Genetic characterization and phylogenetic variations of human adenovirus‐F strains circulating in eastern India during 2017–2020

Abstract

Human adenovirus-F (HAdV-F) (genotype 40/41) is the second-most leading cause of pediatric gastroenteritis after rotavirus, worldwide, accounting for 2.8%-11.8% of infantile diarrheal cases. Earlier studies across eastern India revealed a shift in the predominance of genotypes from HAdV41 in 2007-09 to HAdV40 in 2013-14.Thus, the surveillance for HAdV-F genotypes in this geographical setting was undertaken over 2017-2020 to analyze the viral evolutionary dynamics. A total of 3882 stool samples collected from children (≤5 years) were screened for HAdV-F positivity by conventional PCR. The hypervariable regions of the hexon and the partial shaft region of long fiber genes were amplified, sequenced, and phylogenetically analyzed with respect to the prototype strains. A marginal decrease in enteric HAdV prevalence was observed (9.04%, n = 351/3882) compared to the previous report (11.8%) in this endemic setting. Children <2 years were found most vulnerable to enteric HAdV infection. Reduction in adenovirus-rotavirus coinfection was evident compared to the sole adenovirus infection. HAdV-F genotypes 40 and 41 were found to co-circulate, but HAdV41 was predominant. HAdV40 strains were genetically conserved, whereas HAdV41 strains accumulated new mutations. On the basis of a different set of mutations in their genome, HAdV41 strains segregated into 2 genome type clusters (GTCs). Circulating HAdV41 strains clustered with GTC1 of the fiber gene, for the first time during this study period. This study will provide much-needed baseline data on the emergence and circulation of HAdV40/41 strains for future vaccine development.

Genomic epidemiology of Human Adenovirus F40 and F41 in Coastal Kenya: A retrospective hospital-based surveillance study (2013-2022)

“…HAdV F40/41 genotypes co-circulated similar to what has been reported elsewhere (7–10). In previous studies, the proportion of F40 in sequenced HAdV-F positive samples was lower compared to compared to F41 (3-36% vs 11-97%) partly due to the higher genetic diversity in the F41 genotype that is hypothesised to enable it to outcompete F40 potentially via immune escape (7–11). A similar finding of lower F40 diversity was observed in our study.…”

“…Interestingly, we observe lineage replacement within the lineage 3 sub-types over time. Co-circulation and replacement of multiple HAdV-F41 strains in different genome type clusters based on the fiber gene has also been reported India between 2013 and 2020 (11,26).…”

“…The genome of HAdV-F40/41 is approximately 35,000 base-pairs (6). Previously there have been HAdV studies in Ethiopia, Albania, China, India and Brazil following which the researchers have reported a higher prevalence in HAdV-F41 cases compared to F40 (7–11). Coinfections between F40 and F41, and F41 and C5 were reported in Brazil and Ethiopia (7,10).…”

Genomic epidemiology of human adenovirus F40 and F41 in coastal Kenya: A retrospective hospital-based surveillance study (2013–2022)

“…Co-circulation and replacement of multiple HAdV-F41 strains in different genome type clusters based on the fibre gene have also been reported in India between 2013 and 2020 ( Banerjee et al. 2017 ; Chandra et al. 2021 ).…”

Multi-species co-circulation of adenoviruses identified by next generation sequencing during an outbreak in coastal Kenya in 2023

“…This is likely due to the relaSvely short ~300 base pair hexon region that is amplified and the highly recombinatorial nature of species D HAdVs within the hexon locus 21 . Within HAdV F, there is a high divergence in the strains that have been reported to be circulaSng in Kenya and other regions across the globe 17,[22][23][24] . If this divergence occurs in primer and probe binding sites, nucleic acid amplificaSon methods used for detecSon may be affected.…”