Triple Intergenotype Recombination of Human Astrovirus 5, Human Astrovirus 8, and Human Astrovirus 1 in the Open Reading Frame 1a, Open Reading Frame 1b, and Open Reading Frame 2 Regions of the Human Astrovirus Genome

Wei, Hongyu; Khamrin, Pattara; Yodmeeklin, Arpaporn; Jampanil, Nutthawadee; Phengma, Phitchakorn; Xie, Zhenfeng; Ukarapol, Nuthapong; Ushijima, Hiroshi; Maneekarn, Niwat

doi:10.1128/spectrum.04888-22

Cited by 4 publications

(5 citation statements)

References 34 publications

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“…Recombination is one of the drivers of evolution in RNA viruses and can affect phylogenetic grouping. Typically, in HAstV recombinants display varying topologies across the different ORFs 19,31 . Phylogenetic trees (Figure 6) generated in parallel for ORF1a, ORF1b, and ORF2 to assess for varying phylogeny topologies across the three major ORF regions showed consistency in the topology of the MLB‐3 sequences but inconsistency in tree topology of the three ORFs for MAstV1 (classical HAstV).…”

Section: Resultsmentioning

confidence: 99%

“…1,7,18 Although the role of HAstVs in acute gastroenteritis in children have been established, there exist a substantial dearth of information on the molecular characterization of HAstVs circulating in Nigeria. Also, recombination in Astvs have been reported 13,[19][20][21] in many parts of the world including sub-Saharan Africa, but such occurrence is yet to be investigated in Nigeria. Therefore, leveraging the ongoing national acute flaccid paralysis (AFP) surveillance we explored molecular epidemiology of HAstVs in archived stool samples of Nigerian children (under the age of 15 years) with AFP using viral-likeparticle-based metagenomics approach.…”

Section: Introductionmentioning

confidence: 99%

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Classic human astrovirus 4, 8, MLB‐3, and likely new genotype 5 sublineage in stool samples of children in Nigeria

Ijeomah,

Temitope,

Lander

et al. 2024

Journal of Medical Virology

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Human astrovirus (HAstV) is a nonenveloped RNA virus and has been implicated in acute gastroenteritis among children and elderly. However, there exists a substantial dearth of information on HAstV strains circulating in Nigeria. Viral‐like particles were purified from archived 254 stool samples of children with acute flaccid paralysis between January and December 2020 from five states in Nigeria, using the NetoVIR protocol. Extracted viral RNA and DNA were subjected to a reverse transcription step and subsequent random polymerase chain reaction amplification. Library preparation and Illumina sequencing were performed. Using the virome paired‐end reads pipeline, raw reads were processed into genomic contigs. Phylogenetic and pairwise identity analysis of the recovered HAstV genomes was performed. Six near‐complete genome sequences of HAstV were identified and classified as HAstV4 (n = 1), HAstV5 (n = 1), HAstV8 (n = 1), and MLB‐3 (n = 3). The HAstV5 belonged to a yet unclassified sublineage, which we tentatively named HAstV‐5d. Phylogenetic analysis of open reading frames 1a, 1b, and 2 suggested recombination events inside the MAstV1 species. Furthermore, phylogenetic analysis implied a geographic linkage between the HAstV5 strain from this study with two strains from Cameroon across all the genomic regions. We report for the first time the circulation of HAstV genotypes 4, 8, and MLB‐3 in Nigeria and present data suggestive for the existence of a new sublineage of HAstV5. To further understand the burden, diversity, and evolution of HAstV, increased research interest as well as robust HAstV surveillance in Nigeria is essential.

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Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Classic human astrovirus 4, 8, MLB‐3, and likely new genotype 5 sublineage in stool samples of children in Nigeria

Ijeomah,

Temitope,

Lander

et al. 2024

Journal of Medical Virology

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“…The copyright holder for this preprint this version posted June 28, 2023. ; https://doi.org/10.1101/2023.06.27.546739 doi: bioRxiv preprint 2015; Ha et al, 2017;Wei et al, 2023). The ORF1b-ORF2 overlap region contains sequences that are conserved in HAstV (Méndez and Arias, 2013;Medici et al, 2015), which may increase the probability of homologous recombination, allowing structural protein exchange (Wohlgemuth et al, 2019).…”

Section: Methods and Resultsmentioning

confidence: 99%

Identification of a recombinant human astrovirus type 5 strain from an acute gastroenteritis outbreak in Beijing, China

Mao

Zhang

et al. 2023

Preprint

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Two samples positive for the same strain (2103CP) of human astrovirus (HAstV) were identified during an acute gastroenteritis outbreak in Beijing, China. A full genomic analysis showed that for both samples, open reading frame 1a (ORF1a) clustered with HAstV-1, whereas ORF1b and ORF2 clustered with HAstV-5. The recombination site was detected upstream of the region where ORF1a and ORF1b overlapped. Recombinant HAstV-5 strains were reported previously in China in 2013 and 2021. Our results indicate the need for continuous surveillance of the prevalence and evolution of this recombinant HAstV-5 in China.

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“…3PCM can be used both with comprehensive datasets and with versions of those datasets where known or presumed recombinant sequences have been removed. This option was added because astroviruses exhibit genetic diversity in part through recombination, which is further complicated by concurrent infections with multiple astrovirus taxa and recombination with up to three genomes at once ( Wei et al, 2023 ). The nature of this recombination significantly enhances the genetic diversity of astroviruses and hinders the reconstruction of astrovirus evolutionary history.…”

Section: Methodsmentioning

confidence: 99%

Leveraging machine learning for taxonomic classification of emerging astroviruses

Alipour,

Holmes,

et al. 2024

Front. Mol. Biosci.

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Astroviruses are a family of genetically diverse viruses associated with disease in humans and birds with significant health effects and economic burdens. Astrovirus taxonomic classification includes two genera, Avastrovirus and Mamastrovirus. However, with next-generation sequencing, broader interspecies transmission has been observed necessitating a reexamination of the current host-based taxonomic classification approach. In this study, a novel taxonomic classification method is presented for emergent and as yet unclassified astroviruses, based on whole genome sequence k-mer composition in addition to host information. An optional component responsible for identifying recombinant sequences was added to the method’s pipeline, to counteract the impact of genetic recombination on viral classification. The proposed three-pronged classification method consists of a supervised machine learning method, an unsupervised machine learning method, and the consideration of host species. Using this three-pronged approach, we propose genus labels for 191 as yet unclassified astrovirus genomes. Genus labels are also suggested for an additional eight as yet unclassified astrovirus genomes for which incompatibility was observed with the host species, suggesting cross-species infection. Lastly, our machine learning-based approach augmented by a principal component analysis (PCA) analysis provides evidence supporting the hypothesis of the existence of human astrovirus (HAstV) subgenus of the genus Mamastrovirus, and a goose astrovirus (GoAstV) subgenus of the genus Avastrovirus. Overall, this multipronged machine learning approach provides a fast, reliable, and scalable prediction method of taxonomic labels, able to keep pace with emerging viruses and the exponential increase in the output of modern genome sequencing technologies.

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Triple Intergenotype Recombination of Human Astrovirus 5, Human Astrovirus 8, and Human Astrovirus 1 in the Open Reading Frame 1a, Open Reading Frame 1b, and Open Reading Frame 2 Regions of the Human Astrovirus Genome

Cited by 4 publications

References 34 publications

Classic human astrovirus 4, 8, MLB‐3, and likely new genotype 5 sublineage in stool samples of children in Nigeria

Classic human astrovirus 4, 8, MLB‐3, and likely new genotype 5 sublineage in stool samples of children in Nigeria

Identification of a recombinant human astrovirus type 5 strain from an acute gastroenteritis outbreak in Beijing, China

Leveraging machine learning for taxonomic classification of emerging astroviruses

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