Monitoring Genetic Diversity of Influenza A(H1N1)pdm09 Virus Circulating during the Post-Pandemic Period in Turkey

Abstract

SUMMARY:The aimes of the present study were to monitor genetic alterations in the hemagglutin (HA) gene and oseltamivir resistance-related alterations in the neuraminidase (NA) gene of influenza A(H1N1)pdm09 viral isolates detected during the post-pandemic period in Turkey. A total of 2601 clinical specimens obtained from suspected cases of influenza A(H1N1)pdm09 viral infections were analyzed by real-time reverse transcription polymerase chain reaction. Viral RNA was detected in 233 (9z) clinical specimens. Sequence analysis of the HA gene in 16 random isolates showed À98.7z homology among each other and with the A/California/07/2009 vaccine strain. These 16 isolates had common (75z-100z) amino acid substitiutions at positions P83S, D97N, S203T, R205K, I216V, V249L, I321V, and E374K in the HA gene. In addition, two additional rare mutations were also observed at positions S162N (addition of a glycosylation site, 6.25z) and A186T (receptor binding region, 6.25z). On the basis of amino acid substitutions in the HA1 domain, majority of the Turkish isolates were classified in the genetic group v and others in the genetic groups ii, iii, and vi. In the present study, we observed an increase in the variety and ratio of mutations detected in the HA1 and HA2 domains of the HA gene; however, these alterations have not yet resulted in vaccine escape mutants in Turkey. In addition, analysis of the NA regions of the isolates revealed that oseltamivir resistance was not an issue in Turkey.

Molecular characterization of the influenza A(H1N1)pdm09 isolates collected in the 2015‐2016 season and comparison of HA mutations detected in Turkey since 2009

“…A less common S185P mutation was seen instead of S185T in 10% of our isolates, and we also identified rare mutations (C4S, T72A, I96V, N260D, I266F, L314M, S326F in HA1 and I45V, V66A, R106K, F140L in HA2) in individual isolates. Notably, neither the D222G mutation previously associated with increased virulence, nor the mutations (A186T, R205K, D222E/N, V249L) observed in Turkish isolates of 2009 and 2010‐2011 influenza seasons were detected in our isolates.…”

“…In the 2009‐2010 and 2010‐2011 seasons, the HA nucleotide sequence similarity rates between Turkish isolates and the A/California/07/2009 virus were >98.9% and >98.7%, respectively, but the similarity ranging 96.6% to 97.2% we observed in the 2015‐2016 season was pointing out a rising divergence from the progenitor virus compared to the previous seasons. Accordingly, the total number of amino acid mutations (14 common, 1 less common, and 11 rare) in the 2015‐2016 season was higher than of the previously reported by Guldemir et al The 90%‐100% of our isolates carried 14 common mutations (P83S, S84N, D97N, S162N, K163Q, S185T, S203T, I216T, A256T, K283E, I321V in HA1 and E47K, S124N, E172K in HA2). These mutations have been previously reported from different parts of the world in isolates of the same period .…”

“…The data from Turkish Public Health General Directorate's previous reports and the results from this study revealed that the prevalence of influenza A(H1N1)pdm09 virus varied from year to year since 2009. The observed positivity rates were as following: 47.4% in 2009‐2010, 22.3% in 2010‐2011, 0% in 2011‐2012, 95% in 2012‐2013, 2% in 2013‐2014, 79% in 2014‐2015, and lastly 67.8% in the 2015‐2016 season.…”

“…It is necessary to report all circulating influenza viruses detected in health centers of the country to Turkish Ministry of Health and to transfer the clinical specimens to the National Viral Respiratory Pathogens Reference Laboratory (NVRPRL) of Public Health General Directorate (Ankara, Turkey) where the confirmation of influenza viruses is made by using real‐time reverse transcription‐polymerase chain reactions (RT‐PCR). After identification of the first Turkish influenza A(H1N1)pdm09 infection in 2009 pandemics, three surveillance reports were published from Public Health General Directorate in Turkey . In this follow‐up study, we aimed to identify the ongoing amino acid changes in the HA gene and also determine the oseltamivir sensitivity of influenza A(H1N1)pdm09 isolates circulating in the 2015‐2016 influenza season in Turkey.…”

Substitution in position 222 of haemagglutinin of pandemic influenza A (H1N1) viruses isolated from pigs in Poland

“…Phylogenetic analysis of the 2009 pandemic H1N1 virus (H1N1pdm09) indicated that the genome was a combination of gene segments that had not been previously identified in animal or human influenza viruses (5). The HA gene of H1N1pdm09 belongs to the classical swine lineage distinct from other viruses of human or avian origin that were introduced into pigs more recently, giving rise to 'human-like' and 'avianlike' swine influenza lineages (18).…”