Phylogenomic analysis uncovers a 9-year variation of Uganda influenza type-A strains from the WHO-recommended vaccines and other Africa strains

Nabakooza, G; Owuor, DC; de Laurent, ZR; Galiwango, R; Owor, N; Kayiwa, JT; Jjingo, D; Agoti, CN; Nokes, DJ; Kateete, DP; Kitayimbwa, JM; Frost, SDW; Lutwama, JJ

Journal article

Phylogenomic analysis uncovers a 9-year variation of Uganda influenza type-A strains from the WHO-recommended vaccines and other Africa strains

Abstract:: Genetic characterisation of circulating influenza viruses directs annual vaccine strain selection and mitigation of infection spread. We used next-generation sequencing to locally generate whole genomes from 116 A(H1N1)pdm09 and 118 A(H3N2) positive patient swabs collected across Uganda between 2010 and 2018. We recovered sequences from 92% (215/234) of the swabs, 90% (193/215) of which were whole genomes. The newly-generated sequences were genetically and phylogenetically compared to the WHO-recommended vaccines and other Africa strains sampled since 1994. Uganda strain hemagglutinin (n = 206), neuraminidase (n = 207), and matrix protein (MP, n = 213) sequences had 95.23–99.65%, 95.31–99.79%, and 95.46–100% amino acid similarity to the 2010–2020 season vaccines, respectively, with several mutated hemagglutinin antigenic, receptor binding, and N-linked glycosylation sites. Uganda influenza type-A virus strains sequenced before 2016 clustered uniquely while later strains mixed with other Africa and global strains. We are the first to report novel A(H1N1)pdm09 subclades 6B.1A.3, 6B.1A.5(a,b), and 6B.1A.6 (± T120A) that circulated in Eastern, Western, and Southern Africa in 2017–2019. Africa forms part of the global influenza ecology with high viral genetic diversity, progressive antigenic drift, and local transmissions. For a continent with inadequate health resources and where social distancing is unsustainable, vaccination is the best option. Hence, African stakeholders should prioritise routine genome sequencing and analysis to direct vaccine selection and virus control

Publication status:: Published

Peer review status:: Peer reviewed

Actions

Email

Email this record

Send the bibliographic details of this record to your email address.

Your Email
Please enter the email address that the record information will be sent to.

-
Your message (optional)
Please add any additional information to be included within the email.
Share
Cite

Cite this record

APA Style

Nabakooza, G., Owuor, D. C., de Laurent, Z. R., Galiwango, R., Owor, N., Kayiwa, J. T., Jjingo, D., Agoti, C. N., Nokes, D. J., Kateete, D. P., Kitayimbwa, J. M., Frost, S. D. W., & Lutwama, J. J. (2023). Phylogenomic analysis uncovers a 9-year variation of Uganda influenza type-A strains from the WHO-recommended vaccines and other Africa strains. Scientific Reports, 13(1), 5516–5516.

MLA Style

Nabakooza, G, et al. “Phylogenomic Analysis Uncovers a 9-Year Variation of Uganda Influenza Type-A Strains from the WHO-Recommended Vaccines and Other Africa Strains.” Scientific Reports, vol. 13, no. 1, 2023, pp. 5516–16.

Chicago Style

Nabakooza, G, DC Owuor, ZR de Laurent, et al. 2023. “Phylogenomic Analysis Uncovers a 9-Year Variation of Uganda Influenza Type-A Strains from the WHO-Recommended Vaccines and Other Africa Strains.” Scientific Reports 13 (1): 5516–16.
Print