Table 1.

Summary of sequences and variables used for construction and in-depth analyses of HPV16, HPV18 and HPV52 phylogenetic trees. Data depicting total number of samples and sequence counts stratified by anatomical site, HIV status and cytology results. N represents the total number of women positive for a particular HPV genotype. These numbers were further grouped according to vaginal and anal sites, HIV status and cervical cytology. Cytology was reported according to Bethesda classification, with the following combinations used; Normal cervical cytology signified a Pap smear that was negative for intra-epithelial lesions and malignancy (NILM). ‘Low-grade’ signified any result that was either low-grade squamous intraepithelial lesion (LGSIL) or atypical squamous cells of undetermined significance (ASC-US). ‘High-grade’ represented any result that was either high-grade squamous intra-epithelial lesions (HGSIL) or atypical squamous cells, cannot exclude HGSIL (ASC-H). ‘Unsatisfactory’ results signified that the slide was not satisfactory for evaluation.

HPV types & clades	HPV positive women (N)	HPV positive samples	Variant counts	Variants /samples and site		Sequences/samples and HIV status		Sequences/samples and cervical cytology status
				Anal	Vaginal	Positive	Negative	Normal	Low grade	High grade
16	34	38	4275
16×		13	1377	0/0	1377/13	1333/8	44/5	486/9	596/1	295/3
16Y		27	2898	1247/12	1651/15	2869/20	29/7	722/11	543/7	1631/7
18	37	41	2403
18×		25	1363	211/11	1152/14	1353/16	10/9	150a/16	917/3	294/6
18Y		22	1040	30/4	1010/18	741/12	299/10	561a/14	381/3	94/4
52	44	53	4728
52×		15	1530	319/10	1211/5	1156/10	374/5	1506/11	5/2	19/2
52Y		7	1488	1487/6	1/1	872/6	616/1	1488/7	0/0	0/0
52Z		39	1710	46/2	1664/37	1277/20	433/19	1002/27	561/4	144/6

^aFour samples had unsatisfactory cervical cytology.