Abstract
BackgroundG12 rotaviruses were first observed in sub-Saharan Africa in 2004 and since then have continued to emerge and spread across the continent and are reported as a significant human rotavirus genotype in several African countries, both prior to and after rotavirus vaccine introduction. This study investigated the genetic variability of 15 G12 rotavirus strains associated with either P[6] or P[8] identified between 2010 and 2014 from Ethiopia, Kenya, Rwanda, Tanzania, Togo and Zambia.MethodsThe investigation was carried out by comparing partial VP7 and partial VP4 sequences of the African G12P[6] and G12P[8] strains with the available GenBank sequences and exploring the recognized neutralization epitopes of these strains. Additionally, Bayesian evolutionary analysis was carried out using Markov Chain Monte Carlo (MCMC) implemented in BEAST to estimate the time to the most recent ancestor and evolutionary rate for these G12 rotavirus strains.ResultsThe findings suggested that the VP7 and VP4 nucleotide and amino acid sequences of the G12 strains circulating in African countries are closely related, irrespective of country of origin and year of detection, with the exception of the Ethiopian strains that clustered distinctly. Neutralization epitope analysis revealed that rotavirus VP4 P[8] genes associated with G12 had amino acid sequences similar to those reported globally including the vaccine strains in RotaTeq and Rotarix. The estimated evolutionary rate of the G12 strains was 1.016 × 10− 3 substitutions/site/year and was comparable to what has been previously reported. Three sub-clusters formed within the current circulating lineage III shows the diversification of G12 from three independent ancestries within a similar time frame in the late 1990s.ConclusionsAt present it appears to be unlikely that widespread vaccine use has driven the molecular evolution and sustainability of G12 strains in Africa. Continuous monitoring of rotavirus genotypes is recommended to assess the long-term impact of rotavirus vaccination on the dynamic nature of rotavirus evolution on the continent.
Highlights
G12 rotaviruses were first observed in sub-Saharan Africa in 2004 and since have continued to emerge and spread across the continent and are reported as a significant human rotavirus genotype in several African countries, both prior to and after rotavirus vaccine introduction
It has been estimated that diarrhoeal diseases are significantly more severe in immunocompromised children, especially those infected with Human immunodeficiency virus (HIV) which is relevant to sub-Saharan Africa [4]
Viral protein 7 (VP7) genotype analysis The nucleotide and amino acid sequences of 15 G12 rotavirus strains collected during 2010–2014 rotavirus seasons across Africa, were analysed and compared with the strains from the GenBank database
Summary
G12 rotaviruses were first observed in sub-Saharan Africa in 2004 and since have continued to emerge and spread across the continent and are reported as a significant human rotavirus genotype in several African countries, both prior to and after rotavirus vaccine introduction. Diarrhoeal disease is a major cause of death in infants and young children below the age of 5 years and rotavirus is the most significant pathogen associated with that mortality [1]. The introduction of rotavirus vaccines into 29 sub-Saharan African countries before 2016, resulted in a reduction of approximately 21,000 deaths and 135,000 hospitalizations in 2016 alone [6], highlighting the major impact that rotavirus vaccines have had on rotavirus diarrhoea
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