Sequence analysis of the whole genomes of five African human G9 rotavirus strains
Date
2013Author
Nyaga, Martin M.
Jere, Khuzwayo C.
Mlera, Luwanika
Van Dijk, Alberdina A.
Peenze, Ina
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The G9 rotaviruses are amongst the most common global rotavirus strains causing severe childhood diarrhoea.
However, the whole genomes of only a few G9 rotaviruses have been fully sequenced and characterised
of which only one G9P[6] and one G9P[8] are from Africa. We determined the consensus sequence
of the whole genomes of five African human group A G9 rotavirus strains, four G9P[8] strains and one
G9P[6] strain collected in Cameroon (central Africa), Kenya (eastern Africa), South Africa and Zimbabwe
(southern Africa) in 1999, 2009 and 2010. Strain RVA/Human-wt/ZWE/MRC-DPRU1723/2009/G9P[8]
from Zimbabwe, RVA/Human-wt/ZAF/MRC-DPRU4677/2010/G9P[8] from South Africa, RVA/Human-wt/
CMR/1424/2009/G9P[8] from Cameroon and RVA/Human-wt/KEN/MRC-DPRU2427/2010/G9P[8] from
Kenya were on a Wa-like genetic backbone and were genotyped as G9-P[8]-I1-R1-C1-M1-A1-N1-T1-
E1-H1. Strain RVA/Human-wt/ZAF/MRC-DPRU9317/1999/G9P[6] from South Africa was genotyped as
G9-P[6]-I2-R2-C2-
M2-A2-N1-T2-E2-H2. Rotavirus A strain MRC-DPRU9317 is the second G9 strain to be reported on a DS-
1-like genetic backbone, the other being RVA/Human-wt/ZAF/GR10924/1999/G9P[6]. MRC-DPRU9317
was found to be a reassortant between DS-1-like (I2, R2, C2, M2, A2, T2, E2 and H2) and Wa-like (N1)
genome segments. All the genome segments of the five strains grouped strictly according to their genotype
Wa- or DS-1-like clusters. Within their respective genotypes, the genome segments of the three G9
study strains from southern Africa clustered most closely with rotaviruses from the same geographical
origin and with those with the same G and P types. The highest nucleotide identity of genome segments
of the study strains from eastern and central Africa regions on a Wa-like backbone was not limited to
rotaviruses with G9P[8] genotypes only, they were also closely related to G12P[6], G8P[8], G1P[8] and
G11P[25] rotaviruses, indicating a close inter-genotype relationship between the G9 and other rotavirus
genotypes. Rotavirus strain MRC-DPRU9317 is the first G9P[6] to be characterised on a DS-1-like genetic
backbone with a reassortant segment 8 (NSP2) and fourth G9P[6] to be fully sequenced globally.
URI
http://hdl.handle.net/10394/13995https://doi.org/10.1016/j.meegid.2013.01.005
https://www.sciencedirect.com/science/article/pii/S1567134813000221