Human calicivirus diversity in wastewater in South Africa

Abstract

Aim: To investigate the diversity of human caliciviruses (HuCVs) in wastewater from small-to medium-sized communities in five provinces of South Africa (SA). Methods and Results: Wastewater samples (51) were screened for norovirus (NoV) GI, GII, GIV and sapovirus (SaV) using real-time reverse transcription (RT)-PCR. Partial capsid nucleotide sequences were analysed for genotyping.

Norovirus GII.17 Predominates in Selected Surface Water Sources in Kenya

“…The two NoV GI.1 strains (KDMarch2012-301 and KDMarch2012-304), detected in the urban Mutoine river, showed a high nucleotide sequence identity (97%) to a clinical NoV GI.1 strain (JX416391) from Burkina Faso. Except for studies in South Africa Murray 2013), Botswana (Mattison et al 2010) and Burkino Faso (Nordgren et al 2013), the occurrence of NoV GI.1 does not appear to be widely reported in Africa as no GI.1 strains were detected in diarrhoeal stool samples from children in Nairobi, Kenya (Mans et al 2014) nor in the clinical specimens (Silva et al 2008;Abugalia et al 2011;Ayukekbong et al 2011;Trainor et al 2013) or sewage samples (Sdiri-Loulizi et al 2010) from other African countries. Norovirus GI.3 however, appears to more prevalent in African regions (Ayukekbong et al 2011;Yassin et al 2012;Trainor et al 2013), including Kenya (Mans et al, 2014).…”

“…Strains of NoV GII.17 were identified in clinical specimens collected during 1999-2000 from human immunodeficiency virus (HIV)-infected children at a care center in Kenya (Mans et al 2014) suggesting that GII.17 has been in circulating in urban and rural Kenyan communities for a number of years. Nucleotide sequence information on NoV GII.17 strains from Burkina Faso (Nordgren et al 2013), Morocco (KJ162374), Cameroon (Ayukekbong et al 2011) and South Africa (Murray et al 2013) are available in GenBank. Although NoV GII.17 seems to be prevalent in some parts of Africa this genotype was not identified in clinical specimens (Silva et al 2008;Abugalia et al 2011;Hassine-Zaafrane et al 2013;Huynen et al 2013;) and environmental samples (Sdiri-Loulizi et al 2010) from many other African regions and the GII.17 predominance appears to be peculiar to Kenya.…”

“…In Africa, the prevalence of NoVs has been investigated in both clinical (Mans et al 2010(Mans et al , 2014Hassine-Zaafrane et al 2013;Huynen et al 2013;) and environmental settings (Kamel et al 2010;Kiulia et al 2010;Sdiri-Loulizi et al 2010;Gibson 2011;Mans et al 2013;Murray et al 2013). Noroviruses have also been detected in shellfish collected along the Mediterranean Sea and Atlantic Coast of Morocco (Benabbes et al 2013).…”

Sapovirus prevalence in children less than five years of age hospitalised for diarrhoeal disease in South Africa, 2009–2013

“…Water from three rivers in Gauteng was monitored over two years and SaVs were detected in 18% (3/17), 45% (29/64) and 89% (16/18) of specimens [14]. In Kenya, SaV was detected in 34% (10/29) of river water samples and in 31% (4/13) of urban sewerage samples [15], indicating the widespread distribution of SaVs.…”

“…In addition to clinical case surveillance, river water and sewerage can be monitored for SaV as undertaken in SA [14] and Kenya [15]. Water from three rivers in Gauteng was monitored over two years and SaVs were detected in 18% (3/17), 45% (29/64) and 89% (16/18) of specimens [14].…”