Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2016 Jul;10(4):247-53.
doi: 10.1111/irv.12389. Epub 2016 May 27.

Rapid spread of influenza A(H1N1)pdm09 viruses with a new set of specific mutations in the internal genes in the beginning of 2015/2016 epidemic season in Moscow and Saint Petersburg (Russian Federation)

Andrey Komissarov  1 , Artem Fadeev  1 , Maria Sergeeva  2 , Sergey Petrov  2 , Kseniya Sintsova  1 , Anna Egorova  1 , Maria Pisareva  1 , Zhanna Buzitskaya  1 , Tamila Musaeva  3 , Daria Danilenko  4 , Nadezhda Konovalova  4 , Polina Petrova  4 , Kirill Stolyarov  5 , Elizaveta Smorodintseva  6 , Elena Burtseva  7 , Kirill Krasnoslobodtsev  7 , Elena Kirillova  7 , Lyudmila Karpova  8 , Mikhail Eropkin  4 , Anna Sominina  6 , Mikhail Grudinin  1
Affiliations

Rapid spread of influenza A(H1N1)pdm09 viruses with a new set of specific mutations in the internal genes in the beginning of 2015/2016 epidemic season in Moscow and Saint Petersburg (Russian Federation)

Andrey Komissarov et al. Influenza Other Respir Viruses. 2016 Jul.

Abstract

A dramatic increase of influenza activity in Russia since week 3 of 2016 significantly differs from previous seasons in terms of the incidence of influenza and acute respiratory infection (ARI) and in number of lethal cases. We performed antigenic analysis of 108 and whole-genome sequencing of 77 influenza A(H1N1)pdm09 viruses from Moscow and Saint Petersburg. Most of the viruses were antigenically related to the vaccine strain. Whole-genome analysis revealed a composition of specific mutations in the internal genes (D2E and M83I in NEP, E125D in NS1, M105T in NP, Q208K in M1, and N204S in PA-X) that probably emerged before the beginning of 2015/2016 epidemic season.

Keywords: A(H1N1)pdm09; Russia; high-throughput nucleotide sequencing; influenza.

PubMed Disclaimer

Figures

Figure 1
Figure 1
A. Influenza and ARI morbidity in Russian Federation on weeks 3–5, 2016. Epidemic threshold exceeded by less than 20% is indicated in green, epidemic threshold exceeded by 20 ‐ 50% is indicated by orange and epidemic threshold exceeded by more than 50% is indicated by red. B. Influenza and ARI incidence in Russian Federation in epidemic seasons 2009/2010, 2010/2011, 2011/2012, 2012/2013, 2013/2014, 2014/2015, and 2015/2016. C. Laboratory‐confirmed influenza cases in epidemic season 2015/2016, presented as % positive from all tested samples.
Figure 2
Figure 2
Antigenic map of influenza A(H1N1)pdm09 viruses isolated in Russia in 2009‐2016. The square on the map corresponds to a twofold difference in the homologous HI titer between the vaccine strain and the tested strain. Dots are viruses, squares—antisera. The vaccine strain is shown in red, with bold and underlined text. Strains isolated in epidemic season 2015/2016 are indicated in italicized bold.
Figure 3
Figure 3
Maximum‐likelihood phylogenetic trees based on HA (left) and NA (right) nucleotide sequences of influenza A(H1N1)pdm09 viruses. Vaccine strain is labeled with a green diamond; clade representative strains are highlighted in blue. Amino acid substitutions are indicated above corresponding branches. Bootstrap analysis, 1000 replications. Similar strains are collapsed to triangles (for expanded tree, see Supplement 1). Phylogenetic analysis was conducted in MEGA6 [9].
Figure 4
Figure 4
Frequency plots of selected amino acid substitutions in proteins encoded by internal genes of influenza A(H1N1)pdm09 viruses submitted to EpiFlu GISAID from 2013 to 2016.
Figure 5
Figure 5
Specific mutations in the internal genes of influenza A(H1N1)pdm09 viruses dominating in the beginning of 2015/2016 epidemic season.
See this image and copyright information in PMC

References

    1. Danilenko DM, Konovalova NI, Prokopetz AV, Bildanova ER, Eropkin MY, Sominina AA. Potential use of rat polyclonal antisera in antigenic analysis of human influenza viruses. Epidemiology and Vaccinoprophylaxis 2013; 68:73–79. (in Russian).
    1. Smith D, Lapedes A, Jong J et al Mapping the antigenic and genetic evolution of influenza virus. Science 2004; 35:371–376. - PubMed
    1. Zhou B, Donnelly ME, Scholes DT et al Single‐reaction genomic amplification accelerates sequencing and vaccine production for classical and Swine origin human influenza A viruses. J Virol 2009; 83:10309–10313. - PMC - PubMed
    1. Reid AH, Fanning TG, Janczewski TA, Taubenberger JK. Characterization of the 1918 “Spanish” influenza virus neuraminidase gene. PNAS 2000; 97:6785–6790. - PMC - PubMed
    1. Hale BG, Steel J, Medina RA et al Inefficient Control of Host Gene Expression by the 2009 Pandemic H1N1 Influenza A Virus NS1 Protein. J Virol 2010; 84:6909–6922. - PMC - PubMed

Publication types

MeSH terms