Abstract
A human co-infected with H1N1 and H7N9 subtypes influenza A virus (IAV) causes a complex infectious disease. The identification of molecular-level variations in composition and dynamics of IAV quasispecies will help to understand the pathogenesis and provide guidance for precision medicine treatment. In this study, using single-molecule real-time sequencing (SMRT) technology, we successfully acquired full-length IAV genomic sequences and quantified their genotypes abundance in serial samples from an 81-year-old male co-infected with H1N1 and H7N9 subtypes IAV. A total of 26 high diversity nucleotide loci was detected, in which the A-G base transversion was the most abundant substitution type (67 and 64%, in H1N1 and H7N9, respectively). Seven significant amino acid variations were detected, such as NA:H275Y and HA: R222K in H1N1 as well as PB2:E627K and NA: K432E in H7N9, which are related to viral drug-resistance or mammalian adaptation. Furtherly, we retrieved 25 H1N1 and 22 H7N9 genomic segment haplotypes from the eight samples based on combining high-diversity nucleotide loci, which provided a more concise overview of viral quasispecies composition and dynamics. Our approach promotes the popularization of viral quasispecies analysis in a complex infectious disease, which will boost the understanding of viral infections, pathogenesis, evolution, and precision medicine.
Highlights
Influenza A virus (IAV) is a contagious pathogen that constantly infects many hosts, including but not limited to humans, birds, and pigs (Medina and García-Sastre, 2011)
The α-2,6-SA receptors are dominant in the upper respiratory tract (URT) of humans, while α-2,3-SA receptors are relatively more abundant than α-2,6-SA receptors found in the lower respiratory tract (LRT) of humans (Walther et al, 2013; Lakdawala et al, 2015; Long et al, 2019)
The top eight samples (S1-8) were performed using SMRT with four SMRT cells (S9 and S10 were RT-PCR negative for influenza A virus)
Summary
Influenza A virus (IAV) is a contagious pathogen that constantly infects many hosts, including but not limited to humans, birds, and pigs (Medina and García-Sastre, 2011). Annual influenza virus infections have significant health and economic burdens to mankind and livestock (Gordon and Reingold, 2018). IAV can be subtyped as HxNy by viral surface antigens hemagglutinin (HA) and neuraminidase (NA) proteins, which govern the viral lifecycle at cellular entry and release of virions (Dou et al, 2018). Co-Infected Disease With Influenza Virus subtypes (N1-11) have been observed (Boktor and Hafner, 2019). There are two common IAV cellular receptors:α-2,3-Sialic acid (α-2,3-SA) and α-2,6-Sialic acid (α-2,6-SA) in hosts (Nelli et al, 2010; França et al, 2013; Byrd-Leotis et al, 2017; Chen et al, 2018a; Xu et al, 2019). The α-2,6-SA receptors are dominant in the upper respiratory tract (URT) of humans, while α-2,3-SA receptors are relatively more abundant than α-2,6-SA receptors found in the lower respiratory tract (LRT) of humans (Walther et al, 2013; Lakdawala et al, 2015; Long et al, 2019)
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