ROTAVIRUSES IN UGANDA: MOLECULAR EPIDEMIOLOGY AND POTENTIAL OF ZOONOTIC TRANSMISSION

Abstract

Introduction Rotaviruses are a major cause of diarrhoea in children and young animals. To decrease the burden and mortality due to rotavirus diarrhoea in children, rotavirus vaccination was introduced into the Uganda Expanded Program for Immunisation in June 2018. Objectives The study aimed at generating baseline information on rotavirus prevalence, strain diversity in pre-vaccination era, and information for use in the control of rotavirus diseases in Uganda. Three studies were carried out. Methods Study 1 was a cross sectional study of 712 children hospitalised with acute diarrhoea in four hospitals in Kampala and Masaka districts, conducted from September 2012 to September 2013. Study 2 was a cross sectional study of 281 cattle, 418 goats, 434 pigs and 258 humans sharing households, undertaken in central Uganda in 2013/2014. Rotaviruses in both studies were identified using ProSpecT rotavirus ELISA kit. Rotavirus positive samples were G- and P- typed using reverse transcription polymerase chain reaction (RT-PCR). In Study 3, whole genome analysis was carried out on 18 human and 6 animal (one bovine, one caprine and four porcine) rotavirus strains identified in the same geographical region in Uganda, using the Illumina HiSeq platform. RotaC version 2 program was used to assign the rotavirus genotypes and Phylogenetic analysis was carried out using Maximum Likelihood method in MEGA 6.06 program.

Results Study 1:We found rotavirus infection in 37% of children under- five years old admitted with acute diarrhoea and the most prevalent rotavirus strains were G9P[8] and G12P[4]. Wasting and hospitalisation for more than 5 days were negatively associated with rotavirus infection with adjusted prevalence ratios of 0.66 (95% CI: 0.45, 0.96) and 0.60 (95% CI: 0.38, 0.95), respectively. There was no household transmission of rotavirus. Study 2: The prevalence of rotavirus infection in domestic animals (cows, pigs and goats) was 4%. In the animals six G types: G3,G8,G9,G11.G12 and nine P-types P[1], P[4], P[5], P[6] P[7], P[8], P[9], P[10], P[11] were observed in various combinations. Study 3: Interspecies transmission of rotaviruses occurred in this setting.

Conclusions: Rotavirus infection is common in under five year old children admitted with acute diarrhoea in Central Uganda, with more than 1 in 3 children infected with rotavirus. Factors associated with rotavirus infection were wasting and hospitalisation of children for more than 5 days. The prevalence of rotavirus in domestic animals was low with a high diversity of G and P genotypes. Interspecies transmission of rotavirus occurred in this setting. The study findings will be used to assess the impact of rotavirus vaccination in Uganda.