Genetic Analysis of Influenza A/H1N1pdm Strains Isolated in Bangladesh in Early 2020.

Abu Hasan,Nikhat Ara,Riku Yonezawa,Mizanur Rahman,Suma Mita Biswas,Ritsuko Koketsu,Tadahiro Sasaki,Tatsuo Shioda,Emi E Nakayama,Rummana Rahim,Juthamas Phadungsombat

doi:10.3390/tropicalmed7030038

Abstract

Influenza is one of the most common respiratory virus infections. We analyzed hemagglutinin (HA) and neuraminidase (NA) gene segments of viruses isolated from influenza patients who visited Evercare Hospital Dhaka, Bangladesh, in early 2020 immediately before the coronavirus disease 2019 (COVID-19) pandemic. All of them were influenza virus type A (IAV) H1N1pdm. Sequence analysis of the HA segments of the virus strains isolated from the clinical specimens and the subsequent phylogenic analyses of the obtained sequences revealed that all of the H1N1pdm recent subclades 6B.1A5A + 187V/A, 6B.1A5A + 156K, and 6B.1A5A + 156K with K209M were already present in Bangladesh in January 2020. Molecular clock analysis results suggested that the subclade 6B.1A5A + 156K emerged in Denmark, Australia, or the United States in July 2019, while subclades 6B.1A5A + 187V/A and 6B.1A5A + 156K with K209M emerged in East Asia in April and September 2019, respectively. On the other hand, sequence analysis of NA segments showed that the viruses lacked the H275Y mutation that confers oseltamivir resistance. Since the number of influenza cases in Bangladesh is usually small between November and January, these results indicated that the IAV H1N1pdm had spread extremely rapidly without acquiring oseltamivir resistance during a time of active international flow of people before the COVID-19 pandemic.

Highlights

Seasonal influenza is one of the most common respiratory virus infections
The genome of the influenza virus type A (IAV) H1N1pdm 2009 strains, which caused a pandemic in 2009 and subsequently became a seasonal flu, encodes PB2 and PA derived from the North American avian lineage, PB1 derived from human seasonal influenza A H3N2, NA and M derived from the Eurasian swine lineage, and HA, NP, and NS derived from the North American classical swine lineage [8]
An additional substitution of K209M was detected in this subclade, and the strains that carried K209M formed a distinct subclade with the most recent common ancestor (tMRCA) of 2019.73 (PP = 0.94). These results indicated that all the human IAV H1N1pdm09 subclades that dominated in Bangladesh in 2020 emerged within a year in other countries

Summary

Introduction

Seasonal influenza is one of the most common respiratory virus infections. It is estimated to induce about 3 to 5 million cases of severe illness and about 290,000 to 650,000 respiratory deaths per year prior to the coronavirus disease 2019 (COVID-19) pandemic The antigenicity of influenza virus is known to change by antigenic drift due to point mutations in the influenza virus genome and by antigenic shift that is induced by the reassortment of gene segments of two types of influenza viruses that simultaneously infect the same cell in a host [7]. The genome of the IAV H1N1pdm 2009 strains, which caused a pandemic in 2009 and subsequently became a seasonal flu, encodes PB2 and PA derived from the North American avian lineage, PB1 derived from human seasonal influenza A H3N2, NA and M derived from the Eurasian swine lineage, and HA, NP, and NS derived from the North American classical swine lineage [8]. Antigenic drift is known to induce mutants that can evade the host immune system through the accumulation of random point mutations in the viral genome due to the lack of proofreading ability of influenza RNA polymerase [7,9]. We found that the recent H1N1pdm subclade that emerged in East Asia in September 2019 had appeared in Bangladesh in January 2020

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Conclusion