Molecular epidemiology of influenza A(H1N1)PDM09 hemagglutinin gene circulating in São Paulo State , Brazil: 2016 anticipated influenza season

Katia Corrêa de Oliveira Santos Daniela Bernardes Borges da Silva Norio Augusto Sasaki Margarete Aparecida Benega Rebecca Garten Terezinha Maria de Paiva About the authors

ABSTRACT

Compared to previous years, seasonal influenza activity commenced early in São Paulo State, Brazil, Southern hemisphere during the 2016 year. In order to investigate the genetic pattern of influenza A(H1N1)pdm09 in the State of Sao Paulo a total of 479 respiratory samples, collected in January by Sentinel Surveillance Units, were screened by real-time RT-PCR. A total of 6 Influenza viruses A(H1N1)pdm09 presenting ct values ≤ 30 were sequenced following phylogenetic analysis. The present study identified the circulation of the new 6B.1 subgroup (A/Sao Paulo/10-118/2016 and A/Sao Paulo/3032/2016). In addition, influenza A(H1N1)pdm09 group 6B has also been identified during January in the State of Sao Paulo. Despite amino acid changes and changes in potential glycosylation motifs, 6B.1 viruses were well inhibited by the reference ferret antiserum against A/California/07/2009 virus, the A(H1N1)pdm09 component of the vaccine for the 2016 influenza season.

KEYWORDS:
Influenza; National Influenza Surveillance Network; Molecular epidemiology; Vaccination strategy; Public health

Compared to previous years, seasonal influenza activity commenced early in São Paulo State, Brazil, Southern hemisphere. Influenza A(H1N1)pdm09 virus detection started in January 2016 during the summer season with hot temperatures, and it was the predominating strain in autumn11. Brasil. Ministério da Saúde. Situação epidemiológica/Dados. Brasília: Ministério da Saúde; 2016. [cited 2016 Mar 16]. Available from: http://portalsaude.saude.gov.br/index.php/situacao-epidemiologica-dados-influenza,22. São Paulo. Secretaria da Saúde. Coordenadoria de Controle de Doenças. Centro de Vigilância Epidemiológica "Prof. Alexandre Vranjac". Informe técnico: situação epidemiológica da influenza. São Paulo: Secretaria da Saúde; 2016. [cited 2016 Aug 31]. Available from: http://www.cremesp.org.br/pdfs/Informe_tecnico_flu_17mar2016.pdf.. In contrast, influenza seasonal activity commenced late in some countries in Western Europe, North America and Eastern Asia. Based on the WHO global influenza surveillance, in countries with influenza A(H1N1)pdm09 virus predominance, the hospitalization and intensive care unit (ICU) admission patterns seem to be similar to previous seasons when this virus predominated and young/middle-aged adults experienced severe disease33. World Health Organization. Risk assessment: seasonal influenza A(H1N1)pdm09. Geneva: WHO; 2016 [cited 2016 Feb 08]. Available from: http://www.who.int/influenza/publications/riskassessment_AH1N1pdm09_201602/en/. The aim of this study was to investigate the genetic pattern of influenza A(H1N1)pdm09 in the São Paulo State.

A total of 479 respiratory samples, collected in January by Sentinel Surveillance Units, were screened by real-time RT-PCR (qRT - PCR)44. Shu B, Wu KH, Emery S, Villanueva J, Johnson R, Guthrie E, et al. Design and performance of the CDC real-time reverse transcriptase PCR swine flu panel for detection of 2009 A (H1N1) pandemic influenza virus. J Clin Microbiol. 2011;49:2614-9. 5.. Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acid Res. 2004;32:1792-7.. Among them, 30 Influenza virus A(H1N1)pdm09 presenting ct values ≤ 30 were identified. A total of 6 viruses were sequenced by using an Applied Biosystems BigDye(r) Terminator v3.1 Cycle Sequencing Kit with reaction products resolved on an Applied Biosystems Sequencer 3730 DNA Analyzer. Nucleotide sequences were aligned using MUSCLE55. Edgar RC, MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acid Res. 2004;32 1792-7.. Sequences alignment results were further analyzed using the BioEdit program66. Hall TA. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucl Acids Symp Ser. 1999;41:95-8..

Our Institution is one of the National Influenza Centers accredited by the World Health Organization. The present follow up study of influenza surveillance has been approved by the Conselho Nacional de Ética em Pesquisa (CONEP) -135/2002.

Phylogenetic analyses

The TREESUB phylogenetic program (available from https://github.com/tamuri/treesub) was used to estimate the maximum likelihood phylogenetic trees using RAxML and PAML, followed by branch annotation of amino acid substitutions. The general time reversible+𝚪 (GTR+GAMMA) nucleotide substitution model was selected in RAxML v.7.3.0 for tree inference77. Stamatakis A. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics. 2006;22:2688-90.. Ancestral codon substitutions for each gene were estimated using baseml, as implemented in PAML88. Yang Z. PAML 4: phylogenetic analysis by maximum likelihood. Mol Biol Evol. 2007;24:1586-91. using the ML trees inferred. Nonsynonymous substitutions were then transcribed onto the consensus gene phylogenies and visualized in Figure 1 Tree v1.4.2 (available from http://tree.bio.ed.ac.uk/software/figtree/).

Figure 1
Molecular epidemiology of influenza A(H1N1)pdm09 hemagglutinin gene circulating in São Paulo, state, Brazil: 2016 anticipated influenza season.

Influenza A(H1N1)pdm09 viruses identified in São Paulo State during November 2015 belong to the 6B genetic group, presenting AA changes in the HA at residue E179D and I183V in the HA2 region. Figure 1 shows two viruses from Brazil collected in January that belong to the new 6B.1 subgroup (A/Sao Paulo/10-118/2016 and A/Sao Paulo/3032/2016). The HA sequences from São Paulo State obtained in this study, which were also used in the phylogenetic analysis, were deposited in the EpiFlu database of the Global Initiative on sharing Avian Influenza Data (GISAID) under the following accession numbers: EPI725841, EPI725838.

Influenza A(H1N1)pdm09 group 6B has also been identified during January in São Paulo State as shown in Figure 1, which were also used in the phylogenetic analysis; A/Sao Paulo/3050/2016; A/Sao Paulo/1267/2016; A/Sao Paulo/815/2016; A/Sao Paulo/10-441/2016 deposited in the GISAID under the follow accession numbers EPI725839, EPI725844, EPI704027, EPI725842, respectively.

The phylogenetic analysis of the A(H1N1)pdm09 HA gene demonstrated that HA genes of the recent viruses diverged into genetic groups 6A, 6B or 6C, with all viruses collected since September 1st, 2015 belonging to the genetic subgroup 6B. Subgroups 6B and 6C share AA changes in the HA at residues K283E and E499K (mature A(H1N1)pdm09 numbering after the signal peptide). Subgroup 6B viruses also possess AA changes in the HA at residues K163Q and A256T. Within subgroup 6B, additional subgroups with shared amino acid changes have emerged. The majority of viruses share an AA change at residue S84N; among these more than half share two additional changes at residues S162N (adds a glycosylation motif) and I216T (new subgroup 6B.1). A smaller group of 6B viruses (new subgroup 6B.2) shares AA changes at residues V152T, V173I, E491G and D501E99. Recommended composition of influenza virus vaccines for use in the 2016-2017 northern hemisphere influenza season. Wkly Epidemiol Rec. 2016;91:121-32..

Despite amino acid changes and changes in glycosylation, 6B.1 viruses were well inhibited by the reference ferret antiserum against A/California/07/2009 virus the A(H1N1) pdm09 component of the vaccine for 2016 influenza season99. Recommended composition of influenza virus vaccines for use in the 2016-2017 northern hemisphere influenza season. Wkly Epidemiol Rec. 2016;91:121-32..

In addition, a pool of human post-vaccination sera collected from healthy adults in the United States of America who received influenza vaccine in the 2015-2016 seasons well inhibited all recent viruses tested in the WHO CC at the Centers for Disease Control and Prevention (CDC) in Atlanta99. Recommended composition of influenza virus vaccines for use in the 2016-2017 northern hemisphere influenza season. Wkly Epidemiol Rec. 2016;91:121-32..

According to the literature data, the United Kingdom (UK), as others countries in Europe, has experienced a season dominated by circulation of influenza A(H1N1)pdm09 with reports of increases in hospitalizations and ICU admissions mainly in younger adults. The epidemiological observations are consistent with earlier seasons in the UK dominated by circulation of A(H1N1)pdm09, in particular in 2010/11, the first post-pandemic season1010. Pebody R, Warburton F, Ellis J, Andrews N, Potts A, Cottrell S, et al. Effectiveness of seasonal influenza vaccine in preventing laboratory-confirmed influenza in primary care in the United Kingdom: 2015/16 mid-season results. Euro Surveill. 2016; 21.. In São Paulo State this influenza virus A(H1N1)pdm09 pattern of seasonality occurred in 2013 (personnel communication), and in the currently anticipated influenza virus season 2016, influenza A(H1N1)pdm09 predominated.

Influenza virological surveillance follow-up will provide the antigenic and phylogenetic patterns of influenza A(H1N1)pdm09 virus circulation during the coming winter and early spring period in São Paulo State. Taking into account that Brazilian vacation period corresponds to the North America and Western Europe influenza season (January/February), and also considering the late influenza virus seasonality in these regions, this pattern of seasonality may be considered to interpret the earlier influenza seasonality in São Paulo State in 2016.

ACKNOWLEDGEMENTS

Our gratitude to the personnel of the Biological Sample Management Center/Institute Adolfo Lutz; Nilva Matias dos Reis, Ana Lúcia de Carvalho Avelino and Márcia Theobaldo for laboratorial technique support.

We also would like to thank sentinel nurses, practitioners and physicians of the Sentinel Surveillance Units of São Paulo State, Brazil, who provided quantitative information and collected samples from patients; the personnel from the Epidemiological Surveillance Centre, State Secretariat for Health of São Paulo, SP, Brazil; Municipal and State Secretariat for Health of São Paulo, SP, Brazil; and the personnel of the Ministry of Health of Brazil.

REFERENCES

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    Brasil. Ministério da Saúde. Situação epidemiológica/Dados. Brasília: Ministério da Saúde; 2016. [cited 2016 Mar 16]. Available from: http://portalsaude.saude.gov.br/index.php/situacao-epidemiologica-dados-influenza
  • 2
    São Paulo. Secretaria da Saúde. Coordenadoria de Controle de Doenças. Centro de Vigilância Epidemiológica "Prof. Alexandre Vranjac". Informe técnico: situação epidemiológica da influenza. São Paulo: Secretaria da Saúde; 2016. [cited 2016 Aug 31]. Available from: http://www.cremesp.org.br/pdfs/Informe_tecnico_flu_17mar2016.pdf.
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    World Health Organization. Risk assessment: seasonal influenza A(H1N1)pdm09. Geneva: WHO; 2016 [cited 2016 Feb 08]. Available from: http://www.who.int/influenza/publications/riskassessment_AH1N1pdm09_201602/en/
  • 4
    Shu B, Wu KH, Emery S, Villanueva J, Johnson R, Guthrie E, et al. Design and performance of the CDC real-time reverse transcriptase PCR swine flu panel for detection of 2009 A (H1N1) pandemic influenza virus. J Clin Microbiol. 2011;49:2614-9. 5.. Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acid Res. 2004;32:1792-7.
  • 5
    Edgar RC, MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acid Res. 2004;32 1792-7.
  • 6
    Hall TA. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucl Acids Symp Ser. 1999;41:95-8.
  • 7
    Stamatakis A. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics. 2006;22:2688-90.
  • 8
    Yang Z. PAML 4: phylogenetic analysis by maximum likelihood. Mol Biol Evol. 2007;24:1586-91.
  • 9
    Recommended composition of influenza virus vaccines for use in the 2016-2017 northern hemisphere influenza season. Wkly Epidemiol Rec. 2016;91:121-32.
  • 10
    Pebody R, Warburton F, Ellis J, Andrews N, Potts A, Cottrell S, et al. Effectiveness of seasonal influenza vaccine in preventing laboratory-confirmed influenza in primary care in the United Kingdom: 2015/16 mid-season results. Euro Surveill. 2016; 21.

Supplemental Table   Origin of the haemaglutinin sequences of influenza A(H1N1)pdm09 isolates for the phylogenetic analysis

Publication Dates

  • Publication in this collection
    2017

History

  • Received
    15 July 2016
  • Accepted
    22 Sept 2016
Instituto de Medicina Tropical de São Paulo Av. Dr. Enéas de Carvalho Aguiar, 470, 05403-000 - São Paulo - SP - Brazil, Tel. +55 11 3061-7005 - São Paulo - SP - Brazil
E-mail: revimtsp@usp.br