
| | - Jinyan Gu
- Key Laboratory of Animal Virology of Ministry of Agriculture, Department of Veterinary Medicine, Zhejiang University, Hangzhou, China.
| | - Xin Zhang
- Division of Swine Infectious Diseases, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, No. 427 Maduan Street, Nangang District, Harbin, 150001, China.
| | - Li Feng
- Division of Swine Infectious Diseases, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, No. 427 Maduan Street, Nangang District, Harbin, 150001, China.
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13
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Venkatesh D, Brouwer A, Goujgoulova G, Ellis R, Seekings J, Brown IH, Lewis NS. Regional Transmission and Reassortment of 2.3.4.4b Highly Pathogenic Avian Influenza (HPAI) Viruses in Bulgarian Poultry 2017/18. Viruses 2020; 12:v12060605. [PMID: 32492965 PMCID: PMC7354578 DOI: 10.3390/v12060605] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 05/26/2020] [Accepted: 05/28/2020] [Indexed: 11/20/2022] Open
Abstract
Between 2017 and 2018, several farms across Bulgaria reported outbreaks of H5 highly-pathogenic avian influenza (HPAI) viruses. In this study we used genomic and traditional epidemiological analyses to trace the origin and subsequent spread of these outbreaks within Bulgaria. Both methods indicate two separate incursions, one restricted to the northeastern region of Dobrich, and another largely restricted to Central and Eastern Bulgaria including places such as Plovdiv, Sliven and Stara Zagora, as well as one virus from the Western region of Vidin. Both outbreaks likely originate from different European 2.3.4.4b virus ancestors circulating in 2017. The viruses were likely introduced by wild birds or poultry trade links in 2017 and have continued to circulate, but due to lack of contemporaneous sampling and sequences from wild bird viruses in Bulgaria, the precise route and timing of introduction cannot be determined. Analysis of whole genomes indicates a complete lack of reassortment in all segments but the matrix protein gene (MP), which presents as multiple smaller clusters associated with different European 2.3.4.4b viruses. Ancestral reconstruction of host states of the hemagglutinin (HA) gene of viruses involved in the outbreaks suggests that transmission is driven by domestic ducks into galliform poultry. Thus, according to present evidence, we suggest the surveillance of domestic ducks as they are an epidemiologically relevant species for subclinical infection. Monitoring the spread due to movement between farms within regions and links to poultry production systems in European countries can help to predict and prevent future outbreaks. The 2.3.4.4b lineage which caused the largest recorded poultry epidemic in Europe continues to circulate, and the risk of further transmission by wild birds during migration remains.
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Affiliation(s)
- Divya Venkatesh
- Department of Pathobiology and Population Sciences, Royal Veterinary College, Hatfield, Hertfordshire AL9 7TA, UK;
- Correspondence:
| | - Adam Brouwer
- OIE/FAO/ International Reference Laboratory for avian influenza, swine influenza and Newcastle Disease, Animal and Plant Health Agency (APHA), Weybridge, Addlestone, Surrey KT15 3NB, UK; (A.B.); (J.S.); (I.H.B.)
| | - Gabriela Goujgoulova
- National Diagnostic Research Veterinary Medical Institute, 1231 Sofia, Bulgaria;
| | - Richard Ellis
- Surveillance and Laboratory Services Department, Animal and Plant Health Agency (APHA), Weybridge, Addlestone, Surrey KT15 3NB, UK;
| | - James Seekings
- OIE/FAO/ International Reference Laboratory for avian influenza, swine influenza and Newcastle Disease, Animal and Plant Health Agency (APHA), Weybridge, Addlestone, Surrey KT15 3NB, UK; (A.B.); (J.S.); (I.H.B.)
- Virology Department, Animal and Plant Health Agency (APHA), Weybridge, Addlestone, Surrey KT15 3NB, UK
| | - Ian H. Brown
- OIE/FAO/ International Reference Laboratory for avian influenza, swine influenza and Newcastle Disease, Animal and Plant Health Agency (APHA), Weybridge, Addlestone, Surrey KT15 3NB, UK; (A.B.); (J.S.); (I.H.B.)
| | - Nicola S. Lewis
- Department of Pathobiology and Population Sciences, Royal Veterinary College, Hatfield, Hertfordshire AL9 7TA, UK;
- OIE/FAO/ International Reference Laboratory for avian influenza, swine influenza and Newcastle Disease, Animal and Plant Health Agency (APHA), Weybridge, Addlestone, Surrey KT15 3NB, UK; (A.B.); (J.S.); (I.H.B.)
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14
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Moutelíková R, Sauer P, Dvořáková Heroldová M, Holá V, Prodělalová J. Emergence of Rare Bovine-Human Reassortant DS-1-Like Rotavirus A Strains with G8P[8] Genotype in Human Patients in the Czech Republic. Viruses 2019; 11:v11111015. [PMID: 31683946 PMCID: PMC6893433 DOI: 10.3390/v11111015] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Revised: 10/28/2019] [Accepted: 10/30/2019] [Indexed: 01/09/2023] Open
Abstract
Group A Rotaviruses (RVA) are the leading cause of acute gastroenteritis in children and a major cause of childhood mortality in low-income countries. RVAs are mostly host-specific, but interspecies transmission and reassortment between human and animal RVAs significantly contribute to their genetic diversity. We investigated the VP7 and VP4 genotypes of RVA isolated from 225 stool specimens collected from Czech patients with gastroenteritis during 2016–2019. The most abundant genotypes were G1P[8] (42.7%), G3P[8] (11.1%), G9P[8] (9.8%), G2P[4] (4.4%), G4P[8] (1.3%), G12P[8] (1.3%), and, surprisingly, G8P[8] (9.3%). Sequence analysis of G8P[8] strains revealed the highest nucleotide similarity of all Czech G8 sequences to the G8P[8] rotavirus strains that were isolated in Vietnam in 2014/2015. The whole-genome backbone of the Czech G8 strains was determined with the use of next-generation sequencing as DS-1-like. Phylogenetic analysis of all segments clustered the Czech isolates with RVA strains that were formerly described in Southeast Asia, which had emerged following genetic reassortment between bovine and human RVAs. This is the first time that bovine–human DS-1-like G8P[8] strains were detected at a high rate in human patients in Central Europe. Whether the emergence of this unusual genotype reflects the establishment of a new RVA strain in the population requires the continuous monitoring of rotavirus epidemiology.
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Affiliation(s)
| | - Pavel Sauer
- Institute of Microbiology, University Hospital Olomouc and Faculty of Medicine, Palacký University, 77900 Olomouc, Czech Republic.
| | - Monika Dvořáková Heroldová
- Microbiology Institute of Faculty of Medicine, Masaryk University Brno and University Hospital of St. Anne, 65691 Brno, Czech Republic.
| | - Veronika Holá
- Microbiology Institute of Faculty of Medicine, Masaryk University Brno and University Hospital of St. Anne, 65691 Brno, Czech Republic.
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15
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Wang L, Lanka S, Cassout D, Mateus-Pinilla NE, Li G, Wilson WC, Yoo D, Shelton P, Fredrickson RL. Inter-serotype reassortment among epizootic haemorrhagic disease viruses in the United States. Transbound Emerg Dis 2019; 66:1809-1820. [PMID: 31131970 DOI: 10.1111/tbed.13257] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Revised: 05/21/2019] [Accepted: 05/23/2019] [Indexed: 02/05/2023]
Abstract
First described in 1955 in New Jersey, epizootic haemorrhagic disease (EHD) causes a severe clinical disease in wild and domestic ruminants worldwide. Epizootic haemorrhagic disease outbreaks occur in deer populations each year from summer to late autumn. The etiological agent is EHD virus (EHDV) which is a double-stranded segmented icosahedral RNA virus. EHD virus utilizes point mutations and reassortment strategies to maintain viral fitness during infection. In 2018, EHDV serotype 2 was predominantly detected in deer in Illinois. Whole genome sequencing was conducted for two 2018 EHDV2 isolates (IL41747 and IL42218) and the sequence analyses indicated that IL42218 was a reassortant between different serotypes whereas IL41747 was a genetically stable strain. Our data suggest that multiple strains contribute to outbreaks each year.
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Affiliation(s)
- Leyi Wang
- Department of Veterinary Clinical Medicine and the Veterinary Diagnostic Laboratory, College of Veterinary Medicine, University of Illinois, Urbana, Illinois
| | - Saraswathi Lanka
- Department of Veterinary Clinical Medicine and the Veterinary Diagnostic Laboratory, College of Veterinary Medicine, University of Illinois, Urbana, Illinois
| | - Debbie Cassout
- Department of Veterinary Clinical Medicine and the Veterinary Diagnostic Laboratory, College of Veterinary Medicine, University of Illinois, Urbana, Illinois
| | - Nohra E Mateus-Pinilla
- Illinois Natural History Survey-Prairie Research Institute, University of Illinois Urbana-Champaign, Champaign, Illinois
| | - Ganwu Li
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, Iowa
| | - William C Wilson
- United States Department of Agriculture, Agricultural Research Service, Arthropod-borne Animal Diseases Research Unit, Manhattan, Kansas
| | - Dongwan Yoo
- Department of Pathobiology, College of Veterinary Medicine, University of Illinois at Urbana-Champaign, Urbana, Illinois
| | - Paul Shelton
- Illinois Department of Natural Resources, Division of Wildlife Resources, Springfield, Illinois
| | - Richard L Fredrickson
- Department of Veterinary Clinical Medicine and the Veterinary Diagnostic Laboratory, College of Veterinary Medicine, University of Illinois, Urbana, Illinois
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16
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Abstract
The H8 subtype viruses are rarely isolated from wild ducks. Shanghai is one of the important wintering or stopover sites on the East Asia-Australia Migration Flyway. An influenza virus, subtype H8N4, was firstly isolated from a common teal (Anas crecca) in Shanghai during 2017-2018 in this study. To clarify the genetic characteristics of the H8N4 virus, the whole genome sequences were analyzed. Phylogenetic analysis of the hemagglutinin and neuraminidase genes showed that they shared highest nucleotide identity (99.19%-99.64%) with the Japan duck-origin H8N4 virus collected in 2016 (A/duck/Aichi/231003/2016) and belonged to the Eurasian-like avian lineage. Six other genes of the H8N4 isolated virus were all highly similar to the corresponding genes of a wide range of AIV subtypes including H9N2, H5N7, H3N8, H1N2, H4N6 and H1N1. The results indicated that the H8N4 virus was a multiple reassortant virus. The study emphasized that the continuous surveillance of influenza virus in wild birds should be strengthened. Keywords: avian influenza virus; H8N4; phylogenetic analysis; Shanghai.
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17
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Chen PL, Hu AYC, Lin CY, Weng TC, Lai CC, Tseng YF, Cheng MC, Chia MY, Lin WC, Yeh CT, Su IJ, Lee MS. Development of American-Lineage Influenza H5N2 Reassortant Vaccine Viruses for Pandemic Preparedness. Viruses 2019; 11:v11060543. [PMID: 31212631 PMCID: PMC6631248 DOI: 10.3390/v11060543] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Revised: 06/04/2019] [Accepted: 06/05/2019] [Indexed: 11/23/2022] Open
Abstract
Novel low-pathogenic avian influenza (LPAI) H5N2 viruses hit poultry farms in Taiwan in 2003, and evolved into highly pathogenic avian influenza (HPAI) viruses in 2010. These viruses are reassortant viruses containing HA and NA genes from American-lineage H5N2 and six internal genes from local H6N1 viruses. According to a serological survey, the Taiwan H5N2 viruses can cause asymptomatic infections in poultry workers. Therefore, a development of influenza H5N2 vaccines is desirable for pandemic preparation. In this study, we employed reverse genetics to generate a vaccine virus having HA and NA genes from A/Chicken/CY/A2628/2012 (E7, LPAI) and six internal genes from a Vero cell-adapted high-growth H5N1 vaccine virus (Vero-15). The reassortant H5N2 vaccine virus, E7-V15, presented high-growth efficiency in Vero cells (512 HAU, 107.6 TCID50/mL), and passed all tests for qualification of candidate vaccine viruses. In ferret immunization, two doses of inactivated whole virus antigens (3 μg of HA protein) adjuvanted with alum could induce robust antibody response (HI titre 113.14). In conclusion, we have established reverse genetics to generate a qualified reassortant H5N2 vaccine virus for further development.
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MESH Headings
- Animals
- Antibodies, Viral/blood
- Chlorocebus aethiops
- Ferrets
- Hemagglutinin Glycoproteins, Influenza Virus/genetics
- Hemagglutinin Glycoproteins, Influenza Virus/immunology
- Humans
- Influenza A Virus, H5N2 Subtype/genetics
- Influenza A Virus, H5N2 Subtype/growth & development
- Influenza A Virus, H5N2 Subtype/immunology
- Influenza A Virus, H5N2 Subtype/isolation & purification
- Influenza Vaccines/administration & dosage
- Influenza Vaccines/genetics
- Influenza Vaccines/immunology
- Influenza Vaccines/isolation & purification
- Influenza, Human/prevention & control
- Neuraminidase/genetics
- Neuraminidase/immunology
- Reassortant Viruses/genetics
- Reassortant Viruses/growth & development
- Reassortant Viruses/immunology
- Reassortant Viruses/isolation & purification
- Reverse Genetics
- Taiwan
- Treatment Outcome
- Vaccines, Inactivated/administration & dosage
- Vaccines, Inactivated/immunology
- Vero Cells
- Viral Proteins/genetics
- Viral Proteins/immunology
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Affiliation(s)
- Po-Ling Chen
- National Institution of Infectious Diseases and Vaccinology, National Health Research Institutes (NHRI), Zhunan, Miaoli 35053, Taiwan.
- Institute of Molecular and Cellular Biology, National Tsing Hua University, Hsinchu 30013, Taiwan.
| | - Alan Yung-Chih Hu
- National Institution of Infectious Diseases and Vaccinology, National Health Research Institutes (NHRI), Zhunan, Miaoli 35053, Taiwan.
| | - Chun-Yang Lin
- National Institution of Infectious Diseases and Vaccinology, National Health Research Institutes (NHRI), Zhunan, Miaoli 35053, Taiwan.
| | - Tsai-Chuan Weng
- National Institution of Infectious Diseases and Vaccinology, National Health Research Institutes (NHRI), Zhunan, Miaoli 35053, Taiwan.
| | - Chia-Chun Lai
- National Institution of Infectious Diseases and Vaccinology, National Health Research Institutes (NHRI), Zhunan, Miaoli 35053, Taiwan.
- College of Life Science, National Tsing Hua University, Hsinchu 30013, Taiwan.
| | - Yu-Fen Tseng
- National Institution of Infectious Diseases and Vaccinology, National Health Research Institutes (NHRI), Zhunan, Miaoli 35053, Taiwan.
| | - Ming-Chu Cheng
- Department of Veterinary Medicine, College of Veterinary Medicine, National Pingtung University of Science and Technology, Pingtung 91201, Taiwan.
- Animal Health Research Institutes, Danshui, New Taipei City 25158, Taiwan.
| | - Min-Yuan Chia
- National Institution of Infectious Diseases and Vaccinology, National Health Research Institutes (NHRI), Zhunan, Miaoli 35053, Taiwan.
- Department of Veterinary Medicine, National Chung Hsing University, Taichung 40227, Taiwan.
| | - Wen-Chin Lin
- Institute of Preventive Medicine, National Defence Medical Centre, Taipei 23742, Taiwan.
| | - Chia-Tsui Yeh
- Institute of Preventive Medicine, National Defence Medical Centre, Taipei 23742, Taiwan.
| | - Ih-Jen Su
- National Institution of Infectious Diseases and Vaccinology, National Health Research Institutes (NHRI), Zhunan, Miaoli 35053, Taiwan.
| | - Min-Shi Lee
- National Institution of Infectious Diseases and Vaccinology, National Health Research Institutes (NHRI), Zhunan, Miaoli 35053, Taiwan.
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18
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Pu Z, Yang J, Shen X, Irwin DM, Shen Y. Human-isolated H7N9 obtained internal genes from duck and human influenza viruses. J Infect 2019; 78:491-503. [PMID: 30880145 DOI: 10.1016/j.jinf.2019.03.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Revised: 03/09/2019] [Accepted: 03/12/2019] [Indexed: 02/05/2023]
Affiliation(s)
- Zhiqing Pu
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
| | - Jinjin Yang
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
| | - Xuejuan Shen
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
| | - David M Irwin
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto M5S 1A8, Canada; Banting and Best Diabetes Centre, University of Toronto, Toronto M5S 1A8, Canada
| | - Yongyi Shen
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China; Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, South China Agricultural University, Guangzhou 510642, China; Shantou University Medical College, Shantou 515041, China.
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19
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Ghafouri SA, Fallah Mehrabadi MH, Talakesh SF, Hosseini H, Ziafati Z, Malekan M, Aghaeean L, Ghalyanchilangeroudi A. Full genome characterization of Iranian H5N8 highly pathogenic avian influenza virus from Hooded Crow (Corvus cornix), 2017: The first report. Comp Immunol Microbiol Infect Dis 2019; 64:73-80. [PMID: 31174704 DOI: 10.1016/j.cimid.2019.03.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2018] [Accepted: 03/04/2019] [Indexed: 11/19/2022]
Abstract
During 2014-2017 Clade 2.3.4.4 H5N8 highly pathogenic avian influenza viruses (HPAIVs) have spread worldwide. In 2016, an epidemic of HPAIV H5N8 in Iran caused mass deaths among wild birds, and several commercial poultry farms and captive bird holdings were affected and continue to experience problems. Several outbreaks were reported in 2017. One of them is related to Hooded crow (Corvus cornix) in a national park in Esfahan province in 2017. Whole genome sequencing and characterization have been done on the detected H5N8 sample. Based on HA sequencing results, it belongs to 2.3.4.4 clade, and the cleavage site is (PLREKRRKR/G). Phylogenetic analysis of the HA gene showed that the Iran 2017 H5N8 virus clustered within subgroup Russia 2016 2.3.4.4 b of group B in H5 clade 2.3.4.4 HPAIV. On the other hand, the NA gene of the virus is placed in group C of Eurasian lineage. Complete genome characterization of this virus revealed probable reassortment of the virus with East-Asian low-pathogenic influenza viruses. Furthermore, the virus possessed some phenotypic markers related to the increased potential for transmission and pathogenicity to mammals at internal segments. This study is the first full genome characterization H5N8 HPAIV in Iran. The data complete the puzzle of molecular epidemiology of H5N8 HPAIV in Iran and the region. Our study provides evidence for fast and continuing reassortment of H5 clade 2.3.4.4 viruses, that might lead to changes in virus structural and functional characteristics such as the route and method of transmission of the virus and virus infective, pathogenic and zoonotic potential.
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Affiliation(s)
| | - Mohammad Hossein Fallah Mehrabadi
- Department of Poultry Diseases, Razi Vaccine and Serum Research Institute, Agricultural Research, Education and Extension Organization (AREEO), Tehran, Iran
| | | | - Hossein Hosseini
- Department of Clinical Sciences, Faculty of Veterinary Medicine, Islamic Azad University, Karaj Branch, Karaj, Iran
| | - Zahra Ziafati
- Department of Microbiology and Immunology, Faculty of Veterinary Medicine, University of Tehran, Tehran, Iran
| | - Mohammad Malekan
- Department of Microbiology and Immunology, Faculty of Veterinary Medicine, University of Tehran, Tehran, Iran
| | - Leila Aghaeean
- Department of Microbiology and Immunology, Faculty of Veterinary Medicine, University of Tehran, Tehran, Iran
| | - Arash Ghalyanchilangeroudi
- Department of Microbiology and Immunology, Faculty of Veterinary Medicine, University of Tehran, Tehran, Iran.
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20
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Wiman Å, Enkirch T, Carnahan A, Böttiger B, Hagey TS, Hagstam P, Fält R, Brytting M. Novel influenza A(H1N2) seasonal reassortant identified in a patient sample, Sweden, January 2019. Euro Surveill 2019; 24:1900124. [PMID: 30862332 PMCID: PMC6402178 DOI: 10.2807/1560-7917.es.2019.24.9.1900124] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Accepted: 02/25/2019] [Indexed: 02/05/2023] Open
Abstract
In January 2019, a human seasonal reassortant influenza A(H1N2) virus with a novel 7:1 genetic constellation was identified in a 68-year-old female patient with suspected pneumonia. The virus harboured A(H3N2) neuraminidase and remaining genes from A(H1N1)pdm09. The patient recovered after severe illness. No additional cases have been detected. This is the second identified A(H1N2) seasonal reassortant in a human in Europe within 1 year; a previous case was detected in the Netherlands in March 2018.
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Affiliation(s)
- Åsa Wiman
- Unit for Laboratory Surveillance of Viral Pathogens and Vaccine Preventable Diseases, Department of Microbiology, the Public Health Agency of Sweden, Solna, Sweden
- Authors contributed equally to the work and share first authorship
| | - Theresa Enkirch
- Unit for Laboratory Surveillance of Viral Pathogens and Vaccine Preventable Diseases, Department of Microbiology, the Public Health Agency of Sweden, Solna, Sweden
- Authors contributed equally to the work and share first authorship
| | - AnnaSara Carnahan
- Unit for Vaccination Programmes, Department of Communicable Disease Control and Health Protection, the Public Health Agency of Sweden, Solna, Sweden
| | | | - Tove Samuelsson Hagey
- Unit for Laboratory Surveillance of Viral Pathogens and Vaccine Preventable Diseases, Department of Microbiology, the Public Health Agency of Sweden, Solna, Sweden
| | - Per Hagstam
- Regional Office of Communicable Disease Control and Prevention, Region Skåne, Malmö, Sweden
| | - Rosmarie Fält
- Regional Office of Communicable Disease Control and Prevention, Region Skåne, Malmö, Sweden
| | - Mia Brytting
- Unit for Laboratory Surveillance of Viral Pathogens and Vaccine Preventable Diseases, Department of Microbiology, the Public Health Agency of Sweden, Solna, Sweden
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21
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Souto S, Olveira JG, Alonso MC, Dopazo CP, Bandín I. Betanodavirus infection in bath-challenged Solea senegalensis juveniles: A comparative analysis of RGNNV, SJNNV and reassortant strains. J Fish Dis 2018; 41:1571-1578. [PMID: 30028012 DOI: 10.1111/jfd.12865] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Revised: 06/18/2018] [Accepted: 06/18/2018] [Indexed: 06/08/2023]
Abstract
Senegalese sole has been shown to be highly susceptible to betanodavirus infection, although virulence differences were observed between strains. To study the mechanisms involved in these differences, we have analysed the replication in brain tissue of three strains with different genotypes during 15 days after bath infection. In addition, possible portals of entry for betanodavirus into sole were investigated. The reassortant RGNNV/SJNNV and the SJNNV strain reached the brain after 1 and 2 days postinfection, respectively. Although no RGNNV replication was detected until day 3-4 postinfection, at the end of the experiment this strain yielded the highest viral load; this is in accordance with previous studies in which sole infected with the reassortant showed more acute signs and earlier mortality than the RGNNV and SJNNV strains. Differences between strains were also observed in the possible portals of entry. Thus, whereas the reassortant strain could infect sole mainly through the skin or the oral route, and, to a minor extent, through the gills, the SJNNV strain seems to enter fish only through the gills and the RGNNV strain could use all tissues indistinctly. Taken together, all these results support the hypothesis that reassortment has improved betanodavirus infectivity for sole.
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Affiliation(s)
- Sandra Souto
- Departamento de Microbiología y Parasitología, Instituto de Acuicultura, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - José G Olveira
- Departamento de Microbiología y Parasitología, Instituto de Acuicultura, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - M Carmen Alonso
- Universidad de Málaga, Departamento de Microbiología, Facultad de Ciencias, Málaga, Spain
| | - Carlos P Dopazo
- Departamento de Microbiología y Parasitología, Instituto de Acuicultura, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Isabel Bandín
- Departamento de Microbiología y Parasitología, Instituto de Acuicultura, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
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22
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Glasa M, Šoltys K, Predajňa L, Sihelská N, Nováková S, Šubr Z, Kraic J, Mihálik D. Molecular and Biological Characterisation of Turnip mosaic virus Isolates Infecting Poppy ( Papaversomniferum and P. rhoeas) in Slovakia. Viruses 2018; 10:E430. [PMID: 30110973 PMCID: PMC6116182 DOI: 10.3390/v10080430] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Revised: 08/07/2018] [Accepted: 08/14/2018] [Indexed: 11/30/2022] Open
Abstract
In recent years, the accumulated molecular data of Turnip mosaic virus (TuMV) isolates from various hosts originating from different parts of the world considerably helped to understand the genetic complexity and evolutionary history of the virus. In this work, four complete TuMV genomes (HC9, PK1, MS04, MS15) were characterised from naturally infected cultivated and wild-growing Papaver spp., hosts from which only very scarce data were available previously. Phylogenetic analyses showed the affiliation of Slovak Papaver isolates to the world-B and basal-B groups. The PK1 isolate showed a novel intra-lineage recombination pattern, further confirming the important role of recombination in the shaping of TuMV genetic diversity. Biological assays indicated that the intensity of symptoms in experimentally inoculated oilseed poppy are correlated to TuMV accumulation level in leaves. This is the first report of TuMV in poppy plants in Slovakia.
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Affiliation(s)
- Miroslav Glasa
- Institute of Virology, Biomedical Research Centre, Slovak Academy of Sciences, Dúbravská cesta 9, 845 05 Bratislava, Slovakia.
| | - Katarína Šoltys
- Comenius University Science Park, Comenius University in Bratislava, Ilkovičova 8, 841 04 Bratislava, Slovakia.
| | - Lukáš Predajňa
- Institute of Virology, Biomedical Research Centre, Slovak Academy of Sciences, Dúbravská cesta 9, 845 05 Bratislava, Slovakia.
| | - Nina Sihelská
- Institute of Virology, Biomedical Research Centre, Slovak Academy of Sciences, Dúbravská cesta 9, 845 05 Bratislava, Slovakia.
| | - Slavomíra Nováková
- Institute of Virology, Biomedical Research Centre, Slovak Academy of Sciences, Dúbravská cesta 9, 845 05 Bratislava, Slovakia.
| | - Zdeno Šubr
- Institute of Virology, Biomedical Research Centre, Slovak Academy of Sciences, Dúbravská cesta 9, 845 05 Bratislava, Slovakia.
| | - Ján Kraic
- Department of Biotechnologies, Faculty of Natural Sciences, University of Ss. Cyril and Methodius, J. Herdu 2, 917 01 Trnava, Slovakia.
- National Agriculture and Food Centre, Research Institute of Plant Production, Bratislavská cesta 122, 921 68 Piešťany, Slovakia.
| | - Daniel Mihálik
- Department of Biotechnologies, Faculty of Natural Sciences, University of Ss. Cyril and Methodius, J. Herdu 2, 917 01 Trnava, Slovakia.
- National Agriculture and Food Centre, Research Institute of Plant Production, Bratislavská cesta 122, 921 68 Piešťany, Slovakia.
- Institute of High Mountain Biology, University of Žilina, Univerzitná 8215/1, 010 26 Žilina, Slovakia.
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23
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Wang N, Sun M, Wang W, Ouyang G, Chen Z, Zhang Y, Zhao B, Wu S, Huang J, Sun H, Liao M, Jiao P. Avian Influenza (H7N9) Viruses Co-circulating among Chickens, Southern China. Emerg Infect Dis 2018; 23:2100-2102. [PMID: 29148388 PMCID: PMC5708235 DOI: 10.3201/eid2312.170782] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
In April 2017, three avian influenza (H7N9) viruses were isolated from chickens in southern China. Each virus had different insertion points in the cleavage site of the hemagglutinin protein compared to the first identified H7N9 virus. We determined that these viruses were double or triple reassortant viruses.
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24
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Beerens N, Heutink R, Bergervoet SA, Harders F, Bossers A, Koch G. Multiple Reassorted Viruses as Cause of Highly Pathogenic Avian Influenza A(H5N8) Virus Epidemic, the Netherlands, 2016. Emerg Infect Dis 2018; 23:1974-1981. [PMID: 29148396 PMCID: PMC5708218 DOI: 10.3201/eid2312.171062] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
In 2016, an epidemic of highly pathogenic avian influenza A virus subtype H5N8 in the Netherlands caused mass deaths among wild birds, and several commercial poultry farms and captive bird holdings were affected. We performed complete genome sequencing to study the relationship between the wild bird and poultry viruses. Phylogenetic analysis showed that the viruses are related to H5 clade 2.3.4.4 viruses detected in Russia in May 2016 but contained novel polymerase basic 2 and nucleoprotein gene segments and 2 different variants of the polymerase acidic segment. Molecular dating suggests that the reassortment events most likely occurred in wild birds in Russia or Mongolia. Furthermore, 2 genetically distinct H5N5 reassortant viruses were detected in wild birds in the Netherlands. Our study provides evidence for fast and continuing reassortment of H5 clade 2.3.4.4 viruses, which might lead to rapid changes in virus characteristics, such as pathogenicity, infectivity, transmission, and zoonotic potential.
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25
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Zafari E, Soleimanjahi H, Mohammadi A, Teimoori A, Mahravani H. Molecular and biological characterization of the human-bovine rotavirus-based reassortant rotavirus. Microb Pathog 2018; 121:65-69. [PMID: 29753872 DOI: 10.1016/j.micpath.2018.05.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Revised: 05/09/2018] [Accepted: 05/09/2018] [Indexed: 11/19/2022]
Abstract
Rotaviruses (RV) are the leading cause of acute infantile gastroenteritis, associated with elevated mortality in low-income countries. Morbidity and mortality, length and rates of hospitalization due to RV gastroenteritis are dropping. Improving the quality of newborns life is an ongoing challenge for health-care providers. In this study, homemade reassortant human-bovine rotavirus was developed and biological activity and molecular characterization of candidate vaccine were evaluated for the vaccine stability. Virus titration and purification of reassortant rotavirus strains were evaluated by plaque assays, electropherotyping. The genetic stability after first, third and sixth passage was by sequencing. Due to WHO recommendation, developingment of national capacity for vaccine production in appropriate quantities and at affordable prices is the cornerstone of developing global vaccination policies. Such studies are critical to producing national vaccines and modeling herd protection.
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Affiliation(s)
- Ehsan Zafari
- Department of Virology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Hoorieh Soleimanjahi
- Department of Virology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran.
| | - Ashraf Mohammadi
- Razi Vaccine and Serum Research Institute (RVSRI) Hessark Karadj, Agricultural Research, Education and Extension Organization (AREEO), Tehran, Iran
| | - Ali Teimoori
- Department of Virology, Ahwaz Joundishpor University of Medical Sciences, Ahvaz, IR Iran
| | - Homayon Mahravani
- Razi Vaccine and Serum Research Institute (RVSRI) Hessark Karadj, Agricultural Research, Education and Extension Organization (AREEO), Tehran, Iran
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26
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Bowman AS, Walia RR, Nolting JM, Vincent AL, Killian ML, Zentkovich MM, Lorbach JN, Lauterbach SE, Anderson TK, Davis CT, Zanders N, Jones J, Jang Y, Lynch B, Rodriguez MR, Blanton L, Lindstrom SE, Wentworth DE, Schiltz J, Averill JJ, Forshey T. Influenza A(H3N2) Virus in Swine at Agricultural Fairs and Transmission to Humans, Michigan and Ohio, USA, 2016. Emerg Infect Dis 2018; 23:1551-1555. [PMID: 28820376 PMCID: PMC5572863 DOI: 10.3201/eid2309.170847] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
In 2016, a total of 18 human infections with influenza A(H3N2) virus occurred after exposure to influenza-infected swine at 7 agricultural fairs. Sixteen of these cases were the result of infection by a reassorted virus with increasing prevalence among US swine containing a hemagglutinin gene from 2010–11 human seasonal H3N2 strains.
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27
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Takemae N, Nguyen PT, Le VT, Nguyen TN, To TL, Nguyen TD, Pham VP, Vo HV, Le QVT, Do HT, Nguyen DT, Uchida Y, Saito T. Appearance of reassortant European avian-origin H1 influenza A viruses of swine in Vietnam. Transbound Emerg Dis 2018; 65:1110-1116. [PMID: 29512309 DOI: 10.1111/tbed.12849] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Indexed: 11/26/2022]
Abstract
Three subtypes-H1N1, H1N2 and H3N2-of influenza A viruses of swine (IAVs-S) are currently endemic in swine worldwide, but there is considerable genotypic diversity among each subtype and limited geographical distribution. Through IAVs-S monitoring in Vietnam, two H1N2 influenza A viruses were isolated from healthy pigs in Ba Ria-Vung Tau Province, Southern Vietnam, on 2 December 2016. BLAST and phylogenetic analyses revealed that their HA and NA genes were derived from those of European avian-like H1N2 IAVs-S that contained avian-origin H1 and human-like N2 genes, and were particularly closely related to those of IAVs-S circulating in the Netherlands, Germany or Denmark. In addition, the internal genes of these Vietnamese isolates were derived from human A(H1N1)pdm09 viruses, suggesting that the Vietnamese H1N2 IAVs-S are reassortants between European H1N2 IAVs-S and human A(H1N1)pdm09v. The appearance of European avian-like H1N2 IAVs-S in Vietnam marks their first transmission outside Europe. Our results and statistical analyses of the number of live pigs imported into Vietnam suggest that the European avian-like H1N2 IAVs-S may have been introduced into Vietnam with their hosts through international trade. These findings highlight the importance of quarantining imported pigs to impede the introduction of new IAVs-S.
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Affiliation(s)
- N Takemae
- Division of Transboundary Animal Disease, National Institute of Animal Health, NARO, Tsukuba, Japan
- Thailand-Japan Zoonotic Diseases Collaboration Center, Bangkok, Thailand
| | - P T Nguyen
- Regional Animal Health Office No. 6, Department of Animal Health, Ho Chi Minh City, Vietnam
| | - V T Le
- Regional Animal Health Office No. 6, Department of Animal Health, Ho Chi Minh City, Vietnam
| | - T N Nguyen
- Epidemiology Division, Department of Animal Health, Hanoi, Vietnam
| | - T L To
- National Centre for Veterinary Diagnostics, Department of Animal Health, Hanoi, Vietnam
| | - T D Nguyen
- National Centre for Veterinary Diagnostics, Department of Animal Health, Hanoi, Vietnam
| | - V P Pham
- Regional Animal Health Office No. 6, Department of Animal Health, Ho Chi Minh City, Vietnam
| | - H V Vo
- Regional Animal Health Office No. 6, Department of Animal Health, Ho Chi Minh City, Vietnam
| | - Q V T Le
- Regional Animal Health Office No. 6, Department of Animal Health, Ho Chi Minh City, Vietnam
| | - H T Do
- National Centre for Veterinary Diagnostics, Department of Animal Health, Hanoi, Vietnam
| | - D T Nguyen
- Epidemiology Division, Department of Animal Health, Hanoi, Vietnam
| | - Y Uchida
- Division of Transboundary Animal Disease, National Institute of Animal Health, NARO, Tsukuba, Japan
- Thailand-Japan Zoonotic Diseases Collaboration Center, Bangkok, Thailand
| | - T Saito
- Division of Transboundary Animal Disease, National Institute of Animal Health, NARO, Tsukuba, Japan
- Thailand-Japan Zoonotic Diseases Collaboration Center, Bangkok, Thailand
- United Graduate School of Veterinary Sciences, Gifu University, Gifu, Japan
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28
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Kondo K, Tsugawa T, Ono M, Ohara T, Fujibayashi S, Tahara Y, Kubo N, Nakata S, Higashidate Y, Fujii Y, Katayama K, Yoto Y, Tsutsumi H. Clinical and Molecular Characteristics of Human Rotavirus G8P[8] Outbreak Strain, Japan, 2014. Emerg Infect Dis 2018; 23:968-972. [PMID: 28518031 PMCID: PMC5443423 DOI: 10.3201/eid2306.160038] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
During March–July 2014, rotavirus G8P[8] emerged as the predominant cause of rotavirus gastroenteritis among children in Hokkaido Prefecture, Japan. Clinical characteristics were similar for infections caused by G8 and non-G8 strains. Sequence and phylogenetic analyses suggest the strains were generated by multiple reassortment events between DS-1–like P[8] strains and bovine strains from Asia.
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29
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Selim AA, Erfan AM, Hagag N, Zanaty A, Samir AH, Samy M, Abdelhalim A, Arafa ASA, Soliman MA, Shaheen M, Ibraheem EM, Mahrous I, Hassan MK, Naguib MM. Highly Pathogenic Avian Influenza Virus (H5N8) Clade 2.3.4.4 Infection in Migratory Birds, Egypt. Emerg Infect Dis 2018; 23:1048-1051. [PMID: 28518040 PMCID: PMC5443452 DOI: 10.3201/eid2306.162056] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
We isolated highly pathogenic avian influenza virus (H5N8) of clade 2.3.4.4 from the common coot (Fulica atra) in Egypt, documenting its introduction into Africa through migratory birds. This virus has a close genetic relationship with subtype H5N8 viruses circulating in Europe. Enhanced surveillance to detect newly emerging viruses is warranted.
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MESH Headings
- Amino Acid Sequence
- Animal Migration/physiology
- Animals
- Animals, Wild
- Birds
- Egypt/epidemiology
- Gene Expression
- Hemagglutinin Glycoproteins, Influenza Virus/chemistry
- Hemagglutinin Glycoproteins, Influenza Virus/genetics
- Hemagglutinin Glycoproteins, Influenza Virus/metabolism
- Influenza A Virus, H5N8 Subtype/classification
- Influenza A Virus, H5N8 Subtype/genetics
- Influenza A Virus, H5N8 Subtype/isolation & purification
- Influenza A Virus, H5N8 Subtype/pathogenicity
- Influenza in Birds/epidemiology
- Influenza in Birds/transmission
- Influenza in Birds/virology
- Models, Molecular
- Mutation
- Phylogeny
- Protein Conformation, alpha-Helical
- Protein Conformation, beta-Strand
- Reassortant Viruses/classification
- Reassortant Viruses/genetics
- Reassortant Viruses/isolation & purification
- Reassortant Viruses/pathogenicity
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30
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Takemae N, Tsunekuni R, Sharshov K, Tanikawa T, Uchida Y, Ito H, Soda K, Usui T, Sobolev I, Shestopalov A, Yamaguchi T, Mine J, Ito T, Saito T. Five distinct reassortants of H5N6 highly pathogenic avian influenza A viruses affected Japan during the winter of 2016-2017. Virology 2017; 512:8-20. [PMID: 28892736 DOI: 10.1016/j.virol.2017.08.035] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Revised: 08/22/2017] [Accepted: 08/24/2017] [Indexed: 01/05/2023]
Abstract
To elucidate the evolutionary pathway, we sequenced the entire genomes of 89 H5N6 highly pathogenic avian influenza viruses (HPAIVs) isolated in Japan during winter 2016-2017 and 117 AIV/HPAIVs isolated in Japan and Russia. Phylogenetic analysis showed that at least 5 distinct genotypes of H5N6 HPAIVs affected poultry and wild birds during that period. Japanese H5N6 isolates shared a common genetic ancestor in 6 of 8 genomic segments, and the PA and NS genes demonstrated 4 and 2 genetic origins, respectively. Six gene segments originated from a putative ancestral clade 2.3.4.4 H5N6 virus that was a possible genetic reassortant among Chinese clade 2.3.4.4 H5N6 HPAIVs. In addition, 2 NS clusters and a PA cluster in Japanese H5N6 HPAIVs originated from Chinese HPAIVs, whereas 3 distinct AIV-derived PA clusters were evident. These results suggest that migratory birds were important in the spread and genetic diversification of clade 2.3.4.4 H5 HPAIVs.
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Affiliation(s)
- Nobuhiro Takemae
- Division of Transboundary Animal Disease, National Institute of Animal Health, NARO, 3-1-5 Kannondai, Tsukuba, Ibaraki 305-0856, Japan; Thailand-Japan Zoonotic Diseases Collaboration Center, Kasetklang, Chatuchak, Bangkok 10900, Thailand
| | - Ryota Tsunekuni
- Division of Transboundary Animal Disease, National Institute of Animal Health, NARO, 3-1-5 Kannondai, Tsukuba, Ibaraki 305-0856, Japan; Thailand-Japan Zoonotic Diseases Collaboration Center, Kasetklang, Chatuchak, Bangkok 10900, Thailand
| | - Kirill Sharshov
- Research Institute of Experimental and Clinical Medicine, 2, Timakova street, Novosibirsk 630117, Russia
| | - Taichiro Tanikawa
- Division of Transboundary Animal Disease, National Institute of Animal Health, NARO, 3-1-5 Kannondai, Tsukuba, Ibaraki 305-0856, Japan; Thailand-Japan Zoonotic Diseases Collaboration Center, Kasetklang, Chatuchak, Bangkok 10900, Thailand
| | - Yuko Uchida
- Division of Transboundary Animal Disease, National Institute of Animal Health, NARO, 3-1-5 Kannondai, Tsukuba, Ibaraki 305-0856, Japan; Thailand-Japan Zoonotic Diseases Collaboration Center, Kasetklang, Chatuchak, Bangkok 10900, Thailand
| | - Hiroshi Ito
- The Avian Zoonosis Research Center, Faculty of Agriculture, Tottori University, 4-101 Koyama-cho Minami, Tottori, Tottori 680-8550, Japan
| | - Kosuke Soda
- The Avian Zoonosis Research Center, Faculty of Agriculture, Tottori University, 4-101 Koyama-cho Minami, Tottori, Tottori 680-8550, Japan
| | - Tatsufumi Usui
- The Avian Zoonosis Research Center, Faculty of Agriculture, Tottori University, 4-101 Koyama-cho Minami, Tottori, Tottori 680-8550, Japan
| | - Ivan Sobolev
- Research Institute of Experimental and Clinical Medicine, 2, Timakova street, Novosibirsk 630117, Russia
| | - Alexander Shestopalov
- Research Institute of Experimental and Clinical Medicine, 2, Timakova street, Novosibirsk 630117, Russia
| | - Tsuyoshi Yamaguchi
- The Avian Zoonosis Research Center, Faculty of Agriculture, Tottori University, 4-101 Koyama-cho Minami, Tottori, Tottori 680-8550, Japan
| | - Junki Mine
- Division of Transboundary Animal Disease, National Institute of Animal Health, NARO, 3-1-5 Kannondai, Tsukuba, Ibaraki 305-0856, Japan; Thailand-Japan Zoonotic Diseases Collaboration Center, Kasetklang, Chatuchak, Bangkok 10900, Thailand
| | - Toshihiro Ito
- The Avian Zoonosis Research Center, Faculty of Agriculture, Tottori University, 4-101 Koyama-cho Minami, Tottori, Tottori 680-8550, Japan
| | - Takehiko Saito
- Division of Transboundary Animal Disease, National Institute of Animal Health, NARO, 3-1-5 Kannondai, Tsukuba, Ibaraki 305-0856, Japan; Thailand-Japan Zoonotic Diseases Collaboration Center, Kasetklang, Chatuchak, Bangkok 10900, Thailand; United Graduate School of Veterinary Sciences, Gifu University, 1-1, Yanagito, Gifu, Gifu 501-1112, Japan.
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Patil BL, Dangwal M, Mishra R. Variability of Emaravirus Species Associated with Sterility Mosaic Disease of Pigeonpea in India Provides Evidence of Segment Reassortment. Viruses 2017; 9:E183. [PMID: 28696402 PMCID: PMC5537675 DOI: 10.3390/v9070183] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Revised: 07/04/2017] [Accepted: 07/06/2017] [Indexed: 11/16/2022] Open
Abstract
Sterility mosaic disease (SMD) of pigeonpea is a serious constraint for cultivation of pigeonpea in India and other South Asian countries. SMD of pigeonpea is associated with two distinct emaraviruses, Pigeonpea sterility mosaic virus 1 (PPSMV-1) and Pigeonpea sterility mosaic virus 2 (PPSMV-2), with genomes consisting of five and six negative-sense RNA segments, respectively. The recently published genome sequences of both PPSMV-1 and PPSMV-2 are from a single location, Patancheru from the state of Telangana in India. However, here we present the first report of sequence variability among 23 isolates of PPSMV-1 and PPSMV-2, collected from ten locations representing six states of India. Both PPSMV-1 and PPSMV-2 are shown to be present across India and to exhibit considerable sequence variability. Variability of RNA3 sequences was higher than the RNA4 sequences for both PPSMV-1 and PPSMV-2. Additionally, the sixth RNA segment (RNA6), previously reported to be associated with only PPSMV-2, is also associated with isolates of PPSMV-1. Multiplex reverse transcription PCR (RT-PCR) analyses show that PPSMV-1 and PPSMV-2 frequently occur as mixed infections. Further sequence analyses indicated the presence of reassortment of RNA4 between isolates of PPSMV-1 and PPSMV-2.
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Affiliation(s)
- Basavaprabhu L Patil
- ICAR-National Research Centre on Plant Biotechnology, IARI, Pusa Campus, New Delhi 110012, India.
| | - Meenakshi Dangwal
- ICAR-National Research Centre on Plant Biotechnology, IARI, Pusa Campus, New Delhi 110012, India.
| | - Ritesh Mishra
- ICAR-National Research Centre on Plant Biotechnology, IARI, Pusa Campus, New Delhi 110012, India.
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32
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Urbaniak K, Markowska-Daniel I, Kowalczyk A, Kwit K, Pomorska-Mól M, Frącek B, Pejsak Z. Reassortment process after co-infection of pigs with avian H1N1 and swine H3N2 influenza viruses. BMC Vet Res 2017; 13:215. [PMID: 28688454 PMCID: PMC5501944 DOI: 10.1186/s12917-017-1137-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2016] [Accepted: 06/30/2017] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND The influenza A virus is highly variable, which, to some degree, is caused by the reassortment of viral genetic material. This process plays a major role in the generation of novel influenza virus strains that can emerge in a new host population. Due to the susceptibility of pigs to infections with avian, swine and human influenza viruses, they are considered intermediate hosts for the adaptation of the avian influenza virus to humans. In order to test the reassortment process in pigs, they were co-infected with H3N2 A/swine/Gent/172/2008 (Gent/08) and H1N1 A/duck/Italy/1447/2005 (Italy/05) and co-housed with a group of naïve piglets. RESULTS The Gent/08 strains dominated over Italy/05, but reassortment occurred. The reassortant strains of the H1N1 subtype (12.5%) with one gene (NP or M) of swine-origin were identified in the nasal discharge of the contact-exposed piglets. CONCLUSIONS These results demonstrate that despite their low efficiency, genotypically and phenotypically different influenza A viruses can undergo genetic exchange during co-infection of pigs.
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Affiliation(s)
- Kinga Urbaniak
- Department of Swine Diseases, National Veterinary Research Institute, 57 Partyzantów Avenue, 24-100, Puławy, Poland.
| | - Iwona Markowska-Daniel
- Department of Swine Diseases, National Veterinary Research Institute, 57 Partyzantów Avenue, 24-100, Puławy, Poland
- Present Address: Laboratory of Veterinary Epidemiology and Economics, Faculty of Veterinary Medicine, Warsaw University of Life Sciences, 159c Nowoursynowska Street, 02-776, Warsaw, Poland
| | - Andrzej Kowalczyk
- Department of Swine Diseases, National Veterinary Research Institute, 57 Partyzantów Avenue, 24-100, Puławy, Poland
- Present Address: Wrocław Research Centre EIT+, 147 Stabłowicka Street, 54-066, Wrocław, Poland
| | - Krzysztof Kwit
- Department of Swine Diseases, National Veterinary Research Institute, 57 Partyzantów Avenue, 24-100, Puławy, Poland
| | - Małgorzata Pomorska-Mól
- Department of Swine Diseases, National Veterinary Research Institute, 57 Partyzantów Avenue, 24-100, Puławy, Poland
| | - Barbara Frącek
- Department of Swine Diseases, National Veterinary Research Institute, 57 Partyzantów Avenue, 24-100, Puławy, Poland
| | - Zygmunt Pejsak
- Department of Swine Diseases, National Veterinary Research Institute, 57 Partyzantów Avenue, 24-100, Puławy, Poland
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Zhang Y, Chen M, Huang Y, Zhu W, Yang L, Gao L, Li X, Bi F, Huang C, Kang N, Zhang H, Li Z, Bo H, Wang D, Shu Y. Human infections with novel reassortant H5N6 avian influenza viruses in China. Emerg Microbes Infect 2017; 6:e50. [PMID: 28588293 PMCID: PMC5520314 DOI: 10.1038/emi.2017.38] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2017] [Revised: 03/23/2017] [Accepted: 03/28/2017] [Indexed: 11/16/2022]
Affiliation(s)
- Ye Zhang
- National Institute for Viral Disease Control and Prevention, Collaboration Innovation Center for Diagnosis and Treatment of Infectious Diseases, Chinese Center for Disease Control and Prevention, Key Laboratory for Medical Virology, National Health and Family Planning Commission, Beijing 102206, China
| | - Minmei Chen
- Guangxi Center for Disease Prevention and Control, Nanning 530028, China
| | - Yiwei Huang
- Hunan Provincial Center for Disease Control and Prevention, Changsha 410005, China
| | - Wenfei Zhu
- National Institute for Viral Disease Control and Prevention, Collaboration Innovation Center for Diagnosis and Treatment of Infectious Diseases, Chinese Center for Disease Control and Prevention, Key Laboratory for Medical Virology, National Health and Family Planning Commission, Beijing 102206, China
| | - Lei Yang
- National Institute for Viral Disease Control and Prevention, Collaboration Innovation Center for Diagnosis and Treatment of Infectious Diseases, Chinese Center for Disease Control and Prevention, Key Laboratory for Medical Virology, National Health and Family Planning Commission, Beijing 102206, China
| | - Lidong Gao
- Hunan Provincial Center for Disease Control and Prevention, Changsha 410005, China
| | - Xiaodan Li
- National Institute for Viral Disease Control and Prevention, Collaboration Innovation Center for Diagnosis and Treatment of Infectious Diseases, Chinese Center for Disease Control and Prevention, Key Laboratory for Medical Virology, National Health and Family Planning Commission, Beijing 102206, China
| | - Fuyin Bi
- Guangxi Center for Disease Prevention and Control, Nanning 530028, China
| | - Chaoyang Huang
- Hunan Provincial Center for Disease Control and Prevention, Changsha 410005, China
| | - Ning Kang
- Guangxi Center for Disease Prevention and Control, Nanning 530028, China
| | - Hengjiao Zhang
- Hunan Provincial Center for Disease Control and Prevention, Changsha 410005, China
| | - Zi Li
- National Institute for Viral Disease Control and Prevention, Collaboration Innovation Center for Diagnosis and Treatment of Infectious Diseases, Chinese Center for Disease Control and Prevention, Key Laboratory for Medical Virology, National Health and Family Planning Commission, Beijing 102206, China
| | - Hong Bo
- National Institute for Viral Disease Control and Prevention, Collaboration Innovation Center for Diagnosis and Treatment of Infectious Diseases, Chinese Center for Disease Control and Prevention, Key Laboratory for Medical Virology, National Health and Family Planning Commission, Beijing 102206, China
| | - Dayan Wang
- National Institute for Viral Disease Control and Prevention, Collaboration Innovation Center for Diagnosis and Treatment of Infectious Diseases, Chinese Center for Disease Control and Prevention, Key Laboratory for Medical Virology, National Health and Family Planning Commission, Beijing 102206, China
| | - Yuelong Shu
- National Institute for Viral Disease Control and Prevention, Collaboration Innovation Center for Diagnosis and Treatment of Infectious Diseases, Chinese Center for Disease Control and Prevention, Key Laboratory for Medical Virology, National Health and Family Planning Commission, Beijing 102206, China
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Kim YI, Park SJ, Kwon HI, Kim EH, Si YJ, Jeong JH, Lee IW, Nguyen HD, Kwon JJ, Choi WS, Song MS, Kim CJ, Choi YK. Genetic and phylogenetic characterizations of a novel genotype of highly pathogenic avian influenza (HPAI) H5N8 viruses in 2016/2017 in South Korea. Infect Genet Evol 2017; 53:56-67. [PMID: 28477974 DOI: 10.1016/j.meegid.2017.05.001] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Revised: 04/24/2017] [Accepted: 05/03/2017] [Indexed: 11/30/2022]
Abstract
During the outbreaks of highly pathogenic avian influenza (HPAI) H5N6 viruses in 2016 in South Korea, novel H5N8 viruses were also isolated from migratory birds. Phylogenetic analysis revealed that the HA gene of these H5N8 viruses belonged to clade 2.3.4.4, similarly to recent H5Nx viruses, and originated from A/Brk/Korea/Gochang1/14(H5N8), a minor lineage of H5N8 that appeared in 2014 and then disappeared. At least four reassortment events occurred with different subtypes (H5N8, H7N7, H3N8 and H10N7) and a chicken challenge study revealed that they were classified as HPAI viruses according to OIE criteria.
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MESH Headings
- Animals
- Animals, Wild
- Birds/virology
- Chickens
- Disease Outbreaks/veterinary
- Genotype
- Hemagglutinin Glycoproteins, Influenza Virus/genetics
- Influenza A Virus, H10N7 Subtype/classification
- Influenza A Virus, H10N7 Subtype/genetics
- Influenza A Virus, H10N7 Subtype/isolation & purification
- Influenza A Virus, H3N8 Subtype/classification
- Influenza A Virus, H3N8 Subtype/genetics
- Influenza A Virus, H3N8 Subtype/isolation & purification
- Influenza A Virus, H5N8 Subtype/classification
- Influenza A Virus, H5N8 Subtype/genetics
- Influenza A Virus, H5N8 Subtype/isolation & purification
- Influenza A Virus, H7N7 Subtype/classification
- Influenza A Virus, H7N7 Subtype/genetics
- Influenza A Virus, H7N7 Subtype/isolation & purification
- Influenza in Birds/epidemiology
- Influenza in Birds/virology
- Phylogeny
- Phylogeography
- Reassortant Viruses/classification
- Reassortant Viruses/genetics
- Reassortant Viruses/isolation & purification
- Republic of Korea/epidemiology
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Affiliation(s)
- Young-Il Kim
- College of Medicine and Medical Research Institute, Chungbuk National University, Cheongju 361-763, Republic of Korea
| | - Su-Jin Park
- College of Medicine and Medical Research Institute, Chungbuk National University, Cheongju 361-763, Republic of Korea
| | - Hyeok-Il Kwon
- College of Medicine and Medical Research Institute, Chungbuk National University, Cheongju 361-763, Republic of Korea
| | - Eun-Ha Kim
- College of Medicine and Medical Research Institute, Chungbuk National University, Cheongju 361-763, Republic of Korea
| | - Young-Jae Si
- College of Medicine and Medical Research Institute, Chungbuk National University, Cheongju 361-763, Republic of Korea
| | - Ju-Hwan Jeong
- College of Medicine and Medical Research Institute, Chungbuk National University, Cheongju 361-763, Republic of Korea
| | - In-Won Lee
- College of Medicine and Medical Research Institute, Chungbuk National University, Cheongju 361-763, Republic of Korea
| | - Hiep Dinh Nguyen
- College of Medicine and Medical Research Institute, Chungbuk National University, Cheongju 361-763, Republic of Korea
| | - Jin-Jung Kwon
- College of Medicine and Medical Research Institute, Chungbuk National University, Cheongju 361-763, Republic of Korea
| | - Won Suk Choi
- College of Medicine and Medical Research Institute, Chungbuk National University, Cheongju 361-763, Republic of Korea
| | - Min-Suk Song
- College of Medicine and Medical Research Institute, Chungbuk National University, Cheongju 361-763, Republic of Korea
| | - Chul-Joong Kim
- College of Veterinary Medicine, Chungnam National University, 220 Gung-Dong, Yuseoung-Gu, DaeJeon 305-764, Republic of Korea
| | - Young-Ki Choi
- College of Medicine and Medical Research Institute, Chungbuk National University, Cheongju 361-763, Republic of Korea.
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Kandeil A, El-Shesheny R, Maatouq A, Moatasim Y, Cai Z, McKenzie P, Webby R, Kayali G, Ali MA. Novel reassortant H9N2 viruses in pigeons and evidence for antigenic diversity of H9N2 viruses isolated from quails in Egypt. J Gen Virol 2017; 98:548-562. [PMID: 27902350 PMCID: PMC5817215 DOI: 10.1099/jgv.0.000657] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Accepted: 11/10/2016] [Indexed: 12/21/2022] Open
Abstract
The endemicity of avian influenza viruses (AIVs) among Egyptian poultry represents a public health risk. Co-circulation of low pathogenic AIV H9N2 subtype with highly pathogenic AIV H5N1 subtype in Egyptian farms provides a possibility to generate novel reassortant viruses. Here, the genetic characteristics of surface glycoproteins of 59 Egyptian H9N2 viruses, isolated between 2013 and 2015, were analysed. To elucidate the potential of genetic reassortment, 10 H9N2 isolates were selected based on different avian hosts (chickens, ducks, pigeons and quails) and phylogenetic analyses of their full genome sequences were conducted. Additionally, we performed antigenic analysis to further investigate the antigenic evolution of H9N2 viruses isolated during 2011-2015. Different viral characteristics including receptor-binding affinity and drug resistance of representative Egyptian H9N2 viruses were further investigated. The surface glycoproteins of current Egyptian H9N2 viruses were closely related to viruses of the G1-like lineage isolated from Egypt. Several genetic markers that enhance virulence in poultry and transmission to humans were detected. Analysis of the full genome of 10 H9N2 isolates indicated that two pigeon isolates inherited five internal genes from Eurasian AIVs circulating in wild birds. Antigenic conservation of different Egyptian H9N2 isolates from chickens, pigeons and ducks was observed, whereas quail isolates showed antigenic drift. The Egyptian H9N2 viruses preferentially bound to the human-like receptor rather than to the avian-like receptor. Our results suggest that the endemic H9N2 viruses in Egypt contain elements that may favour avian-to-human transmission and thus represent a public health risk.
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Affiliation(s)
- Ahmed Kandeil
- Center of Scientific Excellence for Influenza Viruses, National Research Centre, Giza, Egypt
| | - Rabeh El-Shesheny
- Center of Scientific Excellence for Influenza Viruses, National Research Centre, Giza, Egypt
- Department of Infectious Diseases, St Jude Children’s Research Hospital, Memphis, TN, USA
| | - Asmaa Maatouq
- Center of Scientific Excellence for Influenza Viruses, National Research Centre, Giza, Egypt
| | - Yassmin Moatasim
- Center of Scientific Excellence for Influenza Viruses, National Research Centre, Giza, Egypt
| | | | - Pamela McKenzie
- Department of Infectious Diseases, St Jude Children’s Research Hospital, Memphis, TN, USA
| | - Richard Webby
- Department of Infectious Diseases, St Jude Children’s Research Hospital, Memphis, TN, USA
| | - Ghazi Kayali
- Department of Epidemiology, Human Genetics, and Environmental Sciences, University of Texas Health Science Center, Houston, TX, USA
- Human Link, Hazmieh, Lebanon
| | - Mohamed A Ali
- Center of Scientific Excellence for Influenza Viruses, National Research Centre, Giza, Egypt
- Environmental Research Division, National Research Centre, Dokki, Giza 12311, Egypt
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36
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Resende PC, Born PS, Matos AR, Motta FC, Caetano BC, Debur MDC, Riediger IN, Brown D, Siqueira MM. Whole-Genome Characterization of a Novel Human Influenza A(H1N2) Virus Variant, Brazil. Emerg Infect Dis 2017; 23:152-154. [PMID: 27983507 PMCID: PMC5176240 DOI: 10.3201/eid2301.161122] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
We report the characterization of a novel reassortant influenza A(H1N2) virus not previously reported in humans. Recovered from a a pig farm worker in southeast Brazil who had influenza-like illness, this virus is a triple reassortant containing gene segments from subtypes H1N2 (hemagglutinin), H3N2 (neuraminidase), and pandemic H1N1 (remaining genes).
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MESH Headings
- Adolescent
- Animal Husbandry
- Animals
- Brazil
- Female
- Genome, Viral
- Hemagglutinin Glycoproteins, Influenza Virus/genetics
- Humans
- Influenza A Virus, H1N1 Subtype/genetics
- Influenza A Virus, H1N1 Subtype/isolation & purification
- Influenza A Virus, H1N2 Subtype/genetics
- Influenza A Virus, H1N2 Subtype/isolation & purification
- Influenza A Virus, H3N2 Subtype/genetics
- Influenza A Virus, H3N2 Subtype/isolation & purification
- Influenza, Human/diagnosis
- Influenza, Human/virology
- Neuraminidase/genetics
- Orthomyxoviridae Infections/veterinary
- Orthomyxoviridae Infections/virology
- Reassortant Viruses/genetics
- Reassortant Viruses/isolation & purification
- Swine
- Swine Diseases/virology
- Workforce
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37
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Nakagomi T, Nguyen MQ, Gauchan P, Agbemabiese CA, Kaneko M, Do LP, Vu TD, Nakagomi O. Evolution of DS-1-like G1P[8] double-gene reassortant rotavirus A strains causing gastroenteritis in children in Vietnam in 2012/2013. Arch Virol 2016; 162:739-748. [PMID: 27878638 PMCID: PMC5329091 DOI: 10.1007/s00705-016-3155-6] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Accepted: 11/09/2016] [Indexed: 12/22/2022]
Abstract
Rotavirus A (RVA) strains, a leading cause of severe gastroenteritis in children worldwide, commonly possess the Wa or DS-1 genotype constellations. During a hospital-based study conducted in Hanoi, Vietnam, in the 2012-2013 rotavirus season, G1P[8] strains with a virtually identical short RNA migration pattern were detected in 20 (14%) of 141 rotavirus-positive samples. Two representatives of these strains were shown by whole-genome sequencing to be double-gene reassortants possessing the genotype constellation of G1-P[8]-I2-R2-C2-M2-A2-N2-T2-E2-H2. Sequencing and a database search revealed that these Vietnamese G1P[8] double-gene reassortant strains shared an immediate ancestor with a locally circulating G2P[4] strain in all of the inner-capsid and non-structural protein genes, whereas they were more closely related in the VP7 and VP4 genes to a Chinese G1P[8] strain and a Chinese G3P[8] strain, respectively, than to locally circulating G1P[8] strains. Despite the marked similarity between Japanese and Thai G1P[8] double-gene reassortant strains, phylogenetic analysis suggested that the Vietnamese and Japanese/Thai G1P[8] double-gene reassortant strains originated from independent reassortment events. Clinically, children infected with Vietnamese G1P[8] double-gene reassortant strains experienced severe diarrhoea, but it was not more severe than that in children infected with ordinary G1P[8] strains. In conclusion, Vietnamese G1P[8] double-gene reassortant strains originated from a locally circulating G2P[4] strain and caused severe diarrhoea, but there was no evidence of increased virulence.
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Affiliation(s)
- Toyoko Nakagomi
- Department of Molecular Epidemiology, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, 852-8523, Japan
| | - Minh Quang Nguyen
- Department of Molecular Epidemiology, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, 852-8523, Japan
- Department of Epidemiology, National Institute of Hygiene and Epidemiology, Hanoi, Vietnam
| | - Punita Gauchan
- Department of Molecular Epidemiology, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, 852-8523, Japan
| | - Chantal Ama Agbemabiese
- Department of Molecular Epidemiology, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, 852-8523, Japan
| | - Miho Kaneko
- Department of Molecular Epidemiology, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, 852-8523, Japan
| | - Loan Phuong Do
- Department of Molecular Epidemiology, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, 852-8523, Japan
- Department of Virology, National Institute of Hygiene and Epidemiology, Hanoi, Vietnam
| | - Thiem Dinh Vu
- Department of Epidemiology, National Institute of Hygiene and Epidemiology, Hanoi, Vietnam
| | - Osamu Nakagomi
- Department of Molecular Epidemiology, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, 852-8523, Japan.
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Zhang Y, Zhou J, Li X, Lu J, Qin K, Shu Y, Wang D. [The Effect of Influenza Type B Inter-lineage Reassortment on the Growth Characteristics of Influenza]. Bing Du Xue Bao 2016; 32:768-772. [PMID: 30004650] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
This study aims to research the effect of inter-lineage reassortment of type B influenza virus on its biological characteristics. The representative strains isolated in 2013~2015were selected, which included wild type viruses and inter-lineage reassortment viruses. We tested the growth curve of each virus based on the value of TCID50 at different time point. And further detected the Km value of virus to analysis the activity of neuraminidase of each virus. The growth curve of viruses in 2013 and 2014reached peak 48 hours after infection, maintained at high level until 72 hours, then the virus titer declined gradually, however the virus isolated in 2015 reached peak 24 hours after infection. The reassortment strain B/Fujian Tongan/1565/2013 has the similar growth characteristics with the wild type virus on the same year. Meanwhile the growth curve of other inter-lineage viruses in 2014 and 2015is lower than that of wild type viruses. We determined neuraminidase kinetic constants of all viruses. The reassortment strain B/Fujian Tongan/1565/2013 has the strongest affinity of neuraminidase. The results of 2014~2015virus suggest that the stronger affinity of neuraminidase of virus the better growth characteristics of virus. But the virus in 2013 is lack of such relationship between the growth characteristics and activity of neuraminidase. The neuraminidase activity and growth characteristics of inter-lineage reassortments due to surface protein gene exchange is not consistent, suggesting internal virus protein might have affected the growth characteristics of the viruses2013-2015,and pending further study.
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Abstract
Avian influenza viruses affect both poultry production and public health. A subtype H5N8 (clade 2.3.4.4) virus, following an outbreak in poultry in South Korea in January 2014, rapidly spread worldwide in 2014-2015. Our analysis of H5N8 viral sequences, epidemiological investigations, waterfowl migration, and poultry trade showed that long-distance migratory birds can play a major role in the global spread of avian influenza viruses. Further, we found that the hemagglutinin of clade 2.3.4.4 virus was remarkably promiscuous, creating reassortants with multiple neuraminidase subtypes. Improving our understanding of the circumpolar circulation of avian influenza viruses in migratory waterfowl will help to provide early warning of threats from avian influenza to poultry, and potentially human, health.
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Matsuzaki Y, Sugawara K, Furuse Y, Shimotai Y, Hongo S, Oshitani H, Mizuta K, Nishimura H. Genetic Lineage and Reassortment of Influenza C Viruses Circulating between 1947 and 2014. J Virol 2016; 90:8251-65. [PMID: 27384661 PMCID: PMC5008092 DOI: 10.1128/jvi.00969-16] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Accepted: 06/28/2016] [Indexed: 11/20/2022] Open
Abstract
Since influenza C virus was first isolated in 1947, the virus has been only occasionally isolated by cell culture; there are only four strains for which complete genome sequences are registered. Here, we analyzed a total of 106 complete genomes, ranging from the first isolate from 1947 to recent isolates from 2014, to determine the genetic lineages of influenza C virus, the reassortment events, and the rates of nucleotide substitution. The results showed that there are six lineages, named C/Taylor, C/Mississippi, C/Aichi, C/Yamagata, C/Kanagawa, and C/Sao Paulo. They contain both antigenic and genetic lineages of the hemagglutinin-esterase (HE) gene, and the internal genes PB2, PB1, P3, NP, M, and NS are divided into two major lineages, a C/Mississippi/80-related lineage and a C/Yamagata/81-related lineage. Reassortment events were found over the entire period of 68 years. Several outbreaks of influenza C virus between 1990 and 2014 in Japan consisted of reassortant viruses, suggesting that the genomic constellation is related to influenza C virus epidemics. The nucleotide sequences were highly homologous to each other. The minimum percent identity between viruses ranged from 91.1% for the HE gene to 96.1% for the M gene, and the rate of nucleotide substitution for the HE gene was the highest, at 5.20 × 10(-4) substitutions/site/year. These results indicate that reassortment is an important factor that increases the genetic diversity of influenza C virus, resulting in its ability to prevail in humans. IMPORTANCE Influenza C virus is a pathogen that causes acute respiratory illness in children and results in hospitalization of infants. We previously demonstrated (Y. Matsuzaki et al., J Clin Virol 61:87-93, 2014, http://dx.doi.org/10.1016/j.jcv.2014.06.017) that periodic epidemics of this virus occurred in Japan between 1996 and 2014 and that replacement of the dominant antigenic group occurred every several years as a result of selection by herd immunity. However, the antigenicity of the HE glycoprotein is highly stable, and antigenic drift has not occurred for at least 30 years. Here, we analyzed a total of 106 complete genomes spanning 68 years for the first time, and we found that influenza C viruses are circulating worldwide while undergoing reassortment as well as selection by herd immunity, resulting in an increased ability to prevail in humans. The results presented in this study contribute to the understanding of the evolution, including reassortment events, underlying influenza C virus epidemics.
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Affiliation(s)
- Yoko Matsuzaki
- Department of Infectious Diseases, Yamagata University Faculty of Medicine, Yamagata, Japan
| | - Kanetsu Sugawara
- Department of Infectious Diseases, Yamagata University Faculty of Medicine, Yamagata, Japan
| | - Yuki Furuse
- Department of Virology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Yoshitaka Shimotai
- Department of Infectious Diseases, Yamagata University Faculty of Medicine, Yamagata, Japan
| | - Seiji Hongo
- Department of Infectious Diseases, Yamagata University Faculty of Medicine, Yamagata, Japan
| | - Hitoshi Oshitani
- Department of Virology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Katsumi Mizuta
- Department of Microbiology, Yamagata Prefectural Institute of Public Health, Yamagata, Japan
| | - Hidekazu Nishimura
- Virus Research Center, Clinical Research Division, Sendai Medical Center, Miyagi, Japan
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Yao Y, He B, Shao Z, Yang W, Liu W, Chen X, Ye S, Chen J. [Molecular Phylogenetic Analysis of a Highly Pathogenic H5N2 Avian Influenza Virus Isolated from Duck]. Bing Du Xue Bao 2016; 32:590-596. [PMID: 30001581] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
In 2016,routine influenza virus surveillance was conducted in the live poultry markets of Wuhan, Hubei Province. An H5N2 subtype avian influenza virus(AIV)was isolated from ducks in Wuhan. The entire genome of this virus isolate was sequenced,and molecular phylogenetic analysis performed. The results indicated that the HA gene belonged to clade 2.3.4.4and contained multiple basic amino acids at the cleavage site, which is characteristic of highly pathogenic AIV. Sequence alignment revealed that the isolate shared a high degree of homology with different H5 subtype AIVs isolated from waterfowl in southern China in recent years. This isolate was likely a natural reassortant from different subtype AIVs. This study provides epidemiological evidence of influenza evolution. Continuation of molecular epidemiology studies of H5 subtype influenza viruses in live poultry markets is important for understanding their role in the variation and evolution of highly pathogenic AIVs and their potential hazardous effects on human health. Furthermore, this information is important for strengthening comprehensive AIV surveillance and control measures.
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Sonnberg S, Ducatez MF, DeBeauchamp J, Crumpton JC, Rubrum A, Sharp B, Hall RJ, Peacey M, Huang S, Webby RJ. Pandemic Seasonal H1N1 Reassortants Recovered from Patient Material Display a Phenotype Similar to That of the Seasonal Parent. J Virol 2016; 90:7647-56. [PMID: 27279619 PMCID: PMC4988147 DOI: 10.1128/jvi.00772-16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2016] [Accepted: 06/06/2016] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED We have previously shown that 11 patients became naturally coinfected with seasonal H1N1 (A/H1N1) and pandemic H1N1 (pdm/H1N1) during the Southern hemisphere winter of 2009 in New Zealand. Reassortment of influenza A viruses is readily observed during coinfection of host animals and in vitro; however, reports of reassortment occurring naturally in humans are rare. Using clinical specimen material, we show reassortment between the two coinfecting viruses occurred with high likelihood directly in one of the previously identified patients. Despite the lack of spread of these reassortants in the community, we did not find them to be attenuated in several model systems for viral replication and virus transmission: multistep growth curves in differentiated human bronchial epithelial cells revealed no growth deficiency in six recovered reassortants compared to A/H1N1 and pdm/H1N1 isolates. Two reassortant viruses were assessed in ferrets and showed transmission to aerosol contacts. This study demonstrates that influenza virus reassortants can arise in naturally coinfected patients. IMPORTANCE Reassortment of influenza A viruses is an important driver of virus evolution, but little has been done to address humans as hosts for the generation of novel influenza viruses. We show here that multiple reassortant viruses were generated during natural coinfection of a patient with pandemic H1N1 (2009) and seasonal H1N1 influenza A viruses. Though apparently fit in model systems, these reassortants did not become established in the wider population, presumably due to herd immunity against their seasonal H1 antigen.
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Affiliation(s)
| | | | | | | | - Adam Rubrum
- St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Bridgett Sharp
- St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Richard J Hall
- Institute of Environmental Science and Research, Upper Hutt, New Zealand
| | - Matthew Peacey
- Institute of Environmental Science and Research, Upper Hutt, New Zealand
| | - Sue Huang
- Institute of Environmental Science and Research, Upper Hutt, New Zealand
| | - Richard J Webby
- St. Jude Children's Research Hospital, Memphis, Tennessee, USA
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Navarro JC, Giambalvo D, Hernandez R, Auguste AJ, Tesh RB, Weaver SC, Montañez H, Liria J, Lima A, Travassos da Rosa JFS, da Silva SP, Vasconcelos JM, Oliveira R, Vianez JLSG, Nunes MRT. Isolation of Madre de Dios Virus (Orthobunyavirus; Bunyaviridae), an Oropouche Virus Species Reassortant, from a Monkey in Venezuela. Am J Trop Med Hyg 2016; 95:328-38. [PMID: 27215299 PMCID: PMC4973178 DOI: 10.4269/ajtmh.15-0679] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Accepted: 04/02/2016] [Indexed: 01/23/2023] Open
Abstract
Oropouche virus (OROV), genus Orthobunyavirus, family Bunyaviridae, is an important cause of human illness in tropical South America. Herein, we report the isolation, complete genome sequence, genetic characterization, and phylogenetic analysis of an OROV species reassortant, Madre de Dios virus (MDDV), obtained from a sick monkey (Cebus olivaceus Schomburgk) collected in a forest near Atapirire, a small rural village located in Anzoategui State, Venezuela. MDDV is one of a growing number of naturally occurring OROV species reassortants isolated in South America and was known previously only from southern Peru.
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Affiliation(s)
- Juan-Carlos Navarro
- Lab Biología de Vectores, Instituto de Zoología y Ecología Tropical, Universidad Central de Venezuela, Caracas, Venezuela. Universidad Internacional SEK, Quito, Ecuador
| | - Dileyvic Giambalvo
- Lab Biología de Vectores, Instituto de Zoología y Ecología Tropical, Universidad Central de Venezuela, Caracas, Venezuela
| | - Rosa Hernandez
- Instituto Nacional de Higiene "Rafael Rangel" (INHRR), Ciudad Universitaria, Caracas, Venezuela
| | - Albert J Auguste
- Department of Microbiology and Immunology, Institute for Human Infections and Immunity, and Department of Pathology, University of Texas Medical Branch, Galveston, Texas
| | - Robert B Tesh
- Department of Microbiology and Immunology, Institute for Human Infections and Immunity, and Department of Pathology, University of Texas Medical Branch, Galveston, Texas
| | - Scott C Weaver
- Department of Microbiology and Immunology, Institute for Human Infections and Immunity, and Department of Pathology, University of Texas Medical Branch, Galveston, Texas
| | - Humberto Montañez
- Dirección General de Salud Ambiental, Ministerio del Poder Popular para la Salud, Caracas, Venezuela
| | - Jonathan Liria
- Departamento de Biología, Facultad Experimental de Ciencias y Tecnología (FACYT), Universidad de Carabobo, Valencia, Venezuela
| | - Anderson Lima
- Center for Technological Innovation, Evandro Chagas Institute, Ministry of Health, Ananindeua, Para, Brazil
| | | | - Sandro P da Silva
- Center for Technological Innovation, Evandro Chagas Institute, Ministry of Health, Ananindeua, Para, Brazil
| | - Janaina M Vasconcelos
- Center for Technological Innovation, Evandro Chagas Institute, Ministry of Health, Ananindeua, Para, Brazil
| | - Rodrigo Oliveira
- Center for Technological Innovation, Evandro Chagas Institute, Ministry of Health, Ananindeua, Para, Brazil
| | - João L S G Vianez
- Center for Technological Innovation, Evandro Chagas Institute, Ministry of Health, Ananindeua, Para, Brazil
| | - Marcio R T Nunes
- Center for Technological Innovation, Evandro Chagas Institute, Ministry of Health, Ananindeua, Para, Brazil.
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Mandal P, Mullick S, Nayak MK, Mukherjee A, Ganguly N, Niyogi P, Panda S, Chawla-Sarkar M. Complete genotyping of unusual species A rotavirus G12P[11] and G10P[14] isolates and evidence of frequent in vivo reassortment among the rotaviruses detected in children with diarrhea in Kolkata, India, during 2014. Arch Virol 2016; 161:2773-85. [PMID: 27447463 DOI: 10.1007/s00705-016-2969-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2016] [Accepted: 07/05/2016] [Indexed: 12/17/2022]
Abstract
Species A rotaviruses (RVA) are the most important cause of acute gastroenteritis in the young of humans and many animal species globally. G1P[8], G2P[4], G3P[8], G4P[8], G9P[6/8] and G12P[6/8] are the predominantly isolated genotypes throughout the world including India. Unusual genotypes from different host species such as G5, G6, G8, G10 and G11 have also been reported in humans with low frequency. In the present study, among >650 RVA positive stool samples collected from children with diarrhea in Kolkata, India, during 2014, two isolates each of the genotype G12P[11] and G10P[14] were obtained and their genomes completely sequenced. The full genotype constellations were G12-P[11]-I1-R1-C1-M2-A1-N1-T2-E1-H1 and G12-P[11]-I1-R1-C1-M1-A5-N1-T1-E1-H1 for G12P[11] viruses, suggesting several reassortments between Wa- and DS-1-like human RVA strains, including possible reassortment of a simian NSP1 gene. The G10P[14] viruses (G10-P[14]-I2-R2-C2-M2-A11-N2-T6-E2-H3) were found to contain multiple genes closely related to RVAs of artiodactyl origin, highlighting the role of inter-host species transmissions of RVAs. From the G/P constellation of all RVA isolates, it could be concluded that approximately one quarter had likely arisen from reassortment events in vivo among RVAs of 'usual' genotypes.
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Affiliation(s)
- Paulami Mandal
- National Institute of Cholera and Enteric Diseases, Kolkata, 700010, India
| | - Satarupa Mullick
- National Institute of Cholera and Enteric Diseases, Kolkata, 700010, India
| | - Mukti Kant Nayak
- National Institute of Cholera and Enteric Diseases, Kolkata, 700010, India
| | - Anupam Mukherjee
- National Institute of Cholera and Enteric Diseases, Kolkata, 700010, India
| | | | | | - Samiran Panda
- National Institute of Cholera and Enteric Diseases, Kolkata, 700010, India
| | - Mamta Chawla-Sarkar
- Division of Virology, National Institute of Cholera and Enteric Diseases, P-33 C.I.T. Road, Scheme XM, Beliaghata, Kolkata, 700010, West Bengal, India.
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Eybpoosh S, Bahrampour A, Karamouzian M, Azadmanesh K, Jahanbakhsh F, Mostafavi E, Zolala F, Haghdoost AA. Spatio-Temporal History of HIV-1 CRF35_AD in Afghanistan and Iran. PLoS One 2016; 11:e0156499. [PMID: 27280293 PMCID: PMC4900578 DOI: 10.1371/journal.pone.0156499] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Accepted: 05/16/2016] [Indexed: 01/28/2023] Open
Abstract
HIV-1 Circulating Recombinant Form 35_AD (CRF35_AD) has an important position in the epidemiological profile of Afghanistan and Iran. Despite the presence of this clade in Afghanistan and Iran for over a decade, our understanding of its origin and dissemination patterns is limited. In this study, we performed a Bayesian phylogeographic analysis to reconstruct the spatio-temporal dispersion pattern of this clade using eligible CRF35_AD gag and pol sequences available in the Los Alamos HIV database (432 sequences available from Iran, 16 sequences available from Afghanistan, and a single CRF35_AD-like pol sequence available from USA). Bayesian Markov Chain Monte Carlo algorithm was implemented in BEAST v1.8.1. Between-country dispersion rates were tested with Bayesian stochastic search variable selection method and were considered significant where Bayes factor values were greater than three. The findings suggested that CRF35_AD sequences were genetically similar to parental sequences from Kenya and Uganda, and to a set of subtype A1 sequences available from Afghan refugees living in Pakistan. Our results also showed that across all phylogenies, Afghan and Iranian CRF35_AD sequences formed a monophyletic cluster (posterior clade credibility> 0.7). The divergence date of this cluster was estimated to be between 1990 and 1992. Within this cluster, a bidirectional dispersion of the virus was observed across Afghanistan and Iran. We could not clearly identify if Afghanistan or Iran first established or received this epidemic, as the root location of this cluster could not be robustly estimated. Three CRF35_AD sequences from Afghan refugees living in Pakistan nested among Afghan and Iranian CRF35_AD branches. However, the CRF35_AD-like sequence available from USA diverged independently from Kenyan subtype A1 sequences, suggesting it not to be a true CRF35_AD lineage. Potential factors contributing to viral exchange between Afghanistan and Iran could be injection drug networks and mass migration of Afghan refugees and labours to Iran, which calls for extensive preventive efforts.
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Affiliation(s)
- Sana Eybpoosh
- Regional Knowledge Hub, and WHO Collaborating Centre for HIV Surveillance, Institute for Futures Studies in Health, Kerman University of Medical Sciences, Kerman, Iran
| | - Abbas Bahrampour
- Modeling in Health Research Centre, Institute for Futures Studies in Health, Kerman University of Medical Sciences, Kerman, Iran
| | - Mohammad Karamouzian
- Regional Knowledge Hub, and WHO Collaborating Centre for HIV Surveillance, Institute for Futures Studies in Health, Kerman University of Medical Sciences, Kerman, Iran
- School of Population and Public Health, Faculty of Medicine, University of British Colombia, Vancouver, BC, Canada
| | | | | | - Ehsan Mostafavi
- Epidemiology Department, Pasteur Institute of Iran, Tehran, Iran
- Emerging and Reemerging Infectious Diseases Research Centre, Pasteur Institute of Iran, Akanlu, Kabudar Ahang, Hamadan, Iran
| | - Farzaneh Zolala
- Modeling in Health Research Centre, Institute for Futures Studies in Health, Kerman University of Medical Sciences, Kerman, Iran
| | - Ali Akbar Haghdoost
- Regional Knowledge Hub, and WHO Collaborating Centre for HIV Surveillance, Institute for Futures Studies in Health, Kerman University of Medical Sciences, Kerman, Iran
- * E-mail:
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Dóró R, Marton S, Bartókné AH, Lengyel G, Agócs Z, Jakab F, Bányai K. Equine-like G3 rotavirus in Hungary, 2015 - Is it a novel intergenogroup reassortant pandemic strain? Acta Microbiol Immunol Hung 2016; 63:243-55. [PMID: 27352976 DOI: 10.1556/030.63.2016.2.8] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Novel, intergenogroup reassortant G3 rotavirus strains are spreading in at least three continents: Asia, Australia, and Europe. The present study provides evidence that a closely related G3P[8] strain circulated in Hungary during 2015. Whole genome sequencing and phylogenetic analysis showed that the identified strain continues to evolve by reassortment. This observation demonstrates the genomic plasticity of the novel strain, which is thought to be a prerequisite of the success of emerging rotavirus genotypes.
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Affiliation(s)
- Renáta Dóró
- Institute for Veterinary Medical Research, Centre for Agricultural Research, Hungarian Academy of Sciences , Budapest, Hungary
| | - Szilvia Marton
- Institute for Veterinary Medical Research, Centre for Agricultural Research, Hungarian Academy of Sciences , Budapest, Hungary
| | - Anett Horváth Bartókné
- Institute for Veterinary Medical Research, Centre for Agricultural Research, Hungarian Academy of Sciences , Budapest, Hungary
| | - György Lengyel
- Medical Centre of Hungarian Defense Forces, Force Health Laboratory Institute , Budapest, Hungary
| | - Zsófia Agócs
- Combined Szent István and Szent László Hospital , Budapest, Hungary
| | - Ferenc Jakab
- János Szentágothai Research Centre, University of Pécs , Pécs, Hungary
| | - Krisztián Bányai
- Institute for Veterinary Medical Research, Centre for Agricultural Research, Hungarian Academy of Sciences , Budapest, Hungary
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Hu T, Zhao H, Zhang Y, Zhang W, Kong Q, Zhang Z, Cui Q, Qiu W, Deng B, Fan Q, Zhang F. Fatal influenza A (H5N1) virus Infection in zoo-housed Tigers in Yunnan Province, China. Sci Rep 2016; 6:25845. [PMID: 27162026 PMCID: PMC4861906 DOI: 10.1038/srep25845] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2015] [Accepted: 04/25/2016] [Indexed: 01/12/2023] Open
Abstract
From 2014 to 2015, three cases of highly pathogenic avian influenza infection occurred in zoo-housed north-east China tigers (Panthera tigris ssp.altaica) and four tigers died of respiratory distress in succession in Yunnan Province, China. We isolated and characterized three highly pathogenic avian influenza A(H5N1) viruses from these tigers. Phylogenetic analysis indicated that A/tiger /Yunnan /tig1404 /2014(H5N1) belongs to the provisional subclade 2.3.4.4e which were novel reassortant influenza A (H5N1) viruses with six internal genes from avian influenza A (H5N2) viruses. The HA gene of the isolated A/tiger /Yunnan /tig1412 /2014(H5N1) virus belongs to the subclade 2.3.2.1b. The isolated A/tiger /Yunnan /tig1508/2015 (H5N1) virus was a novel reassortant influenza A (H5N1) virus with three internal genes (PB2, PB1 and M) from H9N2 virus and belongs to the subclade 2.3.2.1c.
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Affiliation(s)
- Tingsong Hu
- Centre for Disease Control and Prevention, Chengdu Military Region, Kunming 650118, China
| | - Huanyun Zhao
- Centre for Animal Disease Control and Prevention, Yunnan Province, Kunming 650051, China
| | - Yan Zhang
- Department of Biochemistry and Molecular Biology, Fudan University Shanghai Medical College, Shanghai 200030, China
| | - Wendong Zhang
- Centre for Animal Disease Control and Prevention, Yunnan Province, Kunming 650051, China
| | - Qiang Kong
- Centre for Animal Disease Control and Prevention, Yunnan Province, Kunming 650051, China
- Yunnan Agriculture University, Kunming 650223, China
| | - Zhixiao Zhang
- Centre for Disease Control and Prevention, Chengdu Military Region, Kunming 650118, China
| | - Qinghua Cui
- Centre for Disease Control and Prevention, Chengdu Military Region, Kunming 650118, China
| | - Wei Qiu
- Centre for Disease Control and Prevention, Chengdu Military Region, Kunming 650118, China
| | - Bo Deng
- Centre for Disease Control and Prevention, Chengdu Military Region, Kunming 650118, China
| | - Quanshui Fan
- Centre for Disease Control and Prevention, Chengdu Military Region, Kunming 650118, China
| | - Fuqiang Zhang
- Centre for Disease Control and Prevention, Chengdu Military Region, Kunming 650118, China
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Qi X, Gao L, Wang X. [Naturally occurring reassortants of infectious bursal disease virus - A review]. Wei Sheng Wu Xue Bao 2016; 56:740-746. [PMID: 29727135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Infectious bursal disease virus (IBDV) is an important representative of Birnaviridae, which causes infectious bursal disease (IBD), one important immuno-suppressive and fatal disease threatening the poultry husbandry. The naturally occurring reassortants of IBDV induced new risks to disease prevention and control. Here, we reviewed the main types of the genome segments reassortants and intragenic recombination, the inherent mechanism and the biological significances were analyzed, which would give us new insights into the virus genetic evolution research and the disease control strategy.
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Ramey AM, Pearce JM, Reeves AB, Poulson RL, Dobson J, Lefferts B, Spragens K, Stallknecht DE. Surveillance for Eurasian-origin and intercontinental reassortant highly pathogenic influenza A viruses in Alaska, spring and summer 2015. Virol J 2016; 13:55. [PMID: 27036114 PMCID: PMC4815243 DOI: 10.1186/s12985-016-0511-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Accepted: 03/21/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Eurasian-origin and intercontinental reassortant highly pathogenic (HP) influenza A viruses (IAVs) were first detected in North America in wild, captive, and domestic birds during November-December 2014. Detections of HP viruses in wild birds in the contiguous United States and southern Canadian provinces continued into winter and spring of 2015 raising concerns that migratory birds could potentially disperse viruses to more northerly breeding areas where they could be maintained to eventually seed future poultry outbreaks. RESULTS We sampled 1,129 wild birds on the Yukon-Kuskokwim Delta, Alaska, one of the largest breeding areas for waterfowl in North America, during spring and summer of 2015 to test for Eurasian lineage and intercontinental reassortant HP H5 IAVs and potential progeny viruses. We did not detect HP IAVs in our sample collection from western Alaska; however, we isolated five low pathogenic (LP) viruses. Four isolates were of the H6N1 (n = 2), H6N2, and H9N2 combined subtypes whereas the fifth isolate was a mixed infection that included H3 and N7 gene segments. Genetic characterization of these five LP IAVs isolated from cackling (Branta hutchinsii; n = 2) and greater white-fronted geese (Anser albifrons; n = 3), revealed three viral gene segments sharing high nucleotide identity with HP H5 viruses recently detected in North America. Additionally, one of the five isolates was comprised of multiple Eurasian lineage gene segments. CONCLUSIONS Our results did not provide direct evidence for circulation of HP IAVs in the Yukon-Kuskokwim Delta region of Alaska during spring and summer of 2015. Prevalence and genetic characteristics of LP IAVs during the sampling period are concordant with previous findings of relatively low viral prevalence in geese during spring, non-detection of IAVs in geese during summer, and evidence for intercontinental exchange of viruses in western Alaska.
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Affiliation(s)
- Andrew M Ramey
- U.S. Geological Survey, Alaska Science Center, 4210 University Drive, Anchorage, AK, 99508, USA.
| | - John M Pearce
- U.S. Geological Survey, Alaska Science Center, 4210 University Drive, Anchorage, AK, 99508, USA
| | - Andrew B Reeves
- U.S. Geological Survey, Alaska Science Center, 4210 University Drive, Anchorage, AK, 99508, USA
| | - Rebecca L Poulson
- Southeastern Cooperative Wildlife Disease Study, Department of Population Health, College of Veterinary Medicine, 589 D. W. Brooks Drive, University of Georgia, Athens, GA, 30602, USA
| | - Jennifer Dobson
- Yukon-Kuskokwim Health Corporation, 900 Chief Eddie Hoffman Highway, Bethel, AK, 99559, USA
| | - Brian Lefferts
- Yukon-Kuskokwim Health Corporation, 900 Chief Eddie Hoffman Highway, Bethel, AK, 99559, USA
| | - Kyle Spragens
- U.S. Geological Survey, Western Ecological Research Center, San Francisco Bay Estuary, 505 Azuar Drive, Vallejo, CA, 94592, USA
- U.S. Fish and Wildlife Service, Yukon Delta National Wildlife Refuge, 807 Chief Eddie Hoffman Highway, Bethel, AK, 99559, USA
| | - David E Stallknecht
- Southeastern Cooperative Wildlife Disease Study, Department of Population Health, College of Veterinary Medicine, 589 D. W. Brooks Drive, University of Georgia, Athens, GA, 30602, USA
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Dong H, Qian Y, Nong Y, Zhang Y, Mo Z, Li R. [Genomic Characterization of an Unusual Human G3P[3] Rotavirus with Multiple Cross-species Reassortment]. Bing Du Xue Bao 2016; 32:129-140. [PMID: 27396154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
One unusual human G3P[3] group A rotavirus (RVA) strain M2-102 was identified in stool sample collected from a child with diarrhea in Guangxi Province, China in 2014. It is well known that G3P[3] is a genotype commonly identified in feline and canine RVAs. However, the preliminary phylogenetic analyses of the VP7 and VP4 genes of strain M2-102 indicated that these two genes were closely related to bat RVA strain MYAS33 and simian strain RRV, respectively, whereas both clustered distantly to feline/canine-like RVA strains. In this study, full genome sequencing and molecular analyses were conducted to obtain the true origin of strain M2-102. It was revealed that strain RVA/Human-wt/CHN/M2-102/2014/G3P[3] exhibited a G3-P[3]-I3-R3-C3-M3-A9-N3-T3-E3-H6 genotype constellation for VP7-VP4-VP6-VP1-VP2-VP3-NSP1-NSP2-NSP3-NSP4-NSP5 genes. Phylogenetic analyses revealed that 5 genes (VP7, VP1, VP2, NSP2 and NSP3) from strain M2-102 were closely related to those of bat strain MYAS33 from Yunnan Province which was thought a true bat RVA strain rather than a virus transmitted between species, while another 5 genes (VP4, VP3, NSP1, NSP4 and NSP5) clustered closely with those of simian strain RRV, yet the VP6 gene was closely related to that of human G3P[9] strain AU-1 and AU-1-like RVAs. The epidemiological data indicated that the child infected with M2-102 came from a countryside village, located in Dong Autonomous County of Sanjiang (subtropical hilly wooded area), Liuzhou city in Guangxi Province which might provide natural environment for reassortment events occurring among animal and human RVAs. Therefore, the data suggest that human strain M2-102 might originate from multiple reassortment events among bat, simian and human AU-1-like RVAs, yet it is not clear whether the genomic backbone based on bat MYAS33 (5 genes) and simian RRV (5 genes) like rotaviruses had been obtained through reassortment before being transmitted to the human. This is the first report on whole genome analysis of human G3P[3] RVA from China.
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