Exploring the Molecular Epidemiology and Evolutionary Dynamics of Influenza A Virus in Taiwan

Abstract

The evolution and population dynamics of human influenza in Taiwan is a microcosm of the viruses circulating worldwide, which has not yet been studied in detail. We collected 343 representative full genome sequences of human influenza A viruses isolated in Taiwan between 1979 and 2009. Phylogenetic and antigenic data analysis revealed that H1N1 and H3N2 viruses consistently co-circulated in Taiwan, although they were characterized by different temporal dynamics and degrees of genetic diversity. Moreover, influenza A viruses of both subtypes underwent internal gene reassortment involving all eight segments of the viral genome, some of which also occurred during non-epidemic periods. The patterns of gene reassortment were different in the two subtypes. The internal genes of H1N1 viruses moved as a unit, separately from the co-evolving HA and NA genes. On the other hand, the HA and NA genes of H3N2 viruses tended to segregate consistently with different sets of internal gene segments. In particular, as reassortment occurred, H3HA always segregated as a group with the PB1, PA and M genes, while N2NA consistently segregated with PB2 and NP. Finally, the analysis showed that new phylogenetic lineages and antigenic variants emerging in summer were likely to be the progenitors of the epidemic strains in the following season. The synchronized seasonal patterns and high genetic diversity of influenza A viruses observed in Taiwan make possible to capture the evolutionary dynamic and epidemiological rules governing antigenic drift and reassortment and may serve as a “warning” system that recapitulates the global epidemic.

Molecular epidemiologic and clinical characteristics of influenza B-associated complications among hospitalized patients during an outbreak in Taiwan

“…28 These results demonstrate that the vaccine strains recommended by the WHO were circulating in Taiwan one to two influenza seasons earlier. The seasonal patterns synchronized with genetic diversity of influenza B viruses observed in Taiwan make it possible to capture the evolutionary dynamics and epidemiological rules governing antigenic drift 29 and may serve as an early warning system for the detection of an emerging new epidemic strain.…”

Genetic variations on 31 and 450 residues of influenza A nucleoprotein affect viral replication and translation

“…The expression level of NP and β-actin were examined by Western blot and analyzed by Quantity One software from the dominant strain of previous season. Analysis of the human H3N2 whole genome sequences from databases revealed that there are evolutions in codon usage and frequent reassortment events [35][36][37]. A Previous study showed that reassortment occurred whereby A/ Sydney/5/97 converted to A/Fujian/411/02 strain, and A/Fujian/411/02 converted to A/California/7/04 strain [37].…”

Challenges and Strategies of Laboratory Diagnosis for Newly Emerging Influenza Viruses in Taiwan: A Decade after SARS

“…Five influenza seasons were dominated by H1N1, which were preceded by H3N2 during the most recent 5 years. In addition, H3N2 viruses frequently cocirculated with influenza B viruses in several seasons (2000-01, 2004-05, and 2006-07 seasons) [ 8 ]. This illustrates that the influenza A viruses were somewhat more active in Taiwan.…”

“…Influenza A virus is one of the most active pathogens in Taiwan causing regular, yearly islandwide epidemics and associated with significant morbidity and mortality in humans [ 7 , 8 ]. Influenza subtypes H1N1 and H3N2 are currently the major circulating subtypes and have been infecting the human population for several decades.…”

“…Nevertheless, the changing patterns of influenza viruses in Taiwan revealed a dynamic interaction between subtypes; for example, the H1N1 epidemics occurred during winter periods in Taiwan and the H3N2 epidemics often appeared as two separate peaks in summer and winter reflecting the circulation of at least two different H3N2 viruses during that period ( Figure 1 ). Data from Taiwan CDC Lin et al indicate that H3 summer isolates were genetically and antigenically distinct from preceding seasons but were similar to viruses isolated during the following winter [ 8 ]. This observation is consistent with the summer epidemic strains being the progenitors of those dominant in the following flu season.…”