Molecular Epidemiology of Human Rhinoviruses and Enteroviruses Highlights Their Diversity in Sub-Saharan Africa

Abstract

Human rhinoviruses (HRVs) and enteroviruses (HEVs) belong to the Enterovirus genus and are the most frequent cause of infection worldwide, but data on their molecular epidemiology in Africa are scarce. To understand HRV and HEV molecular epidemiology in this setting, we enrolled febrile pediatric patients participating in a large prospective cohort assessing the causes of fever in Tanzanian children. Naso/oropharyngeal swabs were systematically collected and tested by real-time RT-PCR for HRV and HEV. Viruses from positive samples were sequenced and phylogenetic analyses were then applied to highlight the HRV and HEV types as well as recombinant or divergent strains. Thirty-eight percent (378/1005) of the enrolled children harboured an HRV or HEV infection. Although some types were predominant, many distinct types were co-circulating, including a vaccinal poliovirus, HEV-A71 and HEV-D68. Three HRV-A recombinants were identified: HRV-A36/HRV-A67, HRV-A12/HRV-A67 and HRV-A96/HRV-A61. Four divergent HRV strains were also identified: one HRV-B strain and three HRV-C strains. This is the first prospective study focused on HRV and HEV molecular epidemiology in sub-Saharan Africa. This systematic and thorough large screening with careful clinical data management confirms the wide genomic diversity of these viruses, brings new insights about their evolution and provides data about associated symptoms.

High frequency of Polio-like Enterovirus C strains with differential clustering of CVA-13 and EV-C99 subgenotypes in a cohort of Malawian children

“…In our study, 34% of the typed EV strains belonged to species EV-C. Although EV-C is a rather rare species in most of the world [ 3 , 7 , 8 , 49 – 51 ], it accounts for up to 76% of typed EV strains found in African populations [ 18 , 20 , 22 , 25 – 28 ]. The high proportion of EV-C subgroup C as found in our study is in accordance with findings in Cameroon and Madagascar.…”

Human rhinovirus spatial-temporal epidemiology in rural coastal Kenya, 2015-2016, observed through outpatient surveillance

“…A previous study conducted in Kilifi using the same molecular diagnostic assay reported a similar detection of non-HRV enteroviruses 38 . Further, a recent study in Tanzania observed a relatively high prevalence of non-HRV enteroviruses in NPS sample including poliovirus type 1, enterovirus-D68, A71, echovirus-6, 7, 9 , 11 and a variety of coxsackievirus serotypes 40 .…”

Propagation of respiratory viruses in human airway epithelia reveals persistent virus-specific signatures

“…RV-B48 (RV from species B), RV-C15 (RV from species C), RV-C8 (RV from species C, isolated from a patient's serum with disseminated infection), 26 EV-D68 (respiratory EV from species D), influenza A H3N2 Victoria like, RSV subgroup B, and HCoV-OC43 (Table I) 16,[26][27][28][29] directly in reconstituted airway epithelia to prevent acquisition of cell adaptation mutations. Viral RNA copies (10 6 ) corresponding to the average load found in clinical samples [30][31][32] were used in each round of infection.…”