Sub-genotype phylogeny of the non-G, non-P genes of genotype 2 Rotavirus A strains

Abstract

Recent increase in the detection of unusual G1P[8], G3P[8], G8P[8], and G9P[4] Rotavirus A ( RVA ) strains bearing the DS-1-like constellation of the non-G, non-P genes (hereafter referred to as the genotype 2 backbone) requires better understanding of their evolutionary relationship. However, within a genotype, there is lack of a consensus lineage designation framework and a set of common sequences that can serve as references. Phylogenetic analyses were carried out on over 8,500 RVA genotype 2 genes systematically retrieved from the rotavirus database within the NCBI Virus Variation Resource. In line with previous designations, using pairwise comparison of cogent nucleotide sequences and stringent bootstrap support, reference lineages were defined. This study proposes a lineage framework and provides a dataset ranging from 34 to 145 sequences for each genotype 2 gene for orderly lineage designation of global genotype 2 genes of RVAs detected in human and animals. The framework identified five to 31 lineages depending on the gene. The least number of lineages (five to seven) were observed in genotypes A2 (NSP1), T2 (NSP3) and H2 (NSP5) which are limited to human RVA whereas the most number of lineages (31) was observed in genotype E2 (NSP4). Sharing of the same lineage constellations of the genotype 2 backbone genes between recently-emerging, unusual G1P[8], G3P[8], G8P[8] and G9P[4] reassortants and many contemporary G2P[4] strains provided strong support to the hypothesis that unusual genotype 2 strains originated primarily from reassortment events in the recent past involving contemporary G2P[4] strains as one parent and ordinary genotype 1 strains or animal RVA strains as the other. The lineage framework with selected reference sequences will help researchers to identify the lineage to which a given genotype 2 strain belongs, and trace the evolutionary history of common and unusual genotype 2 strains in circulation.

High prevalence of equine‐like G3P[8] rotavirus in children and adults with acute gastroenteritis in Thailand

“…The reliability of the branching was estimated from 1000 bootstrap replicates. In designating lineages, the already established lineages were referenced …”

Whole Genome Analysis of Human Rotaviruses Reveals Single Gene Reassortant Rotavirus Strains in Zambia

“…To understand the genetic relationship of the four Zambian strains with global stains, a phylogenetic tree was resolved for each of the 11 gene segments. For the designation of lineages in the VP7, VP4, and VP1 trees, closely related strains as well as strains on the respective lineages, were selected from the GenBank using previously published articles as reference [ 49 , 50 , 51 , 52 , 53 , 54 ].…”

“…Doan et al [ 52 ] established five lineages for global R2 strains. More recently, Agbemabiese et al [ 49 ] proposed 14 lineages for R2 strains which included human and animal RVA strains. Based on this, one of the two DS-1-like Zambian strains, UFS-NGS-MRC-DPRU13327, clustered in lineage R2 V that mainly comprised of African strains ( Figure 5 ).…”

“…This strain displayed maximum nt (aa) identities of 99.4% (99.7%) with strains from Zimbabwe and Mozambique ( Supplementary data 1 ). In the VP1 phylogenetic tree, a cluster of strains within the R2 genotype could not be classified under any lineage according to the established designations [ 49 , 52 ] and were therefore named “undefined”.…”

Full genome characterization of novel DS-1-like G9P[8] rotavirus strains that have emerged in Thailand

“…The reliability of the branching was estimated from 1000 bootstrap replicates. For designating lineages, the already established lineages were referenced [40].…”