The evolutionary dynamics of H1N1/pdm2009 in India

Luo, Tingting; Liu, Lu; Shen, Xuejuan; Irwin, David M.; Liao, Ming; Shen, Yongyi

doi:10.1016/j.meegid.2018.08.009

Cited by 5 publications

(2 citation statements)

References 33 publications

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“…In addition, viral codon usage patterns significantly govern their replication and fitness in host microenvironment ( Carlini, 2004 ). Viruses depend on host translational machinery, and codon usage patterns that are better adapted to its host facilitate the efficiency and accuracy of protein production at multiple levels while maintaining amino acid sequence ( Tian et al, 2018 ). It has been reported that modern H3N2 viruses are translated more efficiently due to their acquisition of codon usage patterns that better reflect tRNA availability in IFN-treated cells ( Smith et al, 2018 ).…”

Section: Introductionmentioning

confidence: 99%

Origin and Evolution of H1N1/pdm2009: A Codon Usage Perspective

et al. 2020

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The H1N1/pdm2009 virus is a new triple-reassortant virus. While Eurasian avian-like and triple-reassortant swine influenza viruses are the direct ancestors of H1N1/pdm2009, the classic swine influenza virus facilitate the spectrum of influenza A diversity in pig population when the reassortant events occurred during 1998 to April 2009. The factors that facilitate the final formation of this gene constellation for H1N1/pdm2009 virus from this complex gene pool remain unknown. Since a novel successful virus should efficiently replicate and transmit in their hosts, in this study, we estimated the adaptability of the codon usage patterns of the pool of genes from these lineages of swine influenza viruses to the human expression system. We found that the MP and NA genes of Eurasian avian-like swine influenza viruses, and the PB2, PB1 and PA genes of triple-reassortant swine influenza viruses were best adapted to the human codon usage pattern. As these genes participated in the development of H1N1/pdm2009, they might help in viral replication and strengthen its competitiveness during its emergence. After its emergence in the human population, a gradual optimization of codon usage patterns between 2009 and 2019 to the human codon usage for the H1N1/pdm2009 genes was detected. This reveals that ongoing adaptive evolution, after its original incursion, occurred to further increase the adaptability of overall gene cassette to human expression system.

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Section: Introductionmentioning

confidence: 99%

Origin and Evolution of H1N1/pdm2009: A Codon Usage Perspective

et al. 2020

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“…The HA Ind strains, reported with more specific mutations at a higher rate, emerged with enhanced virulence ( Tharakaraman and Sasisekharan, 2015 ) and also became resistant to antiviral drugs such as oseltamivir, zanamivir, and peramivir ( Parida et al, 2016 ; Tandel et al, 2018 ). These viruses with frequent reassortment at the sequence level evolved as more virulent than the previous seasonal H1N1 viruses ( Baillie and Digard, 2013 ; Su et al, 2015 ; Luo et al, 2018a ) and acquired better abilities to infect humans, which caused worse outbreaks ( Luo et al, 2018b ).…”

Section: Discussionmentioning

confidence: 99%

Evolution of Indian Influenza A (H1N1) Hemagglutinin Strains: A Comparative Analysis of the Pandemic Californian HA Strain

Pushan

Samantaray

Rangarajan

et al. 2023

Front. Mol. Biosci.

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The need for a vaccine/inhibitor design has become inevitable concerning the emerging epidemic and pandemic viral infections, and the recent outbreak of the influenza A (H1N1) virus is one such example. From 2009 to 2018, India faced severe fatalities due to the outbreak of the influenza A (H1N1) virus. In this study, the potential features of reported Indian H1N1 strains are analyzed in comparison with their evolutionarily closest pandemic strain, A/California/04/2009. The focus is laid on one of its surface proteins, hemagglutinin (HA), which imparts a significant role in attacking the host cell surface and its entry. The extensive analysis performed, in comparison with the A/California/04/2009 strain, revealed significant point mutations in all Indian strains reported from 2009 to 2018. Due to these mutations, all Indian strains disclosed altered features at the sequence and structural levels, which are further presumed to be associated with their functional diversity as well. The mutations observed with the 2018 HA sequence such as S91R, S181T, S200P, I312V, K319T, I419M, and E523D might improve the fitness of the virus in a new host and environment. The higher fitness and decreased sequence similarity of mutated strains may compromise therapeutic efficacy. In particular, the mutations observed commonly, such as serine-to-threonine, alanine-to-threonine, and lysine-to-glutamine at various regions, alter the physico-chemical features of receptor-binding domains, N-glycosylation, and epitope-binding sites when compared with the reference strain. Such mutations render diversity among all Indian strains, and the structural and functional characterization of these strains becomes inevitable. In this study, we observed that mutational drift results in the alteration of the receptor-binding domain, the generation of new variant N-glycosylation along with novel epitope-binding sites, and modifications at the structural level. Eventually, the pressing need to develop potentially distinct next-generation therapeutic inhibitors against the HA strains of the Indian influenza A (H1N1) virus is also highlighted here.

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No gene communication of HA gene between the human H3N2 and H1N1 pandemic 2009 influenza A viruses

Shen

Irwin

et al. 2019

Journal of Infection

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The evolutionary dynamics of H1N1/pdm2009 in India

Cited by 5 publications

References 33 publications

Origin and Evolution of H1N1/pdm2009: A Codon Usage Perspective

Origin and Evolution of H1N1/pdm2009: A Codon Usage Perspective

Evolution of Indian Influenza A (H1N1) Hemagglutinin Strains: A Comparative Analysis of the Pandemic Californian HA Strain

No gene communication of HA gene between the human H3N2 and H1N1 pandemic 2009 influenza A viruses

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