Molecular epidemiology survey and characterization of human influenza A viruses circulating among Palestinians in East Jerusalem and the West Bank in 2015

Abstract

Frequent typing and molecular characterization of influenza A (IAV) strains are crucial for the identification of circulating subtypes and for the selection of the subtypes' lineages to be included in the annually prepared vaccine cocktail. We investigated IAV sampled from an underrepresented population from Palestine. 200 nasopharyngeal aspirates (NPA) were collected between February and May of 2015 from Palestinians in East Jerusalem and the West Bank suffering from mild to severe symptoms of upper respiratory infections. NPA were screened for the presence of IAV using RT-PCR. Epidemiological data, hemagglutinin (HA) and neuraminidase (NA) gene sequences were analyzed in IAV positive samples. 50 samples tested positive for IAV; 48% of which were identified as A(H1N1)pdm09 and 52% as A(H3N2), respectively. Infection with A(H1N1)pdm09 occurred mainly in April, while A(H3N2) infections were mainly detected in March. Most IAV infections in 6-year-olds and below were attributed to subtype A(H3N2), while A(H1N1)pdm09 was responsible for most infections in adults above 18-year-olds. Analyses of HA and NA amino acid sequences revealed numerous substitutions. Thereafter, and based on the HA analysis, the Palestinian A(H1N1)pdm09 isolates fell into clade 6B, while the A(H3N2) isolates fell into clades 3C.2 and 3C.3, respectively. This study is significant in providing the first insight into the epidemiology and genetic properties of IAV circulating in Palestine. In contrast to international reports for the same season, A(H3N2) was not the dominant subtype as in northern hemisphere, nor was A(H1N1)pdm09 as in WHO reports for the Middle East, however genetic properties of Palestinian A(H3N2) and A(H1N1)pdm09 were in line with global isolates.

Fig 1. Distribution of IAV subtypes in the months of collection.

The percentages reflect the numbers of each subtype in each month in relevance to the 50 total positive IAV cases.

Fig 2. Distribution of A(H1N1)pdm09 and A(H3N2) subtypes in the different age groups.

The distribution of IAV subtypes throughout the different age groups was calculated relative to the 50 total positive IAV samples.

Fig 3. Phylogenetic analysis of the HA gene segment of Palestinian influenza A(H1N1)pdm09 isolates.

Palestinian HA sequences (in red) were compared with those from regional and international isolates, as well as vaccine strain of the season 2014/2015 and the current vaccine strain (in dark blue). NCBI and GISAID accession numbers are indicated for all archived sequences. HA1 aa substitutions are in green and HA2 aa substitutions are in green and underlined.

Fig 4. Phylogenetic analysis of the HA gene segment of Palestinian influenza A(H3N2) isolates.

Palestinian HA sequences (in red) were compared with those from regional and international isolates, as well as vaccine strain of seasons 2014/2015-2017/2018 (in dark blue). NCBI and GISAID accession numbers are indicated for all archived sequences. HA1 aa substitutions are in green and HA2 are in green and underlined.