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Danilenko AV, Kolosova NP, Shvalov AN, Ilyicheva TN, Svyatchenko SV, Durymanov AG, Bulanovich JA, Goncharova NI, Susloparov IM, Marchenko VY, Tregubchak TV, Gavrilova EV, Maksyutov RA, Ryzhikov AB. Evaluation of HA-D222G/N polymorphism using targeted NGS analysis in A(H1N1)pdm09 influenza virus in Russia in 2018-2019. PLoS One 2021; 16:e0251019. [PMID: 33914831 PMCID: PMC8084186 DOI: 10.1371/journal.pone.0251019] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 04/19/2021] [Indexed: 02/07/2023] Open
Abstract
Outbreaks of influenza, which is a contagious respiratory disease, occur throughout the world annually, affecting millions of people with many fatal cases. The D222G/N mutations in the hemagglutinin (HA) gene of A(H1N1)pdm09 are associated with severe and fatal human influenza cases. These mutations lead to increased virus replication in the lower respiratory tract (LRT) and may result in life-threatening pneumonia. Targeted NGS analysis revealed the presence of mutations in major and minor variants in 57% of fatal cases, with the proportion of viral variants with mutations varying from 1% to 98% in each individual sample in the epidemic season 2018-2019 in Russia. Co-occurrence of the mutations D222G and D222N was detected in a substantial number of the studied fatal cases (41%). The D222G/N mutations were detected at a low frequency (less than 1%) in the rest of the studied samples from fatal and nonfatal cases of influenza. The presence of HA D222Y/V/A mutations was detected in a few fatal cases. The high rate of occurrence of HA D222G/N mutations in A(H1N1)pdm09 viruses, their increased ability to replicate in the LRT and their association with fatal outcomes points to the importance of monitoring the mutations in circulating A(H1N1)pdm09 viruses for the evaluation of their epidemiological significance and for the consideration of disease prevention and treatment options.
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Affiliation(s)
- Alexey V. Danilenko
- Vector State Research Center of Virology and Biotechnology, Koltsovo, Novosibirsk Region, Russia
| | - Natalia P. Kolosova
- Vector State Research Center of Virology and Biotechnology, Koltsovo, Novosibirsk Region, Russia
| | - Alexander N. Shvalov
- Vector State Research Center of Virology and Biotechnology, Koltsovo, Novosibirsk Region, Russia
| | - Tatyana N. Ilyicheva
- Vector State Research Center of Virology and Biotechnology, Koltsovo, Novosibirsk Region, Russia
- Novosibirsk State University, Novosibirsk, Russia
| | - Svetlana V. Svyatchenko
- Vector State Research Center of Virology and Biotechnology, Koltsovo, Novosibirsk Region, Russia
| | - Alexander G. Durymanov
- Vector State Research Center of Virology and Biotechnology, Koltsovo, Novosibirsk Region, Russia
| | - Julia A. Bulanovich
- Vector State Research Center of Virology and Biotechnology, Koltsovo, Novosibirsk Region, Russia
| | - Natalia I. Goncharova
- Vector State Research Center of Virology and Biotechnology, Koltsovo, Novosibirsk Region, Russia
| | - Ivan M. Susloparov
- Vector State Research Center of Virology and Biotechnology, Koltsovo, Novosibirsk Region, Russia
| | - Vasiliy Y. Marchenko
- Vector State Research Center of Virology and Biotechnology, Koltsovo, Novosibirsk Region, Russia
| | - Tatyana V. Tregubchak
- Vector State Research Center of Virology and Biotechnology, Koltsovo, Novosibirsk Region, Russia
| | - Elena V. Gavrilova
- Vector State Research Center of Virology and Biotechnology, Koltsovo, Novosibirsk Region, Russia
| | - Rinat A. Maksyutov
- Vector State Research Center of Virology and Biotechnology, Koltsovo, Novosibirsk Region, Russia
| | - Alexander B. Ryzhikov
- Vector State Research Center of Virology and Biotechnology, Koltsovo, Novosibirsk Region, Russia
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2
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Slaine PD, MacRae C, Kleer M, Lamoureux E, McAlpine S, Warhuus M, Comeau AM, McCormick C, Hatchette T, Khaperskyy DA. Adaptive Mutations in Influenza A/California/07/2009 Enhance Polymerase Activity and Infectious Virion Production. Viruses 2018; 10:E272. [PMID: 29783694 PMCID: PMC5977265 DOI: 10.3390/v10050272] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Revised: 05/15/2018] [Accepted: 05/15/2018] [Indexed: 12/16/2022] Open
Abstract
Mice are not natural hosts for influenza A viruses (IAVs), but they are useful models for studying antiviral immune responses and pathogenesis. Serial passage of IAV in mice invariably causes the emergence of adaptive mutations and increased virulence. Here, we report the adaptation of IAV reference strain A/California/07/2009(H1N1) (also known as CA/07) in outbred Swiss Webster mice. Serial passage led to increased virulence and lung titers, and dissemination of the virus to brains. We adapted a deep-sequencing protocol to identify and enumerate adaptive mutations across all genome segments. Among mutations that emerged during mouse-adaptation, we focused on amino acid substitutions in polymerase subunits: polymerase basic-1 (PB1) T156A and F740L and polymerase acidic (PA) E349G. These mutations were evaluated singly and in combination in minigenome replicon assays, which revealed that PA E349G increased polymerase activity. By selectively engineering three PB1 and PA mutations into the parental CA/07 strain, we demonstrated that these mutations in polymerase subunits decreased the production of defective viral genome segments with internal deletions and dramatically increased the release of infectious virions from mouse cells. Together, these findings increase our understanding of the contribution of polymerase subunits to successful host adaptation.
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MESH Headings
- Adaptation, Physiological/genetics
- Amino Acid Substitution
- Animals
- Animals, Outbred Strains
- Cells, Cultured
- Disease Models, Animal
- Dogs
- Female
- Genome, Viral
- Humans
- Influenza A Virus, H1N1 Subtype/enzymology
- Influenza A Virus, H1N1 Subtype/genetics
- Influenza A Virus, H1N1 Subtype/pathogenicity
- Influenza A Virus, H1N1 Subtype/physiology
- Influenza, Human/virology
- Mice
- Mutation, Missense
- Protein Conformation
- RNA-Dependent RNA Polymerase/chemistry
- RNA-Dependent RNA Polymerase/genetics
- RNA-Dependent RNA Polymerase/metabolism
- Serial Passage
- Viral Proteins/chemistry
- Viral Proteins/genetics
- Viral Proteins/metabolism
- Virion/metabolism
- Virulence
- Virus Replication
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Affiliation(s)
- Patrick D Slaine
- Department of Microbiology and Immunology, Dalhousie University, 5850 College Street, Halifax, NS B3H 4R2, Canada.
| | - Cara MacRae
- The Hospital for Sick Children, University Health Network, Toronto, ON M5G 2C4, Canada.
| | - Mariel Kleer
- Department of Microbiology and Immunology, Dalhousie University, 5850 College Street, Halifax, NS B3H 4R2, Canada.
| | - Emily Lamoureux
- CGEB-Integrated Microbiome Resource (IMR) and Department of Pharmacology, Dalhousie University, 5850 College Street, Halifax, NS B3H 4R2, Canada.
| | - Sarah McAlpine
- Division of Microbiology, Department of Pathology and Laboratory Medicine, Nova Scotia Health Authority (NSHA), Halifax, NS B3H 1V8, Canada.
| | - Michelle Warhuus
- Division of Microbiology, Department of Pathology and Laboratory Medicine, Nova Scotia Health Authority (NSHA), Halifax, NS B3H 1V8, Canada.
| | - André M Comeau
- CGEB-Integrated Microbiome Resource (IMR) and Department of Pharmacology, Dalhousie University, 5850 College Street, Halifax, NS B3H 4R2, Canada.
| | - Craig McCormick
- Department of Microbiology and Immunology, Dalhousie University, 5850 College Street, Halifax, NS B3H 4R2, Canada.
| | - Todd Hatchette
- Division of Microbiology, Department of Pathology and Laboratory Medicine, Nova Scotia Health Authority (NSHA), Halifax, NS B3H 1V8, Canada.
| | - Denys A Khaperskyy
- Department of Microbiology and Immunology, Dalhousie University, 5850 College Street, Halifax, NS B3H 4R2, Canada.
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3
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Hashem AM, Azhar EI, Shalhoub S, Abujamel TS, Othman NA, Al Zahrani AB, Abdullah HM, Al-Alawi MM, Sindi AA. Genetic characterization and diversity of circulating influenza A/H1N1pdm09 viruses isolated in Jeddah, Saudi Arabia between 2014 and 2015. Arch Virol 2018; 163:1219-1230. [PMID: 29396684 DOI: 10.1007/s00705-018-3732-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2017] [Accepted: 12/19/2017] [Indexed: 12/28/2022]
Abstract
The emerged influenza A/H1N1pdm09 viruses have replaced the previously circulating seasonal H1N1 viruses. The close antigenic properties of these viruses to the 1918 H1N1 pandemic viruses and their post-pandemic evolution pattern could further enhance their adaptation and pathogenicity in humans representing a major public health threat. Given that data on the dynamics and evolution of these viruses in Saudi Arabia is sparse we investigated the genetic diversity of circulating influenza A/H1N1pdm09 viruses from Jeddah, Saudi Arabia, by analyzing 39 full genomes from isolates obtained between 2014-2015, from patients with varying symptoms. Phylogenetic analysis of all gene segments and concatenated genomes showed similar topologies and co-circulation of clades 6b, 6b.1 and 6b.2, with clade 6b.1 being the most predominate since 2015. Most viruses were more closely related to the vaccine strain (Michigan/45/2015) recommended for the 2017/2018 season, than to the California/07/2009 strain. Low sequence variability was observed in the haemagglutinin protein compared to the neuraminidase protein. Resistance to neuraminidase inhibitors was limited as only one isolate had the H275Y substitution. Interestingly, two isolates had short PA-X proteins of 206 amino acids compared to the 232 amino acid protein found in most influenza A/H1N1pdm09 viruses. Together, the co-circulation of several clades and the predominance of clade 6b.1, despite its low circulation in Asia in 2015, suggests multiple introductions most probably during the mass gathering events of Hajj and Umrah. Jeddah represents the main port of entry to the holy cities of Makkah and Al-Madinah, emphasizing the need for vigilant surveillance in the kingdom.
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MESH Headings
- Amino Acid Substitution
- Female
- Genetic Variation
- Genome, Viral
- Hemagglutinin Glycoproteins, Influenza Virus/genetics
- Humans
- Influenza A Virus, H1N1 Subtype/classification
- Influenza A Virus, H1N1 Subtype/genetics
- Influenza A Virus, H1N1 Subtype/isolation & purification
- Influenza, Human/epidemiology
- Influenza, Human/transmission
- Influenza, Human/virology
- Male
- Nasopharynx/virology
- Neuraminidase/genetics
- Phylogeny
- RNA, Viral/genetics
- Saudi Arabia/epidemiology
- Seasons
- Sequence Analysis, DNA
- Viral Proteins/genetics
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Affiliation(s)
- Anwar M Hashem
- Special Infectious Agent Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Kingdom of Saudi Arabia.
- Department of Medical Microbiology and Parasitology, Faculty of Medicine, King Abdulaziz University, Jeddah, Kingdom of Saudi Arabia.
| | - Esam I Azhar
- Special Infectious Agent Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Kingdom of Saudi Arabia.
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Kingdom of Saudi Arabia.
| | - Sarah Shalhoub
- Division of Infectious Diseases, Department of Medicine, King Fahd Armed Forces Hospital, Jeddah, Kingdom of Saudi Arabia
| | - Turki S Abujamel
- Special Infectious Agent Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Kingdom of Saudi Arabia
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Kingdom of Saudi Arabia
| | - Norah A Othman
- Special Infectious Agent Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Kingdom of Saudi Arabia
| | - Abdulwahab B Al Zahrani
- Molecular Diagnostics Laboratory, King Fahd Armed Forces Hospital, Jeddah, Kingdom of Saudi Arabia
| | - Hanan M Abdullah
- Students' Research and Innovation Unit, Faculty of Medicine, King Abdulaziz University, Jeddah, Kingdom of Saudi Arabia
| | - Maha M Al-Alawi
- Special Infectious Agent Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Kingdom of Saudi Arabia
- Department of Medical Microbiology and Parasitology, Faculty of Medicine, King Abdulaziz University, Jeddah, Kingdom of Saudi Arabia
- Infection Control and Environmental Health Unit, Faculty of Medicine, King Abdulaziz University Hospital, Jeddah, Kingdom of Saudi Arabia
| | - Anees A Sindi
- Department of Anesthesia and Critical Care, Faculty of Medicine, King Abdulaziz University, Jeddah, Kingdom of Saudi Arabia
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4
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Moncla LH, Zhong G, Nelson CW, Dinis JM, Mutschler J, Hughes AL, Watanabe T, Kawaoka Y, Friedrich TC. Selective Bottlenecks Shape Evolutionary Pathways Taken during Mammalian Adaptation of a 1918-like Avian Influenza Virus. Cell Host Microbe 2016; 19:169-80. [PMID: 26867176 PMCID: PMC4761429 DOI: 10.1016/j.chom.2016.01.011] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2015] [Revised: 10/26/2015] [Accepted: 01/25/2016] [Indexed: 01/14/2023]
Abstract
Avian influenza virus reassortants resembling the 1918 human pandemic virus can become transmissible among mammals by acquiring mutations in hemagglutinin (HA) and polymerase. Using the ferret model, we trace the evolutionary pathway by which an avian-like virus evolves the capacity for mammalian replication and airborne transmission. During initial infection, within-host HA diversity increased drastically. Then, airborne transmission fixed two polymerase mutations that do not confer a detectable replication advantage. In later transmissions, selection fixed advantageous HA1 variants. Transmission initially involved a "loose" bottleneck, which became strongly selective after additional HA mutations emerged. The stringency and evolutionary forces governing between-host bottlenecks may therefore change throughout host adaptation. Mutations occurred in multiple combinations in transmitted viruses, suggesting that mammalian transmissibility can evolve through multiple genetic pathways despite phenotypic constraints. Our data provide a glimpse into avian influenza virus adaptation in mammals, with broad implications for surveillance on potentially zoonotic viruses.
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Affiliation(s)
- Louise H Moncla
- Department of Pathobiological Sciences, University of Wisconsin School of Veterinary Medicine, Madison, WI 53706, USA; Wisconsin National Primate Research Center, Madison, WI 53715, USA
| | - Gongxun Zhong
- Department of Pathobiological Sciences, University of Wisconsin School of Veterinary Medicine, Madison, WI 53706, USA
| | - Chase W Nelson
- Department of Biological Sciences, University of South Carolina, Columbia, SC 29208, USA
| | - Jorge M Dinis
- Department of Pathobiological Sciences, University of Wisconsin School of Veterinary Medicine, Madison, WI 53706, USA; Wisconsin National Primate Research Center, Madison, WI 53715, USA
| | - James Mutschler
- Department of Pathobiological Sciences, University of Wisconsin School of Veterinary Medicine, Madison, WI 53706, USA; Wisconsin National Primate Research Center, Madison, WI 53715, USA
| | - Austin L Hughes
- Department of Biological Sciences, University of South Carolina, Columbia, SC 29208, USA
| | - Tokiko Watanabe
- Department of Pathobiological Sciences, University of Wisconsin School of Veterinary Medicine, Madison, WI 53706, USA; Division of Virology, Department of Microbiology and Immunology, Institute of Medical Science, University of Tokyo, 4-6-1, Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
| | - Yoshihiro Kawaoka
- Department of Pathobiological Sciences, University of Wisconsin School of Veterinary Medicine, Madison, WI 53706, USA; Division of Virology, Department of Microbiology and Immunology, Institute of Medical Science, University of Tokyo, 4-6-1, Shirokanedai, Minato-ku, Tokyo 108-8639, Japan.
| | - Thomas C Friedrich
- Department of Pathobiological Sciences, University of Wisconsin School of Veterinary Medicine, Madison, WI 53706, USA; Wisconsin National Primate Research Center, Madison, WI 53715, USA.
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5
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Krasnoslobodtsev KG, Lvov DK, Alkhovsky SV, Burtseva EI, Fedyakina IT, Kolobukhina LV, Kirillova ES, Trushakova SV, Oskerko TA, Shchelkanov MY, Deryabin PG. Amino acid polymorphism at residue 222 of the receptor-binding site of the hemagglutinin of the pandemic influenza A(H1N1)pdm09 from patients 166 with lethal virus pneumonia in 2012-2014. Vopr Virusol 2016; 61:166-171. [PMID: 36494964 DOI: 10.18821/0507-4088-2016-61-4-166-171] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Indexed: 12/13/2022]
Abstract
Survey data from autopsy specimens from patients who died from pneumonia caused by the influenza A(H1N1) pdm09 in 2012-2014 and mutant forms of influenza virus in these patients (position 222 in the receptor-binding region of hemagglutinin) were presented. In total, according to aggregate data, obtained with three different methods (sequencing, next-generation sequencing (NGS), virus isolation) mutant viruses were detected in 17 (41%) from 41 patients. The proportion of the mutant forms in viral populations ranged from 1% to 69.2%. The most frequent mixture was the wild type (D222) and mutant (D222G), with proportion of mutant type ranged from 3.3% to 69.2% in the viral population. Mutation D222N (from 1.1% to 5.5%) was found rarely. Composition of the viral population from one patient is extremely heterogeneous: in left lung there was only wild type D222, meantime in right lung - mixture of mutant forms 222D/N/G (65.4/32.5/1.1%), in trachea - mixture 222D/G/Y/A (61.8/35.6/1.2/1.4%, respectively), and in bronchi compound of 222D/G/N/A (64.3/33.7/1/1%, respectively) were detected. The obtained data indicate that the process of adaptation of the virus in the lower respiratory tract is coupled with the appearance of different virus variants with mutations in the receptor-binding region. Mutant forms of the virus are observed in the lower respiratory tract of the majority of patients with lethal viral pneumonia. However, if they are a minor part of the population, they cannot be detected by the method of conventional sequencing. They can be identified using the NGS methods.
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Affiliation(s)
- K G Krasnoslobodtsev
- «Federal Research Centre of Epidemilogy and Microbiology named after the honorary academician N.F. Gamaleya»
| | - D K Lvov
- «Federal Research Centre of Epidemilogy and Microbiology named after the honorary academician N.F. Gamaleya»
| | - S V Alkhovsky
- «Federal Research Centre of Epidemilogy and Microbiology named after the honorary academician N.F. Gamaleya»
| | - E I Burtseva
- «Federal Research Centre of Epidemilogy and Microbiology named after the honorary academician N.F. Gamaleya»
| | - I T Fedyakina
- «Federal Research Centre of Epidemilogy and Microbiology named after the honorary academician N.F. Gamaleya»
| | - L V Kolobukhina
- «Federal Research Centre of Epidemilogy and Microbiology named after the honorary academician N.F. Gamaleya»
| | - E S Kirillova
- «Federal Research Centre of Epidemilogy and Microbiology named after the honorary academician N.F. Gamaleya»
| | - S V Trushakova
- «Federal Research Centre of Epidemilogy and Microbiology named after the honorary academician N.F. Gamaleya»
| | - T A Oskerko
- «Federal Research Centre of Epidemilogy and Microbiology named after the honorary academician N.F. Gamaleya»
| | - M Y Shchelkanov
- «Federal Research Centre of Epidemilogy and Microbiology named after the honorary academician N.F. Gamaleya»
| | - P G Deryabin
- «Federal Research Centre of Epidemilogy and Microbiology named after the honorary academician N.F. Gamaleya»
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6
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Transmission and pathogenicity of novel reassortants derived from Eurasian avian-like and 2009 pandemic H1N1 influenza viruses in mice and guinea pigs. Sci Rep 2016; 6:27067. [PMID: 27252023 PMCID: PMC4890009 DOI: 10.1038/srep27067] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Accepted: 04/20/2016] [Indexed: 11/08/2022] Open
Abstract
Given the present extensive co-circulation in pigs of Eurasian avian-like (EA) swine H1N1 and 2009 pandemic (pdm/09) H1N1 viruses, reassortment between them is highly plausible but largely uncharacterized. Here, experimentally co-infected pigs with a representative EA virus and a pdm/09 virus yielded 55 novel reassortant viruses that could be categorized into 17 genotypes from Gt1 to Gt17 based on segment segregation. Majority of novel reassortants were isolated from the lower respiratory tract. Most of reassortant viruses were more pathogenic and contagious than the parental EA viruses in mice and guinea pigs. The most transmissible reassortant genotypes demonstrated in guinea pigs (Gt2, Gt3, Gt7, Gt10 and Gt13) were also the most lethal in mice. Notably, nearly all these highly virulent reassortants (all except Gt13) were characterized with possession of EA H1 and full complement of pdm/09 ribonucleoprotein genes. Compositionally, we demonstrated that EA H1-222G contributed to virulence by its ability to bind avian-type sialic acid receptors, and that pdm/09 RNP conferred the most robust polymerase activity to reassortants. The present study revealed high reassortment compatibility between EA and pdm/09 viruses in pigs, which could give rise to progeny reassortant viruses with enhanced virulence and transmissibility in mice and guinea pig models.
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7
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Analysis of the genetic diversity of influenza A viruses using next-generation DNA sequencing. BMC Genomics 2015; 16:79. [PMID: 25758772 PMCID: PMC4342091 DOI: 10.1186/s12864-015-1284-z] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Accepted: 01/26/2015] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Influenza viruses exist as a large group of closely related viral genomes, also called quasispecies. The composition of this influenza viral quasispecies can be determined by an accurate and sensitive sequencing technique and data analysis pipeline. We compared the suitability of two benchtop next-generation sequencers for whole genome influenza A quasispecies analysis: the Illumina MiSeq sequencing-by-synthesis and the Ion Torrent PGM semiconductor sequencing technique. RESULTS We first compared the accuracy and sensitivity of both sequencers using plasmid DNA and different ratios of wild type and mutant plasmid. Illumina MiSeq sequencing reads were one and a half times more accurate than those of the Ion Torrent PGM. The majority of sequencing errors were substitutions on the Illumina MiSeq and insertions and deletions, mostly in homopolymer regions, on the Ion Torrent PGM. To evaluate the suitability of the two techniques for determining the genome diversity of influenza A virus, we generated plasmid-derived PR8 virus and grew this virus in vitro. We also optimized an RT-PCR protocol to obtain uniform coverage of all eight genomic RNA segments. The sequencing reads obtained with both sequencers could successfully be assembled de novo into the segmented influenza virus genome. After mapping of the reads to the reference genome, we found that the detection limit for reliable recognition of variants in the viral genome required a frequency of 0.5% or higher. This threshold exceeds the background error rate resulting from the RT-PCR reaction and the sequencing method. Most of the variants in the PR8 virus genome were present in hemagglutinin, and these mutations were detected by both sequencers. CONCLUSIONS Our approach underlines the power and limitations of two commonly used next-generation sequencers for the analysis of influenza virus gene diversity. We conclude that the Illumina MiSeq platform is better suited for detecting variant sequences whereas the Ion Torrent PGM platform has a shorter turnaround time. The data analysis pipeline that we propose here will also help to standardize variant calling in small RNA genomes based on next-generation sequencing data.
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8
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Kong W, Liu L, Wang Y, He Q, Wu S, Qin Z, Wang J, Sun H, Sun Y, Zhang R, Pu J, Liu J. C-terminal elongation of NS1 of H9N2 influenza virus induces a high level of inflammatory cytokines and increases transmission. J Gen Virol 2015; 96:259-268. [DOI: 10.1099/vir.0.071001-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Affiliation(s)
- Weili Kong
- Key Laboratory of Animal Epidemiology and Zoonosis, Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing 100193, PR China
| | - Lirong Liu
- Key Laboratory of Animal Epidemiology and Zoonosis, Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing 100193, PR China
| | - Yu Wang
- Key Laboratory of Animal Epidemiology and Zoonosis, Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing 100193, PR China
| | - Qiming He
- Key Laboratory of Animal Epidemiology and Zoonosis, Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing 100193, PR China
| | - Sizhe Wu
- Key Laboratory of Animal Epidemiology and Zoonosis, Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing 100193, PR China
| | - Zhihua Qin
- Key Laboratory of Animal Epidemiology and Zoonosis, Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing 100193, PR China
| | - Jinliang Wang
- Key Laboratory of Animal Epidemiology and Zoonosis, Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing 100193, PR China
| | - Honglei Sun
- Key Laboratory of Animal Epidemiology and Zoonosis, Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing 100193, PR China
| | - Yipeng Sun
- Key Laboratory of Animal Epidemiology and Zoonosis, Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing 100193, PR China
| | - Rui Zhang
- Key Laboratory of Animal Epidemiology and Zoonosis, Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing 100193, PR China
| | - Juan Pu
- Key Laboratory of Animal Epidemiology and Zoonosis, Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing 100193, PR China
| | - Jinhua Liu
- Key Laboratory of Animal Epidemiology and Zoonosis, Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing 100193, PR China
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9
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Biophysical characterization of lectin–glycan interactions for therapeutics, vaccines and targeted drug-delivery. Future Med Chem 2014; 6:2113-29. [DOI: 10.4155/fmc.14.130] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Lectin–glycan interactions play a role in biological processes, host–pathogen interactions and in disease. A more detailed understanding of these interactions is not only useful for the elucidation of their biological function but can also be applied in immunology, drug development and delivery and diagnostics. We review some commonly used biophysical techniques for studying lectin–glycan interactions; namely: frontal affinity chromatography, glycan/lectin microarray, surface plasmon resonance, electrochemical impedance spectroscopy, isothermal titration calorimetry, fluorescent assays, enzyme linked lectin sorbent assay and saturation transfer difference nuclear magnetic resonance spectroscopy. Each method is evaluated on efficiency, cost and throughput. We also consider the advantages and limitations of each technique and provide examples of their application in biology, drug discovery and delivery, immunology, glycoprofiling and biosensing.
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