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

Abstract

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.

Host Adaptive Evolution of Avian-Origin H3N2 Canine Influenza Virus

“…However, the present findings reveal a reduction in the distance between H3N2 CIV and the canine codon bias over time (Figure 5B), thus indicating increasing fitness to the canine usage pattern for H3N2 CIV. Similar observations have been reported for canine parvovirus type 2 and H1N1/pdm2009 viruses, where the host shift event from their reservoir host to the new host environment leads to subsequent adaptation in codon usage to better fit the cellular machinery of the new hosts (Franzo et al, 2017;Guo et al, 2020). Analysis of the relative abundance of the 16 possible dinucleotides in the H3N2 CIV genomes revealed a distinct usage preference among the dinucleotides (Figure 5C and Supplementary Table 2).…”

“…Host selection pressure on viral replicative efficacy and adaptation leaves a footprint in the base composition of a viral genome ( Greenbaum et al, 2008 ; Guo et al, 2020 ). The genetic code is degenerate, and the non-random usage of synonymous codons leads to codon usage bias ( Shah and Gilchrist, 2011 ).…”

Evidence for the circulation of genotype 4 Eurasian avian-like lineage swine H1N1 viruses in Korean swine farms using a newly developed one-step multiplex RT-qPCR

“…In terms of analytical specificity, the developed multiplex RT-qPCR can work only with influenza viruses. Even though A/California/04/2009(H1N1), A/Puerto Rico/8/1934(H1N1), and A/wild bird/Korea/SK14/2014(H1N1) viruses have identical subtypes, the multiplex RT-qPCR detects only the Eurasian avian lineage, which is closely related with the EA lineage [1,7] or EA lineage HA1 gene (Table 2 and 3). Interestingly, our PB2 primer and probe set specific to G4 EA swine H1N1 viruses did not work with A/California/04/2009(H1N1) virus, although the genetic lineage of the PB2 gene of the virus was the same as that of the G4 EA H1N1 virus [25] (Table 2 and 3).…”

mRNA vaccines: The future of prevention of viral infections?

“…As estimated, during the first 5 years of circulation, this strain was responsible for 150–575 thousand deaths worldwide 148 . H1N1/pdm2009 has a unique combination of genes resulting from the reassortment process among multiple swine influenza virus lineages: its NA and M gene segments were derived from the Eurasian avian‐like swine H1N1 influenza virus, while its other genes were from the triple‐reassortant (with PB2 and PA derived from avian H1N1, PB1 from human H3N2, and HA, NP, and NS from classical swine H1N1) 149 . In addition to pandemic infections, types A and B viruses (currently belonging to either B/Yamagata or B/Victoria lineage) cause seasonal epidemics on all continents.…”