Epidemiology and genetic diversity of human parechoviruses circulating among children hospitalised with acute gastroenteritis in Pune, Western India: a 5-years study

Abstract

Human parechoviruses (HPeVs) are known to cause various clinical manifestations including acute gastroenteritis. Although HPeV infections and their genotypes have been detected in human patients worldwide, no such reports are available from India to ascertain the association of HPeVs in acute gastroenteritis. The present study was conducted to determine the clinical features and genetic diversity of HPeVs detected in children hospitalised for acute gastroenteritis. Stool specimens (n = 979) collected from children aged ⩽5 years hospitalised for acute gastroenteritis in Pune, western India during January 2006-December 2010 were included. HPeV RNA was detected by reverse transcription-polymerase chain reaction (RT-PCR) (5'UTR) followed by genotyping using VP1 gene-based PCR and phylogenetic analysis. HPeV was detected in 13·9% (136/979) of the cases, co-infections with other enteric viruses were found in 43·4%. HPeV was more frequent in children ⩽1 year age with infections reported throughout the year. A total of 102/136 (75%) HPeV strains were genotyped, which comprised 13 different HPeV genotypes. Of these, HPeV1 was the most predominant genotype detected and phylogenetically clustered with the Harris strain which is rarely reported. The study documents circulation of heterogeneous HPeV genotypes. Two variant strains of HPeV4 and 'RGD absent' HPeV5 and 6 strains were also detected. This is the first report of HPeV with diversified genotypes identified in acute gastroenteritis patients from India.

Genotypic diversity and dynamic nomenclature ofParechovirus A

“…To investigate the likely biases introduced by the use of less robust tree reconstruction approaches such as neighbour joining in combination with inadequate evolutionary models or raw distances prevalently used in literature, we used the unedited nucleotide alignment to reconstruct a neighbour joining tree under a Kimura-2 parameter model. [22][23][24][25][26][27][28] This approach severely underestimates the branch lengths in the global phylogeny, as well as resulting in topological incongruencies for multiple lineages relative to the amino acid reconstructed tree ( Figure 1B). The inadequacy of phylogenetic reconstruction methods and evolutionary models prevalently used to estimate PeV-A divergence has resulted in several documented incidents of inconsistent typing, including PeV-18 (KT879915) which groups with PeV3 and (KJ796882-3) often annotated as PeV-7, which groups with PeV14.…”

“…The current genotyping system also relies on phylogenetic reconstruction approaches such as neighbor joining that can result in severe branch underestimation and topological inconsistencies across studies, which has resulted in inconsistent typing of PeV-A. [22][23][24][25][26][27][28][29] It has also resulted in the designation of PeV-1 subtypes A and B, which do not consistently group as a clade. 30 Many studies also employ BLAST-based nucleotide searches to compare query sequence to a reference dataset representing different genotypes.…”

“…30 Many studies also employ BLAST-based nucleotide searches to compare query sequence to a reference dataset representing different genotypes. [22][23][24][25][26][27][28] However, many of these reference sequences are not representative of the high internal divergence of some genotypes. This is especially pronounced for the progenitor sequences of some genotypes such as PeV-1 and 3, which are genetically and antigenically distinct.…”

“…This is especially pronounced for the progenitor sequences of some genotypes such as PeV-1 and 3, which are genetically and antigenically distinct. [22][23][24][25][26][27][28] Inconsistently typed viruses are incorrectly annotated in public sequence databases, propagating the error into subsequent studies.…”

Frequency of Parechovirus Serotype 1 Among Young Infants With Sepsis

“…HPeVs -A1 genotype is dominant in Europe and USA followed by PeV-A3 and PeV-A4, while PeV-A2, and A7-A19 genotypes are rarely reported (5). In Asia, similar to Europe and the USA, PeV-A1, A3, and A4 genotypes are the most prevalent and a higher diversity of genotypes has been reported in India and Pakistan (6,7,8). In the African continent, PeV-A1, A2, and A3 are the most prevalent but nearly all HPeVs genotypes have been detected, indicating a much wider circulation of genotypes in this continent (9).…”