Investigation of genetic variation: Neuraminidase gene of influenza A virus H1N1/pdm09, Shiraz, Iran (2015–2016)

Oseltamivir and antiviral agents are frequently used for the prevention and treatment of influenza infection. However, resistance to oseltamivir has been reported globally due to a mutation in the Influenza virus neuraminidase gene. Such resistance will be detected by genotyping and phenotyping studies of viral isolates. The recent study aimed to determine the genetic mutation of neuraminidase gene in influenza A (H1N1) viruses isolated from children referred to Shiraz tertiary hospitals during 1 year (2015–2016) with influenza‐like symptoms. A total of 300 patients were registered and throat samples were taken. The throat swabs were used for viral RNA extraction. Detection of influenza A (H1N1) was performed using the one‐step real‐time polymerase chain reaction (qRT‐PCR) method. From positive isolates for H1N1, 51 random samples were evaluated for neuraminidase gene mutation with the nested PCR‐sequencing method. Of 300 cases, 102 (34%) isolates were detected as influenza A (H1N1) pdm09. Based on sequencing results, 2 of the 44 sequenced isolates exhibited H275Y substitution, which presented oseltamivir resistance. In comparison with reference strain, the phylogenetic analysis of sequenced isolates was classified in genogroup 6B. While this result is the first report of emerging oseltamivir‐resistant in the southwest of Iran, it is highly recommended to perform these evaluations on the different geographical regions in any prevalence area to plan treatment strategies for influenza. Highlights oseltamivir‐resistant A(H1N1) pdm09 virus was detected in south Iran. oseltamivir‐resistant A(H1N1) pdm09 viruses may re‐emerge in future seasonal outbreaks. Constant monitoring of oseltamivir‐resistant viral variants is essential for the implementation of the viral treatment strategy.