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. 2016 Nov;10(6):486-492.
doi: 10.1111/irv.12401. Epub 2016 Jul 19.

Whole-genome analysis of influenza A(H1N1)pdm09 viruses isolated in Uganda from 2009 to 2011

Denis K Byarugaba  1   2 , Bernard Erima  3 , Monica Millard  3 , Hannah Kibuuka  3 , Luswa Lkwago  4 , Josephine Bwogi  5 , Derrick Mimbe  3 , Jocelyn B Kiconco  3 , Titus Tugume  3 , Edison A Mworozi  6 , Jasmine Turner  7 , Pamela P Mckenzie  7 , Richard R J Webby  7 , Robert G Webster  7 , Charlotte Foret  8 , Mariette F Ducatez  7   8 , Rodney Coldren  9 , Fred Wabwire-Mangen  3 , Scott Krauss  7
Affiliations

Whole-genome analysis of influenza A(H1N1)pdm09 viruses isolated in Uganda from 2009 to 2011

Denis K Byarugaba et al. Influenza Other Respir Viruses. 2016 Nov.

Abstract

We report a whole-genome analysis of 19 influenza A(H1N1)pdm09 isolates from four Ugandan hospitals between 2009 and 2011. The isolates differed from the vaccine strain A/California/07/2009 by three amino acid substitutions P100S, S220T, and I338V in the hemagglutinin and by two amino acid substitutions V106I and N248D in the neuraminidase proteins with consistent mutations in all gene segments distinguishing isolates from the 2009/2010 to 2010/2011 seasons. Phylogenetic analysis showed low genetic evolution, with genetic distances of 0%-1.3% and 0.1%-1.6% for HA and NA genes, respectively. The amino acid substitutions did not lead to antigenic differences from the reference strains.

Keywords: Uganda; influenza A(H1N1)pdm09; whole-genome sequencing.

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Figures

Figure 1
Figure 1
Occurrence and seasonality of the influenza A(H1N1)pdm09 isolates during the study period (July 2009 to April 2011)
Figure 2
Figure 2
Phylogenetic tree of the hemagglutinin (HA) gene segment of the Ugandan influenza A(H1N1)pdm09 viruses (in bold font) at the nucleotide level. The HA sequences of Ugandan H1N1 isolates were compared with relevant virus sequences available in GenBank: sequences from representative influenza A(H1N1)pdm09 isolates from Africa and closest blast hits from different regions of the world. Ugandan sequences available in the GISAID Epiflu database were also used (GISAID isolates ids: EPI_ISL_94767, EPI_ISL_105881, EPI_ISL_176803, EPI_ISL_176806). Sequences of vaccine strains [A/California/07/2009 (H1N1pdm09) and A/Brisbane/59/2007 (seasonal H1N1)] were also included. Bootstrap values (500 replicates) >50 are indicated on the nodes.*indicates partial sequence data
Figure 3
Figure 3
Phylogenetic tree of the neuraminidase (NA) gene segment of the Ugandan influenza A(H1N1)pdm09 viruses (in bold font) at the nucleotide level. The NA sequences of Ugandan H1N1 isolates were compared with relevant virus sequences available in GenBank: sequences from representative influenza A(H1N1)pdm09 isolates from Africa and closest blast hits from different regions of the world. Ugandan sequences available in the GISAID Epiflu database were also used (GISAID isolates ids: EPI_ISL_94767, EPI_ISL_105881, EPI_ISL_176803, EPI_ISL_176806, EPI_ISL_62338, EPI_ISL_65033, EPI_ISL_65034, EPI_ISL_68760, and EPI_ISL_71429). Sequences from vaccine strains [A/California/07/2009 (H1N1pdm09) and A/Brisbane/59/2007 (seasonal H1N1)] were also included. Bootstrap values (500 replicates) >50 are indicated on the nodes. *indicates partial sequence data
Figure 4
Figure 4
Phylogenetic tree of the polymerase 2 (PB2) gene segment of Ugandan influenza A(H1N1)pdm09 viruses (in bold font) at the nucleotide level. The PB2 sequences of Ugandan H1N1 isolates were compared with relevant virus sequences available in GenBank: sequences from representative influenza A(H1N1)pdm09 isolates from Africa and closest blast hits from different regions of the world. Ugandan sequences available in the GISAID Epiflu database were also used (GISAID isolates ids: EPI_ISL_176803, EPI_ISL_176806, EPI_ISL_62338, EPI_ISL_35548). Sequences from vaccine strains [A/California/07/2009 (H1N1)pdm09) and A/Brisbane/59/2007 (seasonal H1N1)] were also included. Bootstrap values (500 replicates) >50 are indicated on the nodes. *indicates partial sequence data
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