The molecular epidemiology and diversity of gastroenteritis viruses in HIV-infected, -exposed and -unexposed children under the age of five years in Pretoria, South Africa

Abstract

Viruses are common causes of both endemic and epidemic gastroenteritis, infecting millions of people per year, with norovirus, rotavirus and adenovirus-F as the main causative agents, and sapovirus and astrovirus as contributing viruses. These viruses are highly infectious and most severe in the very young, old, or individuals who are immunocompromised. The viral infection usually causes self-limited gastroenteritis, although chronic infection has been observed in highly immunocompromised patients. African and South-East Asian regions are disproportionally affected by diarrhoeal disease. These regions (especially South Africa) are also more severely affected by human immunodeficiency virus (HIV) infections. It has been suggested that immunocompromised individuals may form part of a reservoir for novel virus variants and recombinants. It should be taken into account that not every person is equally susceptible to infection after pathogen exposure and that not all infected persons develop clinical symptoms (Ramani and Giri, 2019). One host genetic factor that can influence susceptibility to enteric infection is the expression of histo-blood group antigens (HBGAs). Histo-blood group antigens are a major group of complex carbohydrates and are determinants of both human and animal ABO blood groups and the Lewis blood group systems, which are distributed in abundance on the mucosal epithelia of the gastrointestinal tract. Histo-blood group antigens have been proven to influence susceptibility to rotavirus and norovirus infections. Saliva, blood and stool specimens (n=205) have previously been collected from children (≤ 5 years of age) hospitalised with gastroenteritis at Kalafong Provincial Tertiary Hospital from June 2016 to December 2017. Follow up stool specimens were then collected six weeks after enrolment when possible. A descriptive questionnaire was completed by each child’s guardian, giving information on age, residential area, HIV status etc. of the participating child. The stool specimens were screened for six gastroenteritis causing viruses (norovirus GI and –GII, rotavirus, sapovirus, astrovirus and adenovirus) by multiplex PCR. Forty-seven percent (96/205) of specimens tested positive for at least one gastroenteritis causing virus. Rotavirus predominated (46/205), followed by norovirus (32/205), adenovirus (15/205), sapovirus (9/205) and astrovirus (3/205). A total of 27/32 norovirus (GI.3, GII.2, GII.3, GII.4, GII.7, GII.12 and GII.21), 44/46 rotavirus (G1P[8], G2P[4], G2P[6], G3P[4], G3P[8], G8P[4], G8P[6], G9P[6] and G9P[8]) and 8/9 sapovirus (GI.1, GI.2, GII.1, GII.4 and GII.8) strains have been genotyped, of which norovirus GII.4 and rotavirus G3P[4] predominated. A total of 46/205 children submitted a follow up stool specimen to be tested. Of the 46 children, 9 tested positive for norovirus infection with initial stool specimen testing. Follow up screening resulted in 13/46 (28%) specimens testing positive for either norovirus GI or GII, with all patients presenting as asymptomatic. After genotyping it was observed that only one of the follow up specimens were identical to the original sequence genotyped, indicating prolonged shedding. FUT2 genotyping of 205/205 children showed a 71%:29% ratio between secretors and non-secretors. Eighty percent (77/96) of the virus-infected children were secretors whereas only 20% (19/96) were non-secretors. Rotavirus (p<0.01) and norovirus GII.4 (p<0.05) specifically were found to be more prevalent in secretors. In this study, no statistical significance was observed in terms of severity of and susceptibility to gastroenteritis viruses between HIV-infected, HIV-exposed uninfected or HIV-uninfected individuals. Histo-blood group phenotyping has resulted in various combinations, with Le(b) being the most prevalent antigen found. Next generation sequencing was unsuccessful. In future, fresh specimens should be considered for testing, with more funding and time for optimisation of this process and to give adequate results. In summary, gastroenteritis is still a leading cause of childhood morbidity and mortality, with all advancements in understanding the disease helping to decrease the impact of it. This study again reinforced the importance of these viruses, as they are circulating in such high abundance. It also reinforced the concept that susceptibility to noro- and rotavirus infection is affected by the secretor status of a person. This could in future help with better understanding the viral infection mechanisms and in turn help with vaccine development and treatment