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Table 1 Phylogenetic relationships and breakpoint location of recombinant norovirus strains circulating in South Africa from 2010–2013

From: Novel norovirus recombinants detected in South Africa

Year of detection Strain name/GenBank accession number Polymerase genotype Capsid genotype Breakpoint: SimPlot/x2 Estimated P-value (x2) GenBank accession number of most closely related NoV strain (%identity/%coverage)# Worldwide detection#
2010 Johannesburg 6108 KC962457 GII.P21 GII.3 −16/+56* 2.154 × 10−13 JX439787 (98%/99%)a China, India, Korea
2010 Bushbuckridge 6387 KC962458 GII.P NA GII.3 ND ND KC597144 (89%/99%)b Novel polymerase region
2011 Cape Town 6745 KJ710245 GII.P4 New Orleans 2009 GII.4 NA ND ND JX448566 (96%/99%)c Novel capsid region
2011 Cape Town 6799 KC962459 GII.Pg GII.1 −27/-88 1.608 × 10−4 JN797508 (93%/99%)a Europe, US
2011 Empangeni 7299 KC962460 GII.P16 GII.17 −6/+17 1.610 × 10−15 JX683114 (93%/99%)a Novel recombinant
2011 Cape Town 8179 KM025143 GII.Pe GII.4 Osaka 2007 ND ND GQ845369 (97%/99%)c Australia, India, Japan, US
2011 Pietermaritzburg 8412 KC962461 GII.P21 GII.2 −29/+14 1.846 × 10−13 AY682549 (96%/97%)a France
2012 Empangeni 8491 KC962462 GII.P4 New Orleans 2009 GII.4 Sydney 2012 −15/-61 1.767 × 10−3 KF509947 (96%/99%)c Australia, Canada, Europe, Asia, US
2012 Bushbuckridge 9306 KJ710246 GII.Pg GII.12 −29/+68 9.441 × 10−9 JQ613568 (98%/99%)a Asia, Australia, Europe, US
2012 Johannesburg 9814 KJ710247 GII.Pe GII.4 Sydney 2012 −59/+20 8.515 × 10−15 KF145148 (98%/99%)c Worldwide
2013 Johannesburg 130930 KJ710248 GII.P7 GII.6 −54/-36 8.238 × 10−10 KJ407072 (96%/98%)a Japan, US
  1. *Breakpoint position relative to the start of ORF2, NA – Not assigned, ND – Not determined, #Based on BLAST analysis of athe polymerase-capsid overlap region (~1090 bp); bthe complete polymerase-capsid overlap region (~1820 bp); and cthe partial polymerase-complete capsid region (~2429 bp).