Epidemiology and molecular detection of human adenovirus and non-polio enterovirus in fecal samples of children with acute gastroenteritis: A five-year surveillance in northern Brazil

Abstract

Acute gastroenteritis (AGE) is a common pediatric infection that remains a significant cause of childhood morbidity and mortality worldwide, especially in low-income regions. Thus, the objective of this study was to detect human adenovirus (HAdV) and non-polio enterovirus (NPEV) in fecal samples from the Gastroenteritis Surveillance Network, and to identify circulating strains by nucleotide sequencing. A total of 801 fecal samples were tested using qPCR/RT-qPCR, and 657 (82.0%) were inoculated into HEp-2C and RD cell lines. The HAdV and NPEV positivity rates obtained using qPCR/RT-qPCR were 31.7% (254/801) and 10.5% (84/801), respectively, with 5.4% (43/801) co-detection. Cytopathic effect was observed in 9.6% (63/657) of patients, 2.7% (18/657) associated with HAdV, and 6.2% (41/657) associated with NPEV after testing by ICC-PCR. A comparison of the two methodologies demonstrated an agreement of 93.5% for EVNP and 64.4% for HAdV. These two viruses were detected throughout the study period, with HAdV positivity rates ranging from 41% in Amapá to 18% in Pará. The NEPV varied from 18% in Pará/Rondônia to 3% in Acre. The most affected age group was over 60 months for both HAdV and NPEV. Samples previously positive for rotavirus and norovirus, which did not show a major difference in the presence or absence of diarrhea, fever, and vomiting, were excluded from the clinical analyses of these two viruses. These viruses circulated over five years, with a few months of absence, mainly during the months corresponding to the waves of SARS-CoV-2 infection in Brazil. Five HAdV species were identified (A, B, C, D, and F), with a greater predominance of HAdV-F41 (56.5%) followed by HAdV-C (15.2%). Three NPEV species (A, B, and C) were detected, with serotypes E14 (19.3%) and CVA-24 (16.1%) being the most prevalent. The present study revealed a high diversity of NPEV and HAdV types circulating in children with AGE symptoms in the northern region of Brazil.

Fig 1. Detection of human adenovirus (HAdV) and non-polio enterovirus (NPEV) detected by qPCR and RT-qPCR in 801 fecal samples from children with acute gastroenteritis, in the northern region of Brazil between 2017 and 2021.

Geographic distribution of positive cases for HAdV, NPEV and co-detection (HAdV+NPEV) in the seven Brazilian federal units. (A) Annual distribution by Brazilian federative unit of positive cases for (B) HAdV and (C) NPEV. Source: The map contains information from OpenStreetMap and OpenStreetMap Foundation, which is made available under the Open Database License. ©OpenStreetMap contributors.

Fig 2. Phylogenetic analysis was based on a conserved nucleotide (nt) region of the hexon gene for adenovirus, detected in samples from children with acute gastroenteritis in the northern region of Brazil between 2017 and 2021.

*Tree was inferred using maximum likelihood method based on Jukes-Cantor model. Genotypes are highlighted in red (HAdV-F41), dark blue (HAdV-F40), pink (HAdV-D), purple (HAdV-C), light blue (HAdV-B3), orange (HAdV-B55), and green (HAdV-A12). Reference strains were obtained from GenBank. A phylogenetic tree was constructed using MEGA 6 software with 2000 bootstrap replicates.

Fig 3. Phylogenetic analysis was based on a partial sequence of VP1 region of enteroviruses detected in samples from children with acute gastroenteritis in northern Brazil between 2017 and 2021.

*The tree was inferred using the neighbor-joining method based on the Jukes-Cantor model. Reference strains were obtained from GenBank. A phylogenetic tree was constructed using the MEGA 6 software with 2000 bootstrap replicates.