Abstract
Objective: Human astrovirus (HAstV) is recognized as an important cause of acute gastroenteritis in children. Recombination between different genotypes of HAstV can contribute to diversity and evolution of the virus. This study aimed to investigate the emergence of HAstV recombinant strains in pediatric patients hospitalized with acute gastroenteritis in Chiang Mai, Thailand, spanning 2011–2020.Methods: A total of 92 archival HAstV strains collected from pediatric patients with acute gastroenteritis during 2011–2020 were further characterized to identify the recombinant strains. The ORF1b and ORF2 junction region of each strain was amplified and sequenced. The obtained sequences were analyzed in comparison with the reference sequences retrieved from GenBank database. Their genotypes were assigned using MEGA X software based on the partial ORF1b (RdRp) and ORF2 (capsid) regions, and the recombination breakpoints of recombinant strains were determined by SimPlot and RDP4 analyses.Results: Five inter-genotype recombinant strains with three recombination patterns of ORF1b/ORF2 of classic HAstV, HAstV8/HAstV1, HAstV8/HAstV3, and HAstV3/HAstV2, were detected. The recombination breakpoints of all strains were located at the 3′-end region of ORF1b close to the ORF1b/ORF2 junction.Conclusion: Several novel inter-genotype recombinant strains of classic HAstV genotypes were detected in pediatric patients with acute gastroenteritis in Chiang Mai, Thailand, during the period of 10 years from 2011 to 2020.
Highlights
Human astrovirus (HAstV) is a non-enveloped, positive-sense, single-stranded RNA virus, which is associated with acute gastroenteritis and systemic diseases (Johnson et al, 2017)
Analysis of the nucleotide sequences of partial ORF1b (RdRp) (342 bp) and ORF2 (329 bp) of 92 HAstV strains detected in this study revealed that assigned genotypes based on ORF1b of only five strains (CMH-N178-12, CMH-N106-13, CMH-S05915, CMH-S062-15, and CMH-S015-20) did not coincide with the genotypes based on ORF2 region
The phylogenetic tree of ORF2 (Figure 1B) of CMHN178-12, CMH-N106-13, CMH-S059-15, and CMH-S062-15 shows that CMH-N178-12, CMH-S059-15, and CMH-S062-15 clustered together with classic HAstV1 reference strains reported previously from the United Kingdom (Z25771), China (FJ755403 and KF211475), Korea (JN887820), Germany (AY720892), Hungary (HQ398856), the United States (MN433703), and Kenya (MW485039) with the nucleotide sequence identities ranging from 91.9–98.1%, whereas CMH-N106-13 clustered together with the HAstV3 reference strains reported previously from Germany (AF141381), the United States (MN444721, MK059951, and KY271946), France (MN510441), Venezuela (MG571777), and Russia (JF491430, GU732187, and GU223905) with the nucleotide sequence identities ranging from 95.7–100%
Summary
Human astrovirus (HAstV) is a non-enveloped, positive-sense, single-stranded RNA virus, which is associated with acute gastroenteritis and systemic diseases (Johnson et al, 2017). The genome of HAstV contains three open reading frames (ORFs), ORF1a, ORF1b, and ORF2 (Bosch et al, 2014). The first evidence of recombination naturally occurring among HAstVs was documented in 2001 by demonstrating that the ORF1b and ORF2 of the new HAstV strain were closely related to those of HAstV3 and HAstV5, respectively, and a putative recombination site was demonstrated at the ORF1b/ORF2 junction (Walter et al, 2001). Many more recombinant strains have been reported even though little is known about the mechanism of astrovirus recombination (Bosch et al, 2014)
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