Determination of the prevalence and diversity of viral gastroenteritis infections and secretor status in the elderly population of the Tshwane region in South Africa

Abstract

Diarrhoeal disease is considered the second most common cause of morbidity and fourth most common cause of mortality, worldwide. Low-income countries such as those in Africa and Asia bear the greatest burden of gastroenteritis. Diarrhoeal disease affects individuals of all ages, however, children <5 years of age, the immunocompromised and the elderly population ≥65 years of age are most severely affected. The elderly population, particularly immunocompromised patients residing in long-term care facilities represent high-risk groups for gastroenteritis and surveillance of these individuals in South Africa is under-represented. It has been observed that an individual’s fucosyltransferase 2 (FUT2) secretor status has been associated with different degrees of infection by rotaviruses and noroviruses. A total of 1 012 stool specimens from elderly patients were collected over an 18-month surveillance period, of which 340 specimens met the inclusion criteria and were tested. Virus screening was performed using a lyophilised real-time multiplex RT-PCR/PCR screening iv assay testing for norovirus GI and GII, rotavirus, human adenovirus, human astrovirus and sapovirus. Careful analysis of the real-time (RT)-PCR amplification plots and export data identified 50 viruses in 40 patient specimens. Seven norovirus GI/GII dual-infections were observed and three co-infections were identified, each with an astrovirus accompanying infection by a rotavirus, sapovirus and human adenovirus. FUT2 genotyping was performed to acquire the secretor status for all the rotavirus- and norovirus-positive individuals. The real-time TaqMan® SNP Genotyping Assay was inconsistent in amplifying the SNP in the FUT2 gene from stool-extracted DNA of elderly patients, and therefore an alternative, conventional genotyping PCR approach was performed. This approach was successful in acquiring the secretor status of 14/21 patient specimens. A total of 10 homozygous secretors, three heterozygous secretors and one homozygous non-secretor were identified. Virus-positive specimens identified in this study were genotyped and subjected to phylogenetic analysis. Overall, 14 norovirus- GI, 12 norovirus- GII, 10 sapovirus-, six human adenovirus-, six human astrovirus- and two rotavirus-positives were identified. From the 14 norovirus GI positives, three polymerase regions and two capsid regions were successfully genotyped. The polymerase strains all belonged to genotype GI.P1 and the capsid sequences were all GI.1 genotypes. Only one virus was successfully dual-genotyped as GI.1[P1]. For norovirus GII, a total of nine polymerase and nine capsid strains were genotyped successfully. All the polymerase sequences belonged to the GII.P31 genotype and eight capsid sequences identified as GII.4 Sydney 2012 strains, with a single GII.6 genotype identified. Three of the six adenovirus positives were genotyped, of which one strain grouped into species C and two strains grouped into species D, and shared a clade with a type 17 reference strain. Human astrovirus dual-genotyping was successful for three strains, which identified as type 2 for both the serine protease and capsid types. A single rotavirus strain was genotyped for VP4 and VP7 and identified as G9P[6]. Only two sapovirus-positives were successfully genotyped as GI.2 and GIV.1, respectively. This study highlights the epidemiological importance of clinical surveillance in the geriatric population, acting as a cornerstone for future studies in South Africa.