BACKGROUND: Noroviruses (NoV) are the leading cause of viral gastroenteritis worldwide. Recombination frequently
occurs within and between NoV genotypes and recombinants have been implicated in sporadic cases, outbreaks
and pandemics of NoV. There is a lack of data on NoV recombinants in Africa and therefore their presence and
diversity was investigated in South Africa (SA).
RESULTS: Between 2010 and 2013, eleven types of NoV recombinants were identified in SA. Amplification of the
polymerase/capsid region spanning the ORF1/2 junction and phylogenetic analysis confirmed each of the
recombinant types. SimPlot and maximum x2 analysis indicated that all recombinants had a breakpoint in the
region of the ORF1/2 junction (P < 0.05). The majority (9/11) were intergenotype recombinants, but two
intragenotype GII.4 recombinants were characterised. Three combinations represent novel recombinants namely GII.
P not assigned (NA)/GII.3, GII.P4 New Orleans 2009/GII.4 NA and GII.P16/GII.17. Several widely reported recombinants
were identified and included GII.P21/GII.2, GII.P21/GII.3, GII.Pe/GII.4 Sydney 2012, and GII.Pg/GII.12. Other
recombinants that were identified were GII.Pg/GII.1, GII.Pe/GII.4 Osaka 2007, GII.P4 New Orleans 2009/GII.4 Sydney
2012, GII.P7/GII.6. To date these recombinant types all have a reportedly restricted geographic distribution. This is
the first report of the GII.P4 New Orleans 2009/GII.4 Sydney 2012 recombinant in Africa.
CONCLUSIONS: Over the past four years, remarkably diverse NoV recombinants have been circulating in SA.
Pandemic strains such as the GII.Pe/GII.4 Sydney 2012 recombinant co-circulated with novel and emerging
recombinant strains. Combined polymerase- and capsid-based NoV genotyping is essential to determine the true
diversity and global prevalence of these viruses.