Prevalence of Human Norovirus GII.4 Sydney 2012 [P31] between 2019 and 2021 among Young Children from Rural Communities in South Africa

Abstract

Acute gastroenteritis (AGE) accounts for considerable morbidity and mortality in the paediatric population worldwide, especially in low-income countries. Human norovirus (HNoV), particularly GII.4 strains, are important agents of AGE. This study aimed to detect and characterise HNoV in children with and without AGE. Between 2019 and 2021, 300 stool samples (200 AGE and 100 without AGE) were collected from children below 5 years of age referred to the healthcare facilities of the rural communities of Vhembe District, South Africa. After detection using real-time RT-PCR, HNoV positive samples were subjected to RT-PCR and Sanger sequencing. Partial nucleotide sequences (capsid/RdRp) were aligned using the Muscle tool, and phylogenetic analysis was performed using MEGA 11. The nucleotides' percent identity among HNoV strains was compared using ClustalW software. A significant difference in HNoV prevalence between AGE children (37%; 74/200) and non-AGE (14%; 14/100) was confirmed (p < 0.0001). Genogroup II (GII) HNoV was predominant in AGE children (80%; 59/74), whereas most non-AGE children were infected by the GI norovirus genogroup (64%; 9/14). GII.4 Sydney 2012 [P31] strains were dominant (59%; 19/32) during the study period. A phylogenetic analysis revealed a close relationship between the HNoV strains identified in this study and those circulating worldwide; however, ClustalW showed less than 50% nucleotide similarity between strains from this study and those from previously reported norovirus studies in the same region. Our findings indicate significant changes over time in the circulation of HNoV strains, as well as the association between high HNoV prevalence and AGE symptoms within the study area. The monitoring of HuNoV epidemiology, along with stringent preventive measures to mitigate the viral spread and the burden of AGE, are warranted.

Keywords: GII and GI genogroups; GII.4 Sydney 2012 [P31]; GII4 Sydney 2012; acute gastroenteritis (AGE); asymptomatic; norovirus; symptomatic.

Figure 1

Phylogenetic analysis of the dual typed (polymerase and capsid junction region, 570 bp (with MON431/G2SKR)) HNoV nucleotide sequence circulating in Vhembe District (South Africa) in 2019–2021. Phylogenetic tree was set using neighbour joining method. Round black dots indicate HNoV genotyped in this study, and reference sequences were randomly selected from GenBank, with their respective accession numbers based on high similarity with our study sequences. All positions containing gaps and missing data were eliminated. The evolutionary distances were computed using the p-distance method and are in the units of the number of base differences per site. Evolutionary analyses were conducted in MEGA 11 (10.0.5) and bootstrap tests (1000 replicates) based on the Kimura two-parameter model. Only bootstrap values greater than 70% are shown.

Figure 2

Phylogenetic tree based on 380 bp (with COG2F/G2SKR) capsid/RdRp junction region of HNoV nucleotide sequence circulating in Vhembe District (South Africa) in 2019–2021. Neighbour joining method was used in building the tree. Triangle black dots indicate the HNoV genotypes obtained during this study, and reference sequences were randomly selected from GenBank, with their respective accession numbers based on high similarity with our study sequences. All positions containing gaps and missing data were eliminated. The evolutionary distances were computed using the p-distance method and are in the units of the number of base differences per site. Evolutionary analyses were conducted in MEGA 11 (10.0.5) and bootstrap tests (1000 replicates) based on the Kimura two-parameter model. Bootstrap values higher than 70% are shown.

Figure 3

Phylogenetic analysis of the partial typed 340 bp (with G2SKF/R) capsid region of HNoV nucleotide sequence circulating in Vhembe District (South Africa) in 2019–2021. Phylogenetic tree was set using neighbour joining method. Squared black dots indicate HNoV genotyped in this study, and reference sequences were randomly selected from GenBank, with their respective accession numbers based on high similarity with our study sequences. All positions containing gaps and missing data were eliminated. The evolutionary distances were computed using the p-distance method and are in the units of the number of base differences per site. Evolutionary analyses were conducted in MEGA 11 (10.0.5) and bootstrap tests (1000 replicates) based on the Kimura two-parameter model. Only bootstrap values greater than 70% are shown.