Sequence based typing of HLA-A and B exons-2 and -3 in a HIV-positive native community with limited HLA diversity from the north of Argentina

DA DILERNIA; D MONACO; RS COLOCCINI; M PANDO; M QUIPILDOR; A DI PAOLO; E HUNTER; H SALOMON

Boston

Congreso; AIDS Vaccine 2012; 2012

AIDS VACCINE 2012

􀀑􀄂􀄐􀅬􀅐􀆌􀅽􀆵􀅶􀄚􀍗􀀃We previously reported a limited diversity of HLAclass I alleles in t􀇁o-di􀅐its typin􀅐 studies of HIV-posi􀆟ve na􀆟ve popula􀆟ons from 􀁋ran, 􀁅ort􀅚 of Ar􀅐en􀆟na􀍘 In t􀅚e present study we determine whether the restricted diversity observed at low-resolu􀆟on re􀅇ects also a restricted 􀅐ene􀆟c diversity in HLA pep􀆟de 􀅐roove􀍘 􀁄􀄞􀆚􀅚􀅽􀄚􀆐􀍗􀀃 We studied 􀏲􀏱 HIV-posi􀆟ve pa􀆟ents whose HLA-A and -􀀑 􀅐enes were previously typed by SS􀁋P techni􀆋ue􀍘 We set-up a se􀆋uence-based typin􀅐 of the most prevalent alleles in 􀁋ran􀍘 HLA-A and 􀀑 were ini􀆟ally PCR-ampli􀄮ed and e􀇆ons-2 and -3 were se􀆋uenced􀍘 􀁅C􀀑I-S􀀑􀁤-Interpreta􀆟on tool was used to con􀄮rm the two-di􀅐its typin􀅐 with previous SS􀁋P data􀍘 We desi􀅐ned a set of primers speci􀄮cs for HLAs hi􀅐hly prevalent in 􀁋ran to achieve di􀄫eren􀆟al PCR-ampli􀄮ca􀆟on of each allele in hetero􀇌y􀅐ote pa􀆟ents􀍘 Phylo􀅐ene􀆟c analysis was used to assi􀅐n e􀇆ons-2 and -3 se􀆋uences to a hi􀅐h-resolu􀆟on HLA 􀅐roup􀍘 R􀄞􀆐􀆵􀅯􀆚􀆐􀍗􀀃Our results show that for HLA-A alleles, 85.1% of A*02 are A*02:01:01:01, 96.7% of A*31 are A*31:01:02 and 92.8% of A*24 are A*24:02:01:01. In the case of A*68, 50% are A*68:01:02 and 31.2% are A*68:17. For HLA-B alleles, B*35 was diverse: B*35:01:01:01 􀍾15.8%􀍿, B*35:04:01 􀍾15.8%􀍿, B*35:05:01 􀍾21.1%􀍿 and B*35:19 􀍾21.1%􀍿. 43.8% of B*39-alleles were B*39:05:01 and 25% were B*39:03. 52.9% of B*48-alleles were B*48:01:01 and 35.3% were B*48:03:01. 62.5% of B*51 alleles were B*51:01:01. 􀁤he men􀆟oned alleles represent the 73.1% of HLA-A 􀅐ene􀆟c diversity and the 45.4% of HLA-B. All the polimorphisms observed lead to non-synonymous changes. 􀀒􀅽􀅶􀄐􀅯􀆵􀆐􀅝􀅽􀅶􀍗􀀃 Our results show that two-digits typing of HLA-A usually corresponds with a speci􀄮c allele in our popula􀆟on. For HLA-B alleles, observed within-subtype diversity was higher. The di􀄫erent protein se􀆋uence encoded by e􀇆ons-2 and -3 may lead to di􀄫erent pep􀆟de speci􀄮ci􀆟es among alleles from the same HLA-B subtype that would be miss-classi􀄮ed as homogeneous in a low-resolu􀆟on typing study.