Sequence analysis of partial VP7 gene of human rotaviruses in clinical specimens, raw sewage and Nile water samples in Egypt

The objective of this study is to estimate the most common G genotypes of human rotaviruses in addition to the most common sequence of partial VP7 gene in clinical specimens, raw sewage, and Nile water samples in Egypt. A total of five hundred and fifty-four stool specimens were collected from December 2020 to April 2022 from children ≤ 3 years old. Of 554 specimens, 182 specimens were positive for rotavirus VP6 using RT-PCR (32.85%). Using multiplex nested and semi-nested RT-PCR, a higher prevalence of common P genotypes than that of common G genotypes was observed in clinical specimens, raw sewage, and Nile water samples. Only common P genotypes could be detected, while P[9] genotype (uncommon P genotype) could not be detected in clinical specimens, raw sewage, and Nile water samples. Of the common G genotypes, G1 was the most prevalent in clinical specimens, raw sewage, and Nile water samples followed by G3. The uncommon G genotypes detected were G9 and G8 in clinical specimens, raw sewage, and Nile water samples. Sequence analysis of 1062 bp of VP7 gene for G1 genotype (the most common G in clinical specimens, raw sewage, and Nile water samples) showed high similarity with human rotavirus Wa strain. In conclusion, the highest frequency of G1 genotype among common G genotypes in clinical specimens, sewage, and Nile water samples may make it a suitable G genotype to be added to the common P genotypes in candidate recombinant subunit vaccine in Egypt and similar patterns in other countries.