Novel norovirus recombinants detected in South Africa

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

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

*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).

ISSN: 1743-422X