Molecular Evolution of Influenza A Viruses From Mauritius, 2017-2019

Abstract

Background: Despite being a vaccine preventable disease, influenza remains a burden in African countries. In Mauritius, influenza virus activity is year-round but evidence-based data to guide vaccination and pandemic preparedness strategies are lacking. This study aimed to describe the genetic diversity of influenza A viruses detected in Mauritius between 2017 and 2019.

Methods: Influenza A/H1N1pdm09 and A/H3N2 virus isolates were sequenced using Oxford Nanopore technology. Sequence reads assembled by CZ ID and Genome Detective web-based tools were uploaded to the EpiFlu database of the Global Initiative on Sharing All Influenza Data (GISAID). Sequence alignments and phylogenetic analysis were performed using Nextclade and MEGA XI software. BioEdit software was used to view amino acid substitutions compared to annual vaccine strains. Prediction of potential N-linked glycosylation (PNG) sites was determined by NetNGlyc 1.0.

Results: Influenza A was predominant (92.6%), with A/H1N1pdm09 prevailing overall (62.5%) but A/H3N2 dominating in 2017 (55.9%). Phylogenetic analysis identified clade 6B dominance for A/H1N1pdm09, with notable substitutions E119K, Q136K and D151E linked to antigenic changes. A/H3N2 exhibited significant genetic diversity, with co-circulation of 3C.2a4 and 3C.2a1 in 2017 while 2018 predominant subclade 3C.2a1b.1 highlights continued antigenic drift. Loss of PNG sites at position 158 (11/21; 52.4%) in HA and position 329 (81.0%, 17/21) in NA of A/H3N2 viruses were observed.

Conclusions: Continued evolution of A/H1N1pdm09 and A/H3N2 viruses in Mauritius highlights the need for sustained genomic surveillance to inform vaccine and antiviral strategies. Data from Mauritius will contribute to understanding of influenza viruses' ecology in the African region and globally.

Keywords: Ct cycle threshold; GISAID Global Initiative on Sharing All Influenza Data; HA Haemagglutinin; ILI Influenza Like Illness; NA Neuraminidase; NGlyc N‐linked glycosylation; PCR Polymerase chain reaction; SARI Severe Acute Respiratory Illness.

FIGURE 1

Maximum‐likelihood (a) HA and (b) NA genes phylogenetic trees from influenza A/H1N1pdm09 viruses detected in Mauritius, 2017–2019. Statistical confidence in branch placements were determined using 1000 bootstrap replicates and significant clusters were defined by bootstrap values > 70%. The vaccine strain is colored bright red. Mauritius strains from each year are indicated by different colors as shown in the color key. The key amino acid substitutions defining clades and subclades are indicated on the branches.

FIGURE 2

Maximum‐likelihood phylogenetic trees for (a) HA and (b) NA gene segments from influenza A/H3N2 viruses detected in Mauritius during 2017–2019. Statistical confidence in branch placements were determined using 1000 bootstrap replicates and significant clusters were defined by bootstrap values > 70%. Mauritius strains from each year are indicated by different colors as shown in the color key and relevant vaccine strains are colored bright red. Key amino acid substitutions defining clades and subclades are indicated on branches.