Genetic and Phylogenetic Analyses of Influenza A H1N1pdm Virus in Buenos Aires, Argentina

Barrero, Paola Roxana; Viegas, Mariana; Valinotto, Laura; Mistchenko, Alicia

doi:10.1128/jvi.00936-10

Cited by 31 publications

(28 citation statements)

References 28 publications

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“…This dominance of circulation of clade 7 viruses throughout the pandemic period and the disappearance of all other clades was observed in other studies in the United Kingdom, Argentina, India and in the United States of America (Baillie et al, 2012;Barrero et al, 2011;Mullick et al, 2011;Nelson et al, 2011). While clade 7 viruses have dominated globally, they have also been the most diverse and their genetic diversity may have arisen from reassortment among clades considering that they co-circulated with all the other clades.…”

Section: Discussionsupporting

confidence: 79%

Whole genome characterization of human influenza A(H1N1)pdm09 viruses isolated from Kenya during the 2009 pandemic

Gachara

Samuel

Otieno

et al. 2016

Infection, Genetics and Evolution

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Section: Discussionsupporting

confidence: 79%

Whole genome characterization of human influenza A(H1N1)pdm09 viruses isolated from Kenya during the 2009 pandemic

Gachara

Samuel

Otieno

et al. 2016

Infection, Genetics and Evolution

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“…The very-high-resolution tracking of individual lineages is achievable only with full genome sequences. Coupled with spatial information, we show that detailed insight into transmission chains and epidemiology becomes apparent, extending what can be observed by use of sequences alone (1,14,21).…”

Section: Discussionmentioning

confidence: 80%

Evolutionary Dynamics of Local Pandemic H1N1/2009 Influenza Virus Lineages Revealed by Whole-Genome Analysis

Baillie

Galiano²,

Agapow³

et al. 2012

J Virol

108

102

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Virus gene sequencing and phylogenetics can be used to study the epidemiological dynamics of rapidly evolving viruses. With complete genome data, it becomes possible to identify and trace individual transmission chains of viruses such as influenza virus during the course of an epidemic. Here we sequenced 153 pandemic influenza H1N1/09 virus genomes from United Kingdom isolates from the first (127 isolates) and second (26 isolates) waves of the 2009 pandemic and used their sequences, dates of isolation, and geographical locations to infer the genetic epidemiology of the epidemic in the United Kingdom. We demonstrate that the epidemic in the United Kingdom was composed of many cocirculating lineages, among which at least 13 were exclusively or predominantly United Kingdom clusters. The estimated divergence times of two of the clusters predate the detection of pandemic H1N1/09 virus in the United Kingdom, suggesting that the pandemic H1N1/09 virus was already circulating in the United Kingdom before the first clinical case. Crucially, three clusters contain isolates from the second wave of infections in the United Kingdom, two of which represent chains of transmission that appear to have persisted within the United Kingdom between the first and second waves. This demonstrates that whole-genome analysis can track in fine detail the behavior of individual influenza virus lineages during the course of a single epidemic or pandemic.

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“…For example, the selection of minority variants with a deletion in the neuraminidase (NA) gene that allows the adaptation of avian influenza viruses from waterfowl to domestic poultry [77], suggests a high frequency of mixed infections and genetic reassortment within these viruses [78, 79, 85]. Other studies described the prevalence and spread patterns of different human influenza viruses in specific geographic areas, based not only on the hemagglutinin (HA) and NA genes but by analyzing all viral segments [86–89]. …”

Section: Applications In General Virologymentioning

confidence: 99%

Deep sequencing: Becoming a critical tool in clinical virology

Quiñones‐Mateu¹,

Ávila²,

Reyes‐Terán³

et al. 2014

Journal of Clinical Virology

116

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Population (Sanger) sequencing has been the standard method in basic and clinical DNA sequencing for almost 40 years; however, next-generation (deep) sequencing methodologies are now revolutionizing the field of genomics, and clinical virology is no exception. Deep sequencing is highly efficient, producing an enormous amount of information at low cost in a relatively short period of time. High-throughput sequencing techniques have enabled significant contributions to multiples areas in virology, including virus discovery and metagenomics (viromes), molecular epidemiology, pathogenesis, and studies of how viruses to escape the host immune system and antiviral pressures. In addition, new and more affordable deep sequencing-based assays are now being implemented in clinical laboratories. Here we review the use of the current deep sequencing platforms in virology, focusing on three of the most studied viruses: human immunodeficiency virus (HIV), hepatitis C virus (HCV), and influenza virus.

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Genetic and Phylogenetic Analyses of Influenza A H1N1pdm Virus in Buenos Aires, Argentina

Cited by 31 publications

References 28 publications

Whole genome characterization of human influenza A(H1N1)pdm09 viruses isolated from Kenya during the 2009 pandemic

Whole genome characterization of human influenza A(H1N1)pdm09 viruses isolated from Kenya during the 2009 pandemic

Evolutionary Dynamics of Local Pandemic H1N1/2009 Influenza Virus Lineages Revealed by Whole-Genome Analysis

Deep sequencing: Becoming a critical tool in clinical virology

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