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
. 2022 Oct 31;14(11):2414.
doi: 10.3390/v14112414.

Evolutionary Dynamics of Whole-Genome Influenza A/H3N2 Viruses Isolated in Myanmar from 2015 to 2019

Wint Wint Phyu  1 , Reiko Saito  1   2 , Yadanar Kyaw  3 , Nay Lin  4 , Su Mon Kyaw Win  2 , Nay Chi Win  2 , Lasham Di Ja  2 , Khin Thu Zar Htwe  5 , Thin Zar Aung  6 , Htay Htay Tin  7 , Eh Htoo Pe  7 , Irina Chon  1   2 , Keita Wagatsuma  1   8 , Hisami Watanabe  2
Affiliations

Evolutionary Dynamics of Whole-Genome Influenza A/H3N2 Viruses Isolated in Myanmar from 2015 to 2019

Wint Wint Phyu et al. Viruses. .

Abstract

This study aimed to analyze the genetic and evolutionary characteristics of the influenza A/H3N2 viruses circulating in Myanmar from 2015 to 2019. Whole genomes from 79 virus isolates were amplified using real-time polymerase chain reaction and successfully sequenced using the Illumina iSeq100 platforms. Eight individual phylogenetic trees were retrieved for each segment along with those of the World Health Organization (WHO)-recommended Southern Hemisphere vaccine strains for the respective years. Based on the WHO clades classification, the A/H3N2 strains in Myanmar from 2015 to 2019 collectively belonged to clade 3c.2. These strains were further defined based on hemagglutinin substitutions as follows: clade 3C.2a (n = 39), 3C.2a1 (n = 2), and 3C.2a1b (n = 38). Genetic analysis revealed that the Myanmar strains differed from the Southern Hemisphere vaccine strains each year, indicating that the vaccine strains did not match the circulating strains. The highest rates of nucleotide substitution were estimated for hemagglutinin (3.37 × 10-3 substitutions/site/year) and neuraminidase (2.89 × 10-3 substitutions/site/year). The lowest rate was for non-structural protein segments (4.19 × 10-5 substitutions/site/year). The substantial genetic diversity that was revealed improved phylogenetic classification. This information will be particularly relevant for improving vaccine strain selection.

Keywords: A/H3N2; evolution; genetic reassortment; mutation; next-generation sequencing; seasonal influenza; variant viruses; whole-genome sequencing.

PubMed Disclaimer

Conflict of interest statement

The authors declare no conflict of interest. The funders had no role in the design of the study; collection, analyses, or interpretation of data; writing of the manuscript; or decision to publish the results.

Figures

Figure 1
Figure 1
Maximum-likelihood phylogenetic trees of all eight segments of influenza A/H3N2 viruses circulating in Myanmar and comparison of sequences from 79 strains isolated in Myanmar between 2015 and 2019 and to the Southern Hemisphere vaccine strains of known clades recommended by the WHO. Southern Hemisphere vaccine strains from 2015 to 2019 are indicated by bold letters according to clade classification by the WHO. (A) HA, (B) PB2, (C) PB1, (D) PA, (E) NP, (F) NA, (G) MP, and (H) NS segments. Amino acid substitutions compared to A/Texas/50/2012 were indicated in HA. The two strains that belonged to 3c.2a1 are highlighted in pink and denoted by pink triangles to clarify the topologies concerning 3c.2a and 3c.2a1b viruses. One revival strain, A/Yangon/18M141/2018, is marked with blue circles. The phylogenetic tree was inferred by the maximum-likelihood method using 1000 bootstrap replicates implemented in MEGA v.7.0.26. Branch values > 70% are indicated at the nodes.
See this image and copyright information in PMC

References

    1. Centers for Disease Control and Prevention Key Facts about Influenza (Flu) [(accessed on 10 February 2022)];2022 Available online: https://www.cdc.gov/flu/about/keyfacts.htm.
    1. World Health Organization Influenza (Seasonal) Fact Sheet. [(accessed on 10 February 2022)];2018 Available online: www.who.int/mediacentre/factsheets/fs211/en/
    1. Thompson W.W., Weintraub E., Dhankhar P., Cheng P.Y., Brammer L., Meltzer M.I., Bresee J.S., Shay D.K. Estimates of US influenza-associated deaths made using four different methods. Influenza Other Respir. Viruses. 2009;3:37–49. doi: 10.1111/j.1750-2659.2009.00073.x. - DOI - PMC - PubMed
    1. Nair H., Brooks W.A., Katz M., Roca A., Berkley J.A., Madhi S.A., Simmerman J.M., Gordon A., Sato M., Howie S., et al. Global burden of respiratory infections due to seasonal influenza in young children: A systematic review and meta-analysis. Lancet. 2011;378:1917–1930. doi: 10.1016/S0140-6736(11)61051-9. - DOI - PubMed
    1. Webster R.G., Bean W.J., Gorman O.T., Chambers T.M., Kawaoka Y. Evolution and ecology of influenza A viruses. Microbiol. Rev. 1992;56:152–179. doi: 10.1128/mr.56.1.152-179.1992. - DOI - PMC - PubMed

Publication types

Substances