Phylogenomic analysis of Uganda influenza type-A viruses to assess their relatedness to the vaccine strains and other Africa viruses: a molecular epidemiology study

Simple item page
dc.contributor.authorNabakooza, Grace
dc.contributor.authorOwuor, David Collins
dc.contributor.authorLaurent, Zaydah R. de
dc.contributor.authorOwor, Nicholas
dc.contributor.authorKayiwa, John Timothy
dc.contributor.authorJjingo, Daudi
dc.contributor.authorNyaigoti Agoti, Charles
dc.contributor.authorNokes, David James
dc.contributor.authorKateete, David Patrick
dc.contributor.authorMulindwa Kitayimbwa, John
dc.contributor.authorFrost, Simon David William
dc.contributor.authorLutwama, Julius Julian
dc.date.accessioned2022-06-06T15:25:55Z
dc.date.available2022-06-06T15:25:55Z
dc.date.issued2021
dc.description.abstractGenetic characterisation of circulating influenza viruses is essential for vaccine selection and mitigation of viral transmission. The current scantiness of viral genomic data and underutilisation of advanced molecular analysis methods on influenza viruses circulating in Africa has limited their extensive study and representation in the global influenza ecology. We aimed to sequence influenza type-A viruses (IAVs) that previously circulated in Uganda and characterised their genetic relatedness to the vaccine viruses and publicly available Africa IAVs. Methods: This was an observational study nested to the Uganda national influenza surveillance programme. We used Next-generation sequencing to locally generate genomes from 116 A(H1N1)pdm09 and 118 A(H3N2) viruses collected between 2010 and 2018 from 7 districts across Uganda. A total of 206 hemagglutinin (HA), 207 neuraminidase (NA), and 213 matrix protein (MP) sequences were genetically compared to the WHO-recommended vaccines and other viruses isolated from Africa since 1994. Viral temporal and spatial divergence and circulating genetic clades were characterised using phylogenetic methods. Findings: We successfully generated gene sequences for 91·9% (215/234) viruses. Uganda A(H1N1)pdm09 and A(H3N2) virus HA, NA, and MP proteins had 96·36-99·09%, 96·49-99·39%, and 97·48-99·95% amino acid similarity, respectively, to vaccines recommended from 2010 through 2020. The local viruses incorporated amino acid substitutions (AAS) in their antigenic, receptor binding, and glycosylation sites each year causing them to antigenically drift away from vaccines. For seasons when vaccine formulations differed, Uganda IAV antigenic sites had 1-2 extra AAS relative to the Southern than Northern hemisphere vaccine viruses. All Uganda IAVs carried the adamantine-resistance marker S31N but not the neuraminidase inhibitor (NAI) resistance markers H274Y and H275Y. However, some A(H1N1)pdm09 viruses had permissive substitutions V234I, N369K, and V241I typical of NAI-resistant viruses.en_US
dc.identifier.citationNabakooza, G., Owuor, DC, de Laurent, ZR, Owor, N., Kayiwa, JT, Jjingo, D., ... & Lutwama, JJ (2021). Phylogenomic analysis of Uganda influenza type-A viruses to assess their relatedness to the vaccine strains and other Africa viruses: a molecular epidemiology study. bioRxiv . https://doi.org/10.1101/2021.07.05.451078en_US
dc.identifier.urihttps://doi.org/10.1101/2021.07.05.451078
dc.identifier.urihttps://nru.uncst.go.ug/handle/123456789/3768
dc.language.isoenen_US
dc.publisherbioRxiven_US
dc.titlePhylogenomic analysis of Uganda influenza type-A viruses to assess their relatedness to the vaccine strains and other Africa viruses: a molecular epidemiology studyen_US
dc.typeArticleen_US
Files
Original bundle
Now showing 1 - 1 of 1
Thumbnail Image
Name:
Phylogenomic analysis of Uganda influenza type-A viruses to assess their relatedness to the.pdf
Size:
1.48 MB
Format:
Adobe Portable Document Format
Description:
Article
Download
License bundle
Now showing 1 - 1 of 1
No Thumbnail Available
Name:
license.txt
Size:
1.71 KB
Format:
Item-specific license agreed upon to submission
Description:
Download
Collections
Medical and Health Sciences