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.
Highlights
Rotaviruses A (RVA) within the genus Rotavirus of the Reoviridae family, are a major cause of severe acute gastroenteritis in children and the young of various mammals and birds
Examination of over 8,500 RVA genotype 2 genes retrieved from the NCBI Viral Genomes Resource (Table 1) revealed that six genotypes I2 (VP6), R2 (VP1), C2 (VP2), M2 (VP3), N2 (NSP2), and E2 (NSP4) were detected in a diverse pool of hosts whereas the A2 (NSP1), T2 (NSP3), and H2 (NSP5) genotypes were unique to human RVA strains
Examining clinical and surveillance specimens of RVA infecting humans at the level of the whole genotype constellation has provided a grand view of Wa-like, genotype 1 RVA originating from porcine RVA and DS-1-like, genotype 2 RVA originating from bovine RVA in the evolutionary perspective [2]
Summary
Rotaviruses A (RVA) within the genus Rotavirus of the Reoviridae family, are a major cause of severe acute gastroenteritis in children and the young of various mammals and birds. Phylogenetic framework for Rotavirus A genotype 2 genes possess a triple-layered capsid that contains a genome of 11 segments of double-stranded RNA encoding six structural viral proteins (VP1-VP4, VP6, VP7) and five to six non-structural proteins (NSP1-NSP5/NSP6) [1]. The non-structural proteins NSP1-NSP5/ NSP6 play diverse roles during the complex virus replication cycle that is orchestrated by an interplay between the rotavirus structural and non-structural proteins. These inner capsid proteins (VP1, VP2, VP3, and VP6) and the non-structural protein genes (hereafter referred to as the backbone genes) of the genotype 2 strains have recently attracted renewed attention. G1P[4], G3P[4], G9P[4] and G12P[6] strains have been reported to possess the genotype 2 backbone genes [29,30,31,32,33,34,35,36,37]
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