Characterization of influenza A(H1N1)pdm09 viruses isolated from Nepalese and Indian outbreak patients in early 2015

Abstract

We characterized influenza A(H1N1)pdm09 isolates from large‐scale outbreaks that occurred in Nepal and India in early 2015. Although no specific viral features, which may have caused the outbreaks, were identified, an S84N substitution in hemagglutinin was frequently observed. Chronological phylogenetic analysis revealed that these Nepalese and Indian viruses possessing the S84N substitution constitute potential ancestors of the novel genetic subclade 6B.1 virus that spread globally in the following (2015/16) influenza season. Thus, active surveillance of circulating influenza viruses in the Southern Asia region, including Nepal and India, would be beneficial for detecting novel variant viruses prior to their worldwide spread.

Epidemic of influenza A(H1N1)pdm09 analyzed by full genome sequences and the first case of oseltamivir-resistant strain in Myanmar 2017

“…In NA phylogeny, amino acid substitutions V13I, I34V, and I314M were found in all Myanmar strains. These substitutions were also detected in Indian and Nepalese A(H1N1) pdm09 outbreak strains in early 2015, which suggests the coevolution of HA and NA [16]. According to our investigation (unpublished data), influenza A(H3N2) and B viruses, which were the predominant circulating strains in Myanmar during 2016, could be a possible reason for this big outbreak of A(H1N1)pdm09 and it may be responsible for the reduced herd immunity against A(H1N1)pdm09, when the new 6B.1 clade virus was introduced in Myanmar in 2017.…”

“…According to the phylogenetic analysis, the 2017 Myanmar influenza A(H1N1)pdm09 strains belonged to clade 6B.1 and were closely related to the strains that circulated in India and other countries during the same period. India reported several outbreaks and severe cases caused by influenza A(H1N1)pdm09 of Clade 6B and 6B.1 during 2015-2017 [16][17][18][19][20]31]. We suspect the possibility of transmission from India or other countries situated to the west of Myanmar because early cases of this outbreak were reported from Chin State, which shares its western border with Bangladesh.…”

“…Reference strains such as the influenza vaccine strains for the 2017-2018 Japanese vaccine, A/Singapore/GP1908/2015, and the 2017 southern hemisphere vaccine, A/Michigan/45/2015, as well as strains collected in India during May and August of 2017 (GISAID Isolate ID: EPI_ISL_281596, EPI_ISL_281597, EPI_ISL_281600, EPI_ISL_281601, EPI_ISL_281602, EPI_ISL_281603, EPI_ISL_281604, and EPI_ISL_282867) were downloaded from GISAID. India is specifically included in this analysis because A(H1N1)pdm09 outbreaks due to Clade 6B and 6B.1 viruses were repeatedly reported in India during 2015-2017, thus suggesting the possibility that the Myanmar strains may have originated in India [16][17][18][19][20]. Phylogenetic analysis was performed using the Hasegawa-Kishino-Yano model with discrete Gamma distribution (HKY+G) and the General Time Reversible model with discrete Gamma distribution incorporating Invariant sites (GTR + G + I) as the best-fit nucleotide substitution models for the HA and NA datasets, respectively, as implemented in the MEGA 6.0 software (Molecular Evolutionary Genetics Analysis) [21].…”

Differential Disease Severity and Whole Genome Sequence Analysis for Human Influenza A/H1N1pdm Virus in 2015-2016 Influenza Season

“…Severe and fatal outbreaks occurred in early 2015 in Nepal and India [42]. A study in Taiwan showed patients with laboratory-confirmed H1N1pdm 6B, 6B.1 and 6B.2 in 2013-14 and 2015-16 had higher risk for influenza-related complications compared to patients from seasons where 6B, 6B.1 and 6B.2 viruses did not dominate [43].…”

Mortality and severity related factors during the admission: H1N1 pneumonia

“…In our country, between 2015 and 2016 years a mild outbreak of H1N1 viruses has emerged, and lethal cases were detected as seen in Nepal and India in early 2015 (16). During the admission to the hospital, a prediction for severity and mortality should be assessed in patients with H1N1 pneumonia since some factors may have resulted in death.…”