Genetic Diversity of Enteric Viruses in Children under Five Years Old in Gabon

Abstract

Enteric viruses are the leading cause of diarrhea in children globally. Identifying viral agents and understanding their genetic diversity could help to develop effective preventive measures. This study aimed to determine the detection rate and genetic diversity of four enteric viruses in Gabonese children aged below five years. Stool samples from children <5 years with (n = 177) and without (n = 67) diarrhea were collected from April 2018 to November 2019. Norovirus, astrovirus, sapovirus, and aichivirus A were identified using PCR techniques followed by sequencing and phylogenetic analyses. At least one viral agent was identified in 23.2% and 14.9% of the symptomatic and asymptomatic participants, respectively. Norovirus (14.7%) and astrovirus (7.3%) were the most prevalent in children with diarrhea, whereas in the healthy group norovirus (9%) followed by the first reported aichivirus A in Gabon (6%) were predominant. The predominant norovirus genogroup was GII, consisting mostly of genotype GII.P31-GII.4 Sydney. Phylogenetic analysis of the 3CD region of the aichivirus A genome revealed the presence of two genotypes (A and C) in the study cohort. Astrovirus and sapovirus showed a high diversity, with five different astrovirus genotypes and four sapovirus genotypes, respectively. Our findings give new insights into the circulation and genetic diversity of enteric viruses in Gabonese children.

Keywords: Gabon; children; diarrhea; enteric viruses; phylogenetic analysis.

Figure 1

Seasonal distribution of enteric viruses among diarrhea cases within the sampling period, 2018–2019.

Figure 2

Phylogenetic tree of a 248 bp alignment of ORF1 region of the GI and GII NoV strains from Gabon and NoV reference sequences (accession nos. are indicated). Samples from symptomatic patients are marked with a dot and samples from asymptomatic with a rhombus. The tree was constructed using the neighbor-joining method with bootstrap test (1000 replicates) and the Kimura 2-parameter method available in MEGA7. Bootstrap values above 70 are shown. The bar indicates the nucleotide substitution per site.

Figure 3

Phylogenetic tree of a 691 bp alignment of P2 region (ORF2) of the GI and GII NoV strains from Gabon and NoV reference sequences (accession nos. are indicated). Samples from symptomatic patients are marked with a dot and samples from asymptomatic patients with a rhombus. The tree was constructed using the neighbor-joining method with the bootstrap test (1000 replicates) and the Kimura 2-parameter method available in MEGA7. Bootstrap values above 70 are shown. The bar indicates the nucleotide substitution per site.

Figure 4

Phylogenetic tree of a 419 bp alignment of ORF1b region of astrovirus strains from Gabon and HAstV reference strains (accession nos. are indicated). Samples from symptomatic patients are marked with a dot and samples from asymptomatic patients with a rhombus. The tree was constructed using the maximum likelihood method with the bootstrap test (1000 replicates) and Tamura 3-parameter method available in MEGA7. The bar indicates the nucleotide substitution per site.

Figure 5

Phylogenetic tree of a 593 bp alignment of polymerase region (ORF1) of sapoviruses (SaV) strains from Gabon and SaV reference sequences (accession nos. are indicated). Samples from symptomatic patients are marked with a dot and samples from asymptomatic patients with a rhombus. The tree was constructed using the neighbor-joining method with the Bootstrap test (1000 replicates) and the Kimura 2-parameter method available in MEGA7. The bar indicates the nucleotide substitution per site.

Figure 6

Phylogenetic tree of a 459 bp alignment of 3CD region of aichivirus (AiV) strains from Gabon and AiV reference sequences (accession nos. are indicated). Samples from symptomatic patients are marked with a dot and samples from asymptomatic patients with a rhombus. The tree was constructed using the neighbor-joining method with the bootstrap test (1000 replicates) and Tamura 3-parameter method available in MEGA7. Bootstraps value above 70 are shown. The bar indicates the variation scale.