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Ciuoderis K, Usuga J, Pérez-Restrepo LS, Gonzalez-Ramirez M, Carvajal L, Cardona A, Moreno I, Diaz A, Peña M, Hernández-Ortiz JP, Osorio JE. Genomic diversity and evolutionary dynamics of Influenza A viruses in Colombian swine: implications for one health surveillance and control. Emerg Microbes Infect 2024; 13:2368202. [PMID: 38970562 PMCID: PMC11229761 DOI: 10.1080/22221751.2024.2368202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2024] [Accepted: 06/10/2024] [Indexed: 07/08/2024]
Abstract
Influenza A viruses (IAV) impose significant respiratory disease burdens in both swine and humans worldwide, with frequent human-to-swine transmission driving viral evolution in pigs and highlighting the risk at the animal-human interface. Therefore, a comprehensive One Health approach (interconnection among human, animal, and environmental health) is needed for IAV prevention, control, and response. Animal influenza genomic surveillance remains limited in many Latin American countries, including Colombia. To address this gap, we genetically characterized 170 swine specimens from Colombia (2011-2017). Whole genome sequencing revealed a predominance of pandemic-like H1N1 lineage, with a minority belonging to H3N2 and H1N2 human seasonal-like lineage and H1N1 early classical swine lineages. Significantly, we have identified reassortant and recombinant viruses (H3N2, H1N1) not previously reported in Colombia. This suggests a broad genotypic viral diversity, likely resulting from reassortment between classical endemic viruses and new introductions established in Colombia's swine population (e.g. the 2009 H1N1 pandemic). Our study highlights the importance of a One Health approach in disease control, particularly in an ecosystem where humans are a main source of IAV to swine populations, and emphasizes the need for continued surveillance and enhanced biosecurity measures. The co-circulation of multiple subtypes in regions with high swine density facilitates viral exchange, underscoring the importance of monitoring viral evolution to inform vaccine selection and public health policies locally and globally.
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MESH Headings
- Animals
- Swine
- Colombia/epidemiology
- Orthomyxoviridae Infections/virology
- Orthomyxoviridae Infections/veterinary
- Orthomyxoviridae Infections/epidemiology
- Swine Diseases/virology
- Swine Diseases/epidemiology
- Influenza A Virus, H3N2 Subtype/genetics
- Influenza A Virus, H3N2 Subtype/classification
- Influenza A Virus, H3N2 Subtype/isolation & purification
- Influenza A Virus, H1N1 Subtype/genetics
- Influenza A Virus, H1N1 Subtype/classification
- Influenza A Virus, H1N1 Subtype/isolation & purification
- Evolution, Molecular
- Genetic Variation
- Phylogeny
- One Health
- Humans
- Influenza A virus/genetics
- Influenza A virus/classification
- Influenza A virus/isolation & purification
- Whole Genome Sequencing
- Genome, Viral
- Epidemiological Monitoring
- Reassortant Viruses/genetics
- Reassortant Viruses/classification
- Reassortant Viruses/isolation & purification
- Influenza A Virus, H1N2 Subtype/genetics
- Influenza A Virus, H1N2 Subtype/isolation & purification
- Influenza A Virus, H1N2 Subtype/classification
- Influenza, Human/virology
- Influenza, Human/epidemiology
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Affiliation(s)
- Karl Ciuoderis
- GHI One Health Colombia, Universidad Nacional de Colombia, Medellín, Colombia
| | - Jaime Usuga
- GHI One Health Colombia, Universidad Nacional de Colombia, Medellín, Colombia
| | | | | | - Leidi Carvajal
- GHI One Health Colombia, Universidad Nacional de Colombia, Medellín, Colombia
| | - Andrés Cardona
- GHI One Health Colombia, Universidad Nacional de Colombia, Medellín, Colombia
| | - Isabel Moreno
- GHI One Health Colombia, Universidad Nacional de Colombia, Medellín, Colombia
| | - Andrés Diaz
- Pig Improvement Company, Hendersonville, NC, USA
| | - Mario Peña
- PorkColombia Association, Bogotá, Colombia
| | - Juan P. Hernández-Ortiz
- GHI One Health Colombia, Universidad Nacional de Colombia, Medellín, Colombia
- Faculty of Life Sciences, Universidad Nacional de Colombia, Medellín, Colombia
| | - Jorge E. Osorio
- GHI One Health Colombia, Universidad Nacional de Colombia, Medellín, Colombia
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin, Madison, WI, USA
- Global Health Institute, University of Wisconsin, Madison, WI, USA
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He CQ, Kong C, He M, Chen GX, Liu SM, Ding NZ. Intrasegmental recombination as an evolutionary force of Lassa fever virus. Front Microbiol 2024; 15:1411537. [PMID: 38832113 PMCID: PMC11144899 DOI: 10.3389/fmicb.2024.1411537] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Accepted: 04/29/2024] [Indexed: 06/05/2024] Open
Abstract
Lassa fever (LF), caused by Lassa virus (LASV), is one of the most dangerous diseases to public health. Homologous recombination (HR) is a basic genetic power driving biological evolution. However, as a negative-stranded RNA virus, it is unknown whether HR occurs between LASVs and its influence on the outbreak of LF. In this study, after analyzing 575 S and 433 L segments of LASV collected in Africa, we found that LASV can achieve HR in both of its segments. Interestingly, although the length of S segment is less than half of the L segment, the proportion of LASVs with S recombinants is significantly higher than that with L recombinants. These results suggest that HR may be a feature of LASV, which can be set by natural selection to produce beneficial or eliminate harmful mutations for the virus, so it plays a role in LASV evolution during the outbreak of LF.
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Affiliation(s)
- Cheng-Qiang He
- Shandong Provincial Key Laboratory of Animal Resistance Biology, College of Life Science, Shandong Normal University, Jinan, China
| | | | | | | | | | - Nai-Zheng Ding
- Shandong Provincial Key Laboratory of Animal Resistance Biology, College of Life Science, Shandong Normal University, Jinan, China
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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] [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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Deviatkin AA, Simonov RA, Trutneva KA, Maznina AA, Khavina EM, Volchkov PY. Universal Flu mRNA Vaccine: Promises, Prospects, and Problems. Vaccines (Basel) 2022; 10:vaccines10050709. [PMID: 35632465 PMCID: PMC9145388 DOI: 10.3390/vaccines10050709] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 04/26/2022] [Accepted: 04/28/2022] [Indexed: 02/05/2023] Open
Abstract
The seasonal flu vaccine is, essentially, the only known way to prevent influenza epidemics. However, this approach has limited efficacy due to the high diversity of influenza viruses. Several techniques could potentially overcome this obstacle. A recent first-in-human study of a chimeric hemagglutinin-based universal influenza virus vaccine demonstrated promising results. The coronavirus pandemic triggered the development of fundamentally new vaccine platforms that have demonstrated their effectiveness in humans. Currently, there are around a dozen messenger RNA and self-amplifying RNA flu vaccines in clinical or preclinical trials. However, the applicability of novel approaches for a universal influenza vaccine creation remains unclear. The current review aims to cover the current state of this problem and to suggest future directions for RNA-based flu vaccine development.
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Affiliation(s)
- Andrei A. Deviatkin
- The National Medical Research Center for Endocrinology, 117036 Moscow, Russia; (A.A.D.); (K.A.T.)
- Genome Engineering Lab, Life Sciences Research Center, Moscow Institute of Physics and Technology (National Research University), 141700 Dolgoprudniy, Russia; (R.A.S.); (A.A.M.); (E.M.K.)
| | - Ruslan A. Simonov
- Genome Engineering Lab, Life Sciences Research Center, Moscow Institute of Physics and Technology (National Research University), 141700 Dolgoprudniy, Russia; (R.A.S.); (A.A.M.); (E.M.K.)
| | - Kseniya A. Trutneva
- The National Medical Research Center for Endocrinology, 117036 Moscow, Russia; (A.A.D.); (K.A.T.)
- Genome Engineering Lab, Life Sciences Research Center, Moscow Institute of Physics and Technology (National Research University), 141700 Dolgoprudniy, Russia; (R.A.S.); (A.A.M.); (E.M.K.)
| | - Anna A. Maznina
- Genome Engineering Lab, Life Sciences Research Center, Moscow Institute of Physics and Technology (National Research University), 141700 Dolgoprudniy, Russia; (R.A.S.); (A.A.M.); (E.M.K.)
| | - Elena M. Khavina
- Genome Engineering Lab, Life Sciences Research Center, Moscow Institute of Physics and Technology (National Research University), 141700 Dolgoprudniy, Russia; (R.A.S.); (A.A.M.); (E.M.K.)
| | - Pavel Y. Volchkov
- The National Medical Research Center for Endocrinology, 117036 Moscow, Russia; (A.A.D.); (K.A.T.)
- Genome Engineering Lab, Life Sciences Research Center, Moscow Institute of Physics and Technology (National Research University), 141700 Dolgoprudniy, Russia; (R.A.S.); (A.A.M.); (E.M.K.)
- Correspondence:
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5
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Abstract
Because of their replication mode and segmented dsRNA genome, homologous recombination is assumed to be rare in the rotaviruses. We analyzed 23,627 complete rotavirus genome sequences available in the NCBI Virus Variation database, and found 109 instances of homologous recombination, at least eleven of which prevailed across multiple sequenced isolates. In one case, recombination may have generated a novel rotavirus VP1 lineage. We also found strong evidence for intergenotypic recombination in which more than one sequence strongly supported the same event, particularly between different genotypes of segment 9, which encodes the glycoprotein, VP7. The recombined regions of many putative recombinants showed amino acid substitutions differentiating them from their major and minor parents. This finding suggests that these recombination events were not overly deleterious, since presumably these recombinants proliferated long enough to acquire adaptive mutations in their recombined regions. Protein structural predictions indicated that, despite the sometimes substantial amino acid replacements resulting from recombination, the overall protein structures remained relatively unaffected. Notably, recombination junctions appear to occur nonrandomly with hot spots corresponding to secondary RNA structures, a pattern seen consistently across segments. In total, we found strong evidence for recombination in nine of eleven rotavirus A segments. Only segments 7 (NSP3) and 11 (NSP5) did not show strong evidence of recombination. Collectively, the results of our computational analyses suggest that, contrary to the prevailing sentiment, recombination may be a significant driver of rotavirus evolution and may influence circulating strain diversity.
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Affiliation(s)
- Irene Hoxie
- Biology Department, Queens College of The City University of New York, 65-30 Kissena Blvd, Queens, NY 11367, USA.,The Graduate Center of The City University of New York, Biology Program, 365 5th Ave, New York, NY 10016, USA
| | - John J Dennehy
- Biology Department, Queens College of The City University of New York, 65-30 Kissena Blvd, Queens, NY 11367, USA.,The Graduate Center of The City University of New York, Biology Program, 365 5th Ave, New York, NY 10016, USA
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6
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Soli R, Kaabi B, Barhoumi M, Maktouf C, Ahmed SBH. Bayesian phylogenetic analysis of the influenza-A virus genomes isolated in Tunisia, and determination of potential recombination events. Mol Phylogenet Evol 2019; 134:253-268. [DOI: 10.1016/j.ympev.2019.01.019] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Revised: 12/27/2018] [Accepted: 01/22/2019] [Indexed: 11/24/2022]
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7
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Esmaelizad M, Mayahi V. Analysis of natural recombination and host-related evolutionary dynamics of avian avulavirus 1 isolates based on positive and negative selection from 1948 to 2017. Arch Virol 2019; 164:717-724. [DOI: 10.1007/s00705-018-04130-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Accepted: 11/08/2018] [Indexed: 12/26/2022]
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8
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Xiang D, Shen X, Pu Z, Irwin DM, Liao M, Shen Y. Convergent Evolution of Human-Isolated H7N9 Avian Influenza A Viruses. J Infect Dis 2018; 217:1699-1707. [PMID: 29438519 DOI: 10.1093/infdis/jiy082] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Accepted: 02/08/2018] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND Avian influenza A virus H7N9 has caused 5 epidemic waves of human infections in China since 2013. Avian influenza A viruses may face strong selection to adapt to novel conditions when establishing themselves in humans. In this study, we sought to determine whether adaptive evolution had occurred in human-isolated H7N9 viruses. METHODS We evaluated all available genomes of H7N9 avian influenza A virus. Maximum likelihood trees were separately reconstructed for all 8 genes. Signals of positive selection and convergent evolution were then detected on branches that lead to changes in host tropism (from avian to human). RESULTS We found that 3 genes had significant signals of positive selection (all of them P < .05). In addition, we detected 34 sites having significant signals for parallel evolution in 8 genes (all of them P < .05), including 7 well-known sites (Q591K, E627K, and D701N in PB2 gene; R156K, V202A, and L244Q in HA; and R289K in NA) that play roles in crossing species barriers for avian influenza A viruses. CONCLUSION Our study suggests that, during infection in humans, H7N9 viruses have undergone adaptive evolution to adapt to their new host environment and that the sites where parallel evolution occurred might play roles in crossing species barriers and respond to the new selection pressures arising from their new host environments.
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Affiliation(s)
- Dan Xiang
- College of Veterinary Medicine, South China Agricultural University, Guangzhou
- Shantou University Medical College, Guangzhou, China
| | - Xuejuan Shen
- College of Veterinary Medicine, South China Agricultural University, Guangzhou
| | - Zhiqing Pu
- College of Veterinary Medicine, South China Agricultural University, Guangzhou
| | - David M Irwin
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Canada
- Banting and Best Diabetes Centre, University of Toronto, Canada
| | - Ming Liao
- College of Veterinary Medicine, South China Agricultural University, Guangzhou
- Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, Guangzhou, China
| | - Yongyi Shen
- College of Veterinary Medicine, South China Agricultural University, Guangzhou
- Shantou University Medical College, Guangzhou, China
- Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, Guangzhou, China
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9
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Evolution of Influenza A Virus by Mutation and Re-Assortment. Int J Mol Sci 2017; 18:ijms18081650. [PMID: 28783091 PMCID: PMC5578040 DOI: 10.3390/ijms18081650] [Citation(s) in RCA: 188] [Impact Index Per Article: 26.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2017] [Revised: 07/20/2017] [Accepted: 07/24/2017] [Indexed: 12/13/2022] Open
Abstract
Influenza A virus (IAV), a highly infectious respiratory pathogen, has continued to be a significant threat to global public health. To complete their life cycle, influenza viruses have evolved multiple strategies to interact with a host. A large number of studies have revealed that the evolution of influenza A virus is mainly mediated through the mutation of the virus itself and the re-assortment of viral genomes derived from various strains. The evolution of influenza A virus through these mechanisms causes worldwide annual epidemics and occasional pandemics. Importantly, influenza A virus can evolve from an animal infected pathogen to a human infected pathogen. The highly pathogenic influenza virus has resulted in stupendous economic losses due to its morbidity and mortality both in human and animals. Influenza viruses fall into a category of viruses that can cause zoonotic infection with stable adaptation to human, leading to sustained horizontal transmission. The rapid mutations of influenza A virus result in the loss of vaccine optimal efficacy, and challenge the complete eradication of the virus. In this review, we highlight the current understanding of influenza A virus evolution caused by the mutation and re-assortment of viral genomes. In addition, we discuss the specific mechanisms by which the virus evolves.
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De A, Sarkar T, Nandy A. Bioinformatics studies of Influenza A hemagglutinin sequence data indicate recombination-like events leading to segment exchanges. BMC Res Notes 2016; 9:222. [PMID: 27083561 PMCID: PMC4832483 DOI: 10.1186/s13104-016-2017-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Accepted: 03/31/2016] [Indexed: 01/14/2023] Open
Abstract
BACKGROUND The influenza genome is highly variable due primarily to two mechanisms: antigenic drift and antigenic shift. A third mechanism for genetic change, known as copy choice or template switching, can arise during replication when, if two viral strains infect a cell, a part of a gene from the second viral strain can be copied into the growing progeny of a gene of the first viral strain as replacement leading to a new variety of the virus. This template switching between the same genes of the two strains is known as homologous recombination. While genetic drift and shift are well-understood, the presence or absence of intra-segment homologous recombination in influenza genomes is controversial. CONTEXT AND PURPOSE OF STUDY We are interested to study the possibility of subunit-wise homologous recombination. The idea is that where well-defined subunits are separated by consensus sequences, it might be possible for template switching to take place at such junctions. The influenza hemagglutinin gene has basically two subunits, HA1 and HA2, with HA1 being mostly surface exposed and containing the active site for binding to cells, while HA2 secures the hemagglutinin to the viral coat. We undertook a thorough search of the major human infecting influenza hemagglutinin gene sequences, viz., the H1N1, H5N1, H3N2 and H7N9 subtypes, over the period 2010-2014 in Asia to determine if certain sequences could be identified that had HA1 from a previous strain and HA2 from another. RESULTS Our search yielded several instances where sequence identities between segments of various strains could be interpreted as indicating possibilities of segment exchange. In some cases, on closer examination they turn out to differ by a few mutations in each segment, due perhaps to the short time span of our database. CONCLUSIONS AND POTENTIAL IMPLICATIONS The study reported here, and in combination with our earlier observations on the neuraminidase, shows that subunit-wise recombination-like events in the influenza genes may be occurring more often than have been accounted for and merits further detailed studies.
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Affiliation(s)
- Antara De
- Centre for Interdisciplinary Research and Education, 404B Jodhpur Park, Kolkata, 700068, India.
| | - Tapati Sarkar
- Physics Department, Jadavpur University, Jadavpur, Kolkata, 700032, India
| | - Ashesh Nandy
- Centre for Interdisciplinary Research and Education, 404B Jodhpur Park, Kolkata, 700068, India
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11
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Chen L, Sun L, Li R, Chen Y, Zhang Z, Xiong C, Zhao G, Jiang Q. Is a highly pathogenic avian influenza virus H5N1 fragment recombined in PB1 the key for the epidemic of the novel AIV H7N9 in China, 2013? Int J Infect Dis 2016; 43:85-89. [PMID: 26778522 DOI: 10.1016/j.ijid.2016.01.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Revised: 01/04/2016] [Accepted: 01/05/2016] [Indexed: 10/22/2022] Open
Abstract
BACKGROUND A novel avian influenza A H7N9 virus that infects humans was identified in China in 2013. This study is the first to comprehensively investigate the characteristics of genomic recombination, rather than reassortment, which has been the subject of investigation in previously reported studies. METHODS Novel avian influenza virus (AIV) H7N9 genome sequences were obtained from the NCBI Influenza Virus Sequence Database and the Global Initiative on Sharing Avian Influenza Database (GISAID) and a representative isolate was subjected to homogeneity analysis. A phylogenetic tree was constructed. Eight segments of the isolate were analyzed to identify segments with recombination events, the corresponding recombination fragments, and breakpoints. The evolutionary history of the recombined fragments was tracked by constructing phylogenetic trees of the recombination fragments. RESULTS Among the eight segments of the novel AIV H7N9 analyzed, only the PB1 segment showed a marked recombination phenomenon, with 11 recombination events; these included five actual recombination events and six possible misalignment artifact recombination events. The most notable was the recombination of a 291-nucleotide (nt) fragment at the 490-780 nt site that was affiliated to a highly pathogenic avian influenza virus (HPAIV) H5N1 (A/tree sparrow/Thailand/VSMU-16-RBR/2005). The phylogenetic tree of the 291-nt recombination fragment on the PB1 segment showed that the novel AIV H7N9 had a close genetic relationship to H9N2 and H5N1. CONCLUSIONS The novel AIV H7N9 might have reassorted its PB1 segment from H9N2 circulating in China, and this H9N2 PB1 might have been recombined into a highly pathogenic fragment from HPAIV H5N1, which could be the reason for the high fatality rate among patients with AIV H7N9 influenza.
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Affiliation(s)
- Liang Chen
- Department of Public Health Microbiology, School of Public Health, Fudan University, Bldg 8#, Rd. Dong'an 130, Shanghai 200032, People's Republic of China; Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, People's Republic of China
| | - Liqian Sun
- Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, People's Republic of China; Department of Epidemiology and Biostatistics, School of Public Health, Fudan University, Bldg 8#, Rd. Dong'an 130, Shanghai 200032, People's Republic of China; Laboratory for Spatial Analysis and Modeling, School of Public Health, Fudan University, Shanghai, People's Republic of China
| | - Rui Li
- Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, People's Republic of China; Department of Epidemiology and Biostatistics, School of Public Health, Fudan University, Bldg 8#, Rd. Dong'an 130, Shanghai 200032, People's Republic of China; Laboratory for Spatial Analysis and Modeling, School of Public Health, Fudan University, Shanghai, People's Republic of China
| | - Yue Chen
- Department of Epidemiology and Community Medicine, Faculty of Medicine, University of Ottawa, Ontario, Canada
| | - Zhijie Zhang
- Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, People's Republic of China; Department of Epidemiology and Biostatistics, School of Public Health, Fudan University, Bldg 8#, Rd. Dong'an 130, Shanghai 200032, People's Republic of China; Laboratory for Spatial Analysis and Modeling, School of Public Health, Fudan University, Shanghai, People's Republic of China.
| | - Chenglong Xiong
- Department of Public Health Microbiology, School of Public Health, Fudan University, Bldg 8#, Rd. Dong'an 130, Shanghai 200032, People's Republic of China; Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, People's Republic of China.
| | - Genming Zhao
- Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, People's Republic of China; Department of Epidemiology and Biostatistics, School of Public Health, Fudan University, Bldg 8#, Rd. Dong'an 130, Shanghai 200032, People's Republic of China
| | - Qingwu Jiang
- Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, People's Republic of China
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12
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Published sequences do not support transfer of oseltamivir resistance mutations from avian to human influenza A virus strains. BMC Infect Dis 2015; 15:162. [PMID: 25887656 PMCID: PMC4387679 DOI: 10.1186/s12879-015-0860-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2014] [Accepted: 02/26/2015] [Indexed: 01/06/2023] Open
Abstract
Background Tamiflu (oseltamivir phosphate ester, OE) is a widely used antiviral active against influenza A virus. Its active metabolite, oseltamivir carboxylate (OC), is chemically stable and secreted into wastewater treatment plants. OC contamination of natural habitats of waterfowl might induce OC resistance in influenza viruses persistently infecting waterfowl, and lead to transfer of OC-resistance from avian to human influenza. The aim of this study was to evaluate whether such has occurred. Methods A genomics approach including phylogenetic analysis and probability calculations for homologous recombination was applied on altogether 19,755 neuraminidase (N1 and N2) genes from virus sampled in humans and birds, with and without resistance mutations. Results No evidence for transfer of OE resistance mutations from avian to human N genes was obtained, and events suggesting recombination between human and avian influenza virus variants could not be traced in the sequence material studied. Conclusions The results indicate that resistance in influenza viruses infecting humans is due to the selection pressure posed by the global OE administration in humans rather than transfer from avian influenza A virus strains carrying mutations induced by environmental exposure to OC. Electronic supplementary material The online version of this article (doi:10.1186/s12879-015-0860-9) contains supplementary material, which is available to authorized users.
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13
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Park ES, Suzuki M, Kimura M, Maruyama K, Mizutani H, Saito R, Kubota N, Furuya T, Mizutani T, Imaoka K, Morikawa S. Identification of a natural recombination in the F and H genes of feline morbillivirus. Virology 2014; 468-470:524-531. [PMID: 25262470 DOI: 10.1016/j.virol.2014.09.003] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2014] [Revised: 07/31/2014] [Accepted: 09/04/2014] [Indexed: 01/11/2023]
Abstract
Feline morbillivirus (FmoPV) has recently been identified in Hong Kong and Japan. FmoPV is considered to belong to the genus Morbillivirus, in the family Paramyxoviridae. In this study, the complete nucleotide sequences of three strains of FmoPV detected in cats in Japan were determined. Among the six genes in FmoPV; N, P/V/C, M, F, H and L, the P gene showed the highest polymorphism in the nucleotide and putative amino acid sequences among the FmoPV strains. There was no geographical association in terms of the FmoPV phylogeny; however, from extensive phylogenetic and recombination analyses, we found that one Japanese FmoPV strain, MiJP003, was a probable recombinant between two virus strains in the independent lineages found in Japan and Hong Kong, respectively. The recombination was considered to have occurred within the F and H genes. Such recombination is thought to be involved in the evolution of FmoPV.
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Affiliation(s)
- Eun-Sil Park
- Department of Veterinary Science, National Institute of Infectious Diseases, Tokyo 162-8640, Japan
| | - Michio Suzuki
- Department of Veterinary Science, National Institute of Infectious Diseases, Tokyo 162-8640, Japan
| | - Masanobu Kimura
- Department of Veterinary Science, National Institute of Infectious Diseases, Tokyo 162-8640, Japan
| | - Keiji Maruyama
- Tokyo Metropolitan Animal Care and Consultation Center Jounanjima Branch Office, Tokyo 143-0002, Japan
| | - Hiroshi Mizutani
- Tokyo Metropolitan Animal Care and Consultation Center Jounanjima Branch Office, Tokyo 143-0002, Japan
| | - Ryuichi Saito
- Tokyo Metropolitan Animal Care and Consultation Center Jounanjima Branch Office, Tokyo 143-0002, Japan
| | - Nami Kubota
- Tokyo Metropolitan Animal Care and Consultation Center Jounanjima Branch Office, Tokyo 143-0002, Japan
| | - Tetsuya Furuya
- Research and education center for prevention of global infectious diseases of animals, Tokyo University of Agriculture and Technology, Tokyo 183-8509, Japan
| | - Tetsuya Mizutani
- Research and education center for prevention of global infectious diseases of animals, Tokyo University of Agriculture and Technology, Tokyo 183-8509, Japan
| | - Koichi Imaoka
- Department of Veterinary Science, National Institute of Infectious Diseases, Tokyo 162-8640, Japan
| | - Shigeru Morikawa
- Department of Veterinary Science, National Institute of Infectious Diseases, Tokyo 162-8640, Japan.
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14
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Severe fever with thrombocytopenia syndrome, an emerging tick-borne zoonosis. THE LANCET. INFECTIOUS DISEASES 2014; 14:763-772. [DOI: 10.1016/s1473-3099(14)70718-2] [Citation(s) in RCA: 310] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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15
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The adaptive potential of hybridization demonstrated with bacteriophages. J Mol Evol 2014; 77:221-30. [PMID: 24078088 DOI: 10.1007/s00239-013-9586-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2013] [Accepted: 09/18/2013] [Indexed: 10/26/2022]
Abstract
The success or failure of hybrids and the factors that determine their fitness have ecological, evolutionary, medical, and economic implications. Hybrid fitness is a major determinant of the size of hybrid zones and the maintenance of related species with overlapping ranges. It also influences the evolution of emerging pathogens and the success of economically important crop species experimentally hybridized in search of strains with increased yields or disease resistance. Hybrid fitness may largely be determined by the pervasiveness of epistasis in the genome, as epistasis is known to debilitate hybrids through disrupted inter- and intragenic interactions. We identified two bacteriophages isolated from their natural environment, one the result of a past hybridization event involving an ancestor of the other phage and a third, unknown phage. By performing a reciprocal cross of the affected region of the genome, consisting of a single complete gene, we both approximately recreated and reversed this original hybridization event in two chimeric bacteriophage genomes. Subsequent adaptation of the hybrid phages allowed for the recovery of fitness losses incurred by the hybrid genotypes. Furthermore, adaptation led to the ascension of a substantially higher and previously inaccessible adaptive peak. We show that by allowing genotypes to take large leaps across the adaptive landscape rather than single mutational steps, hybridization can lead to huge long-term fitness gains in spite of short-term costs resulting from disrupted epistatic interactions, demonstrating that the success or failure of hybrids may be determined not by their initial fitness, but rather by their adaptive potential.
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16
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Systematic phylogenetic analysis of influenza A virus reveals many novel mosaic genome segments. INFECTION GENETICS AND EVOLUTION 2013; 18:367-78. [PMID: 23548803 DOI: 10.1016/j.meegid.2013.03.015] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2013] [Revised: 03/04/2013] [Accepted: 03/09/2013] [Indexed: 11/24/2022]
Abstract
Recombination plays an important role in shaping the genetic diversity of a number of DNA and RNA viruses. Although some recent studies have reported bioinformatic evidence of mosaic sequences in a variety of influenza A viruses, it remains controversial as to whether these represent bona fide natural recombination events or laboratory artifacts. Importantly, mosaic genome structures can create significant topological incongruence during phylogenetic analyses, which can mislead additional phylogeny-based molecular evolutionary analyses such as molecular clock dating, the detection of selection pressures and phylogeographic inference. As a result, there is a strong need for systematic screenings for mosaic structures within the influenza virus genome database. We used a combination of sequence-based and phylogeny-based methods to identify 388 mosaic influenza genomic segments, of which 332 are previously unreported and are significantly supported by phylogenetic methods. It is impossible, however, to ascertain whether these represent natural recombinants. To facilitate the future identification of recombinants, reference sets of non-recombinant sequences were selected for use in an automatic screening protocol for detecting mosaic sequences. Tests using real and simulated mosaic sequences indicate that our screening protocol is both sensitive (average >90%) and accurate (average >77%) enough to identify a range of different mosaic patterns. The relatively high prevalence of mosaic influenza virus sequences implies that efficient systematic screens, such as that proposed here, should be performed routinely to detect natural recombinant strains, potential laboratory artifacts, and sequencing contaminants either prior to sequences being deposited in GenBank or before they are used for phylogenetic analyses.
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17
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Suzuki Y, Kobayashi Y. Evolution of complementary nucleotides in 5' and 3' untranslated regions of influenza A virus genomic segments. INFECTION GENETICS AND EVOLUTION 2012; 13:175-9. [PMID: 23146832 DOI: 10.1016/j.meegid.2012.10.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2012] [Revised: 09/29/2012] [Accepted: 10/08/2012] [Indexed: 10/27/2022]
Abstract
The genome of influenza A virus comprises 8 segments (segments 1-8) of single-stranded RNA (virion RNA: vRNA) with negative-polarity. All vRNAs share 13 and 12 terminal nucleotides in the 5' and 3' untranslated regions (UTRs), respectively, which are partially complementary and constitute panhandle and corkscrew structures. Here, it is shown, from the analysis of genomic sequences for 506 strains of influenza A virus, that the number of contiguous complementary nucleotides in the 5' and 3' UTRs varies from 4 to 7 among segments. Complementary nucleotides were segment specific and highly conserved in all segments except for segment 6, where in the phylogenetic analysis co-evolution was observed to have occurred between and within subtypes of neuraminidase (NA). Mutations in the terminal sequences sometimes appeared to have caused convergence between subtypes, involving changes in multiple nucleotide positions. These observations suggest that intra-segmental (homologous) recombinations may have taken place for transferring terminal sequences in segment 6.
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Affiliation(s)
- Yoshiyuki Suzuki
- Graduate School of Natural Sciences, Nagoya City University, 1 Yamanohata, Nagoya-shi, Aichi-ken 467-8501, Japan.
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18
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Shapshak P, Chiappelli F, Somboonwit C, Sinnott J. The Influenza Pandemic of 2009. Mol Diagn Ther 2012; 15:63-81. [DOI: 10.1007/bf03256397] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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19
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He CQ, Ding NZ, Mou X, Xie ZX, Si HL, Qiu R, Ni S, Zhao H, Lu Y, Yan HY, Gao YX, Chen LL, Shen XH, Cao RN. Identification of three H1N1 influenza virus groups with natural recombinant genes circulating from 1918 to 2009. Virology 2012; 427:60-6. [DOI: 10.1016/j.virol.2012.01.012] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2011] [Revised: 11/29/2011] [Accepted: 01/17/2012] [Indexed: 11/16/2022]
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20
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Castro-Nallar E, Cortez-San Martín M, Mascayano C, Molina C, Crandall KA. Molecular phylodynamics and protein modeling of infectious salmon anemia virus (ISAV). BMC Evol Biol 2011; 11:349. [PMID: 22132866 PMCID: PMC3267707 DOI: 10.1186/1471-2148-11-349] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2011] [Accepted: 12/02/2011] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND ISAV is a member of the Orthomyxoviridae family that affects salmonids with disastrous results. It was first detected in 1984 in Norway and from then on it has been reported in Canada, United States, Scotland and the Faroe Islands. Recently, an outbreak was recorded in Chile with negative consequences for the local fishing industry. However, few studies have examined available data to test hypotheses associated with the phylogeographic partitioning of the infecting viral population, the population dynamics, or the evolutionary rates and demographic history of ISAV. To explore these issues, we collected relevant sequences of genes coding for both surface proteins from Chile, Canada, and Norway. We addressed questions regarding their phylogenetic relationships, evolutionary rates, and demographic history using modern phylogenetic methods. RESULTS A recombination breakpoint was consistently detected in the Hemagglutinin-Esterase (he) gene at either side of the Highly Polymorphic Region (HPR), whereas no recombination breakpoints were detected in Fusion protein (f) gene. Evolutionary relationships of ISAV revealed the 2007 Chilean outbreak group as a monophyletic clade for f that has a sister relationship to the Norwegian isolates. Their tMRCA is consistent with epidemiological data and demographic history was successfully recovered showing a profound bottleneck with further population expansion. Finally, selection analyses detected ongoing diversifying selection in f and he codons associated with protease processing and the HPR region, respectively. CONCLUSIONS Our results are consistent with the Norwegian origin hypothesis for the Chilean outbreak clade. In particular, ISAV HPR0 genotype is not the ancestor of all ISAV strains, although SK779/06 (HPR0) shares a common ancestor with the Chilean outbreak clade. Our analyses suggest that ISAV shows hallmarks typical of RNA viruses that can be exploited in epidemiological and surveillance settings. In addition, we hypothesized that genetic diversity of the HPR region is governed by recombination, probably due to template switching and that novel fusion gene proteolytic sites confer a selective advantage for the isolates that carry them. Additionally, protein modeling allowed us to relate the results of phylogenetic studies with the predicted structures. This study demonstrates that phylogenetic methods are important tools to predict future outbreaks of ISAV and other salmon pathogens.
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Affiliation(s)
- Eduardo Castro-Nallar
- Department of Biology, 401 Widtsoe Building, Brigham Young University, Provo, UT 84602-5181, USA.
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21
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No evidence for intra-segment recombination of 2009 H1N1 influenza virus in swine. Gene 2011; 494:242-5. [PMID: 22226809 DOI: 10.1016/j.gene.2011.10.041] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2011] [Revised: 10/10/2011] [Accepted: 10/20/2011] [Indexed: 11/21/2022]
Abstract
Hao (2011) reported that the PB2 genes of three swine influenza A viruses were likely generated through homologous recombination between two closely related parental strains. However, we show that Hao's observation is an artifact of incorrect taxon sampling arising through the lack of an appropriate evolutionary context. Through rigorous phylogenetic analyses we explain the evolutionary origins of these stains and confirm the lack of any statistical support for intra-segmental recombination.
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22
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Homologous recombination in negative sense RNA viruses. Viruses 2011; 3:1358-73. [PMID: 21994784 PMCID: PMC3185808 DOI: 10.3390/v3081358] [Citation(s) in RCA: 92] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2011] [Revised: 07/12/2011] [Accepted: 07/22/2011] [Indexed: 01/05/2023] Open
Abstract
Recombination is an important process that influences biological evolution at many different levels. More and more homologous recombination events have been reported among negative sense RNA viruses recently. While sporadic authentic examples indicate that homologous recombination does occur, recombination seems to be generally rare or even absent in most negative sense RNA viruses, and most of the homologous recombination events reported in the literature were likely generated artificially due to lab contamination or inappropriate bioinformatics methods. Homologous recombination in negative sense RNA viruses should be reported with caution in the future, and only after stringent quality control efforts. Moreover, co-infection experiments should be performed to confirm whether recombination can occur.
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23
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Hao W. Evidence of intra-segmental homologous recombination in influenza A virus. Gene 2011; 481:57-64. [PMID: 21571048 PMCID: PMC7127770 DOI: 10.1016/j.gene.2011.04.012] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2011] [Revised: 04/24/2011] [Accepted: 04/25/2011] [Indexed: 10/26/2022]
Abstract
The evolution of influenza viruses is remarkably dynamic. Influenza viruses evolve rapidly in sequence and undergo frequent reassortment of different gene segments. Homologous recombination, although commonly seen as an important component of dynamic genome evolution in many other organisms, is believed to be rare in influenza. In this study, 256 gene segments from 32 influenza A genomes were examined for homologous recombination, three recombinant H1N1 strains were detected and they most likely resulted from one recombination event between two closely rated parental sequences. These findings suggest that homologous recombination in influenza viruses tends to take place between strains sharing high sequence similarity. The three recombinant strains were isolated at different time periods and they form a clade, indicating that recombinant strains could circulate. In addition, the simulation results showed that many recombinant sequences might not be detectable by currently existing recombinant detection programs when the parental sequences are of high sequence similarity. Finally, possible ways were discussed to improve the accuracy of the detection for recombinant sequences in influenza.
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Affiliation(s)
- Weilong Hao
- Department of Laboratory Medicine and Pathobiology, University of Toronto, ON, Canada.
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24
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Dong CZ. [Advances on genomic evolution of influenza virus]. YI CHUAN = HEREDITAS 2011; 33:189-197. [PMID: 21402525 DOI: 10.3724/sp.j.1005.2011.00189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Four influenza virus pandemics occurred since the beginning of the 20th century. In 1918, 1957, 1968 and 2009, this disease threatened human health and social living greatly. The progress in genomic evolution of influenza virus promoted exploring pathogenic mechanism, surveilling epidemic, preparing influenza vaccine and developing anti-virus drugs. Here, we reviewed the progress in genomic evolution of influenza virus that included evolution mechanism, antigenic evolution, and anti-drug.
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25
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Resistance characteristics of influenza to amino-adamantyls. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2011; 1808:547-53. [DOI: 10.1016/j.bbamem.2010.06.018] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2010] [Revised: 06/14/2010] [Accepted: 06/18/2010] [Indexed: 12/17/2022]
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Abstract
Influenza is a highly contagious respiratory pathogen that continues to evolve and threaten both veterinary and human public health. Influenza A viruses are continually undergoing molecular changes through mutations, reassortment, and, in rare instances, recombination. While they generally cause benign enteric infection in their natural reservoir of wild aquatic birds, they can cause catastrophic and potentially lethal disease outbreaks in humans, domestic poultry, and pigs when they cross the host species barrier. The continuing circulation of highly pathogenic (HP) H5N1 influenza viruses in domestic poultry in parts of Eurasia and the emergence and global spread of pandemic H1N1 2009 are current examples of influenza evolution. The spread of both HP H5N1 and pandemic H1N1 to multiple hosts emphasizes the potential for continued evolution. In this review, we discuss the current understanding of influenza A virus structure and strategies of variation, with a specific focus on the HP H5N1 and pandemic H1N1 influenza viruses. Additionally, we attempt to identify the gaps in our knowledge of H5N1 and pandemic H1N1 influenza viruses. These gaps include (i) an understanding of the molecular determinants of influenza virus and the host that permit efficient transmissibility and pandemic potential, (ii) the urgent need for prospective surveillance in apparently healthy swine, (iii) the molecular determinants of high pathogenicity in poultry, pigs, and people, (iv) the genetic basis of host susceptibility, (v) antigenic variability, (vi) the use of vaccine to control influenza, (vii) the role of wild birds as the reservoir of highly pathogenic avian influenza, (viii) the problems with vaccines, (ix) seasonality, (x) co-infections, and (xi) anti-influenza drug resistance. Our failure to eradicate HP H5N1 globally and to explain why H5N1 does not transmit efficiently in humans while an H1N1 pandemic virus of swine origin spread globally in months are key examples that emphasize the critical need to bridge these knowledge gaps. Future directions in influenza research that will help us resolve each of the above-mentioned knowledge gaps include complete genomic and proteomic analysis of both the virus and the host with the prospect of designing new control strategies and the development of genetically resistant hosts.
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27
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Han GZ, Boni MF, Li SS. No observed effect of homologous recombination on influenza C virus evolution. Virol J 2010; 7:227. [PMID: 20840780 PMCID: PMC2949832 DOI: 10.1186/1743-422x-7-227] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2010] [Accepted: 09/14/2010] [Indexed: 11/10/2022] Open
Abstract
The occurrence of homologous recombination in influenza viruses has been under some debate recently. To determine the extent of homologous recombination in influenza C virus, recombination analyses of all available gene sequences of influenza C virus were carried out. No recombination signal was found. With the previous evidence in influenza A and B viruses, it seems that homologous recombination has minimal or no effect on influenza virus evolution.
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Affiliation(s)
- Guan-Zhu Han
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an, Shandong 271018, China
- Current Address: Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona 85721, USA
| | - Maciej F Boni
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- MRC Centre for Genomics and Global Health, University of Oxford, Oxford, UK
| | - Si-Shen Li
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an, Shandong 271018, China
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28
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Boni MF, de Jong MD, van Doorn HR, Holmes EC. Guidelines for identifying homologous recombination events in influenza A virus. PLoS One 2010; 5:e10434. [PMID: 20454662 PMCID: PMC2862710 DOI: 10.1371/journal.pone.0010434] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2010] [Accepted: 04/06/2010] [Indexed: 11/22/2022] Open
Abstract
The rapid evolution of influenza viruses occurs both clonally and non-clonally through a variety of genetic mechanisms and selection pressures. The non-clonal evolution of influenza viruses comprises relatively frequent reassortment among gene segments and a more rarely reported process of non-homologous RNA recombination. Homologous RNA recombination within segments has been proposed as a third such mechanism, but to date the evidence for the existence of this process among influenza viruses has been both weak and controversial. As homologous recombination has not yet been demonstrated in the laboratory, supporting evidence, if it exists, may come primarily from patterns of phylogenetic incongruence observed in gene sequence data. Here, we review the necessary criteria related to laboratory procedures and sample handling, bioinformatic analysis, and the known ecology and evolution of influenza viruses that need to be met in order to confirm that a homologous recombination event occurred in the history of a set of sequences. To determine if these criteria have an effect on recombination analysis, we gathered 8307 publicly available full-length sequences of influenza A segments and divided them into those that were sequenced via the National Institutes of Health Influenza Genome Sequencing Project (IGSP) and those that were not. As sample handling and sequencing are executed to a very high standard in the IGSP, these sequences should be less likely to be exposed to contamination by other samples or by laboratory strains, and thus should not exhibit laboratory-generated signals of homologous recombination. Our analysis shows that the IGSP data set contains only two phylogenetically-supported single recombinant sequences and no recombinant clades. In marked contrast, the non-IGSP data show a very large amount of potential recombination. We conclude that the presence of false positive signals in the non-IGSP data is more likely than false negatives in the IGSP data, and that given the evidence to date, homologous recombination seems to play little or no role in the evolution of influenza A viruses.
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Affiliation(s)
- Maciej F Boni
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam.
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29
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Liu X, Wu C, Chen AYH. Codon usage bias and recombination events for neuraminidase and hemagglutinin genes in Chinese isolates of influenza A virus subtype H9N2. Arch Virol 2010; 155:685-93. [DOI: 10.1007/s00705-010-0631-2] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2009] [Accepted: 02/08/2010] [Indexed: 10/19/2022]
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30
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Ghosh A, Nandy A, Nandy P, Gute BD, Basak SC. Computational Study of Dispersion and Extent of Mutated and Duplicated Sequences of the H5N1 Influenza Neuraminidase over the Period 1997−2008. J Chem Inf Model 2009; 49:2627-38. [DOI: 10.1021/ci9001662] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Ambarnil Ghosh
- Physics Department, Jadavpur University, and School of Environmental Studies, Jadavpur University, 188 Raja S.C. Mallick Road, Jadavpur, Kolkata, 700032 West Bengal, India, and Natural Resources Research Institute, University of Minnesota Duluth, 5013 Miller Trunk Highway, Duluth, Minnesota 55811
| | - Ashesh Nandy
- Physics Department, Jadavpur University, and School of Environmental Studies, Jadavpur University, 188 Raja S.C. Mallick Road, Jadavpur, Kolkata, 700032 West Bengal, India, and Natural Resources Research Institute, University of Minnesota Duluth, 5013 Miller Trunk Highway, Duluth, Minnesota 55811
| | - Papiya Nandy
- Physics Department, Jadavpur University, and School of Environmental Studies, Jadavpur University, 188 Raja S.C. Mallick Road, Jadavpur, Kolkata, 700032 West Bengal, India, and Natural Resources Research Institute, University of Minnesota Duluth, 5013 Miller Trunk Highway, Duluth, Minnesota 55811
| | - Brian D. Gute
- Physics Department, Jadavpur University, and School of Environmental Studies, Jadavpur University, 188 Raja S.C. Mallick Road, Jadavpur, Kolkata, 700032 West Bengal, India, and Natural Resources Research Institute, University of Minnesota Duluth, 5013 Miller Trunk Highway, Duluth, Minnesota 55811
| | - Subhash C. Basak
- Physics Department, Jadavpur University, and School of Environmental Studies, Jadavpur University, 188 Raja S.C. Mallick Road, Jadavpur, Kolkata, 700032 West Bengal, India, and Natural Resources Research Institute, University of Minnesota Duluth, 5013 Miller Trunk Highway, Duluth, Minnesota 55811
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31
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Ding NZ, Wang XM, Sun SW, Song Q, Li SN, He CQ. Appearance of mosaic enterovirus 71 in the 2008 outbreak of China. Virus Res 2009; 145:157-61. [PMID: 19540282 DOI: 10.1016/j.virusres.2009.06.006] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2009] [Revised: 06/02/2009] [Accepted: 06/03/2009] [Indexed: 01/05/2023]
Abstract
Enterovirus 71 (EV71) is a pathogen of hand-foot-and-mouth disease (HFMD). In the last year and this spring, HFMD caused by EV71 repeatedly broke out and has resulted in at least 50 children's death in China. It is important to know the mechanism effecting genetic diversity of the virus circulating in China in order to prevent future outbreaks in the country. Homologous recombination has been proved to play a role in evolution of the virus. In this study, we have performed a phylogenetic analysis of full-length EV71 isolated in the last year in China to detect if recombination exerts its influence on the EV71 outbreak. Among EV71 isolates from China, 5 isolates were identified as mosaic. This finding suggests that homologous recombination has played some roles in generating genetic diversity in the outbreak of EV71 in China.
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Affiliation(s)
- Nai-Zheng Ding
- School of Biological Science and Technology, Central South University, Hunan Province, China.
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32
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He CQ, Xie ZX, Han GZ, Dong JB, Wang D, Liu JB, Ma LY, Tang XF, Liu XP, Pang YS, Li GR. Homologous recombination as an evolutionary force in the avian influenza A virus. Mol Biol Evol 2008; 26:177-87. [PMID: 18931384 DOI: 10.1093/molbev/msn238] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Avian influenza A viruses (AIVs), including the H5N1, H9N2, and H7N7 subtypes, have been directly transmitted to humans, raising concerns over the possibility of a new influenza pandemic. To prevent a future avian influenza pandemic, it is very important to fully understand the molecular basis driving the change in AIV virulence and host tropism. Although virulent variants of other viruses have been generated by homologous recombination, the occurrence of homologous recombination within AIV segments is controversial and far from proven. This study reports three circulating H9N2 AIVs with similar mosaic PA genes descended from H9N2 and H5N1. Additionally, many homologous recombinants are also found deposited in GenBank. Recombination events can occur in PB2, PB1, PA, HA, and NP segments and between lineages of the same/different serotype. These results collectively demonstrate that intragenic recombination plays a role in driving the evolution of AIVs, potentially resulting in effects on AIV virulence and host tropism changes.
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Affiliation(s)
- Cheng-Qiang He
- Department of Biotechnology College of Life Science, Shandong Normal University, Shandong Province, Jinan, China.
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