The Phylodynamics of Seasonal Influenza A/H1N1pdm Virus in China Between 2009 and 2019

Abstract

Since its first introduction into China in 2009, influenza A/H1N1pdm virus has undergone a rapid expansion and replaced the classical seasonal A(H1N1) virus. To characterize the ongoing evolution and national transmission dynamics of this virus, we analyzed 335 complete genome, 1259 HA, and 1043 NA sequences of the A/H1N1pdm strains detected in China. We found that the dN/dS value and relative genetic diversity of the A/H1N1pdm virus experienced a decrease from 2009 to 2017, and then a rapid increase during 2018-2019. Importantly, elevated relative genetic diversity was observed in the A/H1N1pdm and the A/H3N2 viruses, as well as two lineages (Victoria and Yamagata) of influenza B virus during 2018-2019, suggesting the simultaneous changes of these viruses in terms of genetic diversity might be associated with the recent large outbreak of seasonal influenza epidemic in China during 2018-2019. Fifteen amino acid mutations were found to be fixed along the main trunks of both HA and NA phylogenetic trees, and some of them are located in the antigen binding site or the receptor binding site. A sequential accumulation of mutations relative to the 2009-vaccine strain was observed in the circulating A/H1N1pdm strains during 2009-2016, while a rapid accumulation of mutations relative to the 2015-vaccine strain appeared in the emerging variants in 2017 shortly after the release of the vaccine. Multiple introductions of the A/H1N1pdm lineages into China were observed during 2009-2019, and East China and South China were found to serve as two major epicenters responsible for the national migration of the virus. In summary, these data provide important insights into the understanding of the evolution, epidemiology and transmission of the A/H1N1pdm virus, and highlight the importance of strengthening influenza surveillance in East China and South China.

Keywords: A/H1N1pdm; genetic diversity; genetic drift; transmission; viral evolution.

FIGURE 1

The dN/dS values for major genes of A/H1N1pdm virus. Colored bars correspond to different years. This dN/dS value represents an average over all sites and lineages.

FIGURE 2

Phylogeny of A/H1N1pdm virus by HA gene and three-dimensional structure of HA glycoprotein. (A) Maximum likelihood tree inferred from 1259 A/H1N1pdm virus HA sequences in China from 2009 to 2019. The color of the branch is marked by the isolation year of the strain. Fixed amino acid mutations are mapped at the major nodes of the tree. Positively selected sites are highlighted by asterisks (*). Scale bar represents number of substitutions per site. (B) Three-dimensional structure map of HA monomer of A/H1N1pdm virus (Protein Data Bank code: 3LZG). Antigenic sites were shown in red in the three-dimensional structure.

FIGURE 3

Phylogeny of A/H1N1pdm virus by NA gene. The ML tree inferred from 1043 A/H1N1pdm virus NA sequences in China from 2009 to 2019. The color of the branch is marked by the isolation year of the strain. Fixed amino acid mutations are mapped at the major nodes of the tree. Positively selected sites are highlighted by asterisks (*).

FIGURE 4

Amino acid variations of HA (A) and NA (B) glycoproteins of A/H1N1pdm virus during 2009–19 compared to the vaccine strains. The small dots indicate identical amino acids to the vaccine stain A/California/07/2009. The number of identical sequences is shown in parenthesis.

FIGURE 5

Population dynamics of genetic diversity of A/H1N1pdm virus in China during 2009–2019. The relative genetic diversity of each gene was estimated using the Gaussian Markov Random Fields (GMRF) Skyride model.

FIGURE 6

Comparative phylogenetic analysis, population dynamics and positive rate of A/H1N1pdm (A), A/H3N2 (B), influenza B/Victoria (C), and influenza B/Yamagata (D) viruses. Phylogenies were inferred using the strict clock model and relative genetic diversity estimated using the Gaussian Markov Random Field (GMRF) model. The branches were colored by sampling year. Solid black lines in the GMRF plot represent mean relative genetic diversity, and the gray shades indicate the 95% HPD (highest probability density) intervals. The positive rate of A/H1N1pdm virus (2009–2019), A/H3N2 (2009–2019), influenza B/Victoria (2015–2019), influenza B/Yamagata (2015–2019) by week of specimen collection in China was retrieved from Chinese National Influenza Center.

FIGURE 7

Spatial diffusion of A/H1N1pdm virus. Thickness of lines represents supported migration rates: solid black arrows, decisive support with BF > 1000; dashed black arrows, very strongly supported with 100 < BF < 1000; solid gray arrows, strongly support with 10 < BF < 100; dashed gray arrows, support with 3 < BF < 10. In the phylogenetic tree, colored branches represent different regions. North China (NC), Northeast China (NEC), Northwest China (NWC), Central China (CC), East China (EC), South China (SC), and Southwest China (SWC).