title: Development and application of a broadly sensitive dried-blood-spot-based genotyping assay for global surveillance of HIV-1 drug resistance.
abstract: As antiretroviral therapy (ART) is scaled up in resource-limited countries, surveillance for HIV drug resistance (DR) is vital to ensure sustained effectiveness of first-line ART. We have developed and applied a broadly sensitive dried-blood-spot (DBS)-based genotyping assay for surveillance of HIV-1 DR in international settings. In 2005 and 2006, 171 DBS samples were collected under field conditions from newly diagnosed HIV-1-infected individuals from Malawi (n = 58), Tanzania (n = 60), and China (n =53). In addition, 30 DBS and 40 plasma specimens collected from ART patients in China and Cameroon, respectively, were also tested. Of the 171 DBS analyzed at the protease and RT regions, 149 (87.1%) could be genotyped, including 49 (81.7%) from Tanzania, 47 (88.7%) from China, and 53 (91.4%) from Malawi. Among the 70 ART patient samples analyzed, 100% (30/30) of the Chinese DBS and 90% (36/40) of the Cameroonian plasma specimens were genotyped, including 8 samples with a viral load of <400 copies/ml. The results of phylogenetic analyses indicated that the subtype, circulating recombinant form (CRF), and unique recombinant form (URF) distribution was as follows: 73 strains were subtype C (34%), 37 were subtype B (17.2%), 24 each were CRF01_AE or CRF02_AG (11.2% each), 22 were subtype A1 (10.2%), and 9 were unclassifiable (UC) (4.2%). The remaining samples were minor strains comprised of 6 that were CRF07_BC (2.8%), 5 that were CRF10_CD (2.3%), 3 each that were URF_A1C and CRF08_BC (1.4%), 2 each that were G, URF_BC, and URF_D/UC (0.9%), and 1 each that were subtype F1, subtype F2, and URF_A1D (0.5%). Our results indicate that this broadly sensitive genotyping assay can be used to genotype DBS collected from areas with diverse HIV-1 group M subtypes and CRFs. Thus, the assay is likely to become a useful screening tool in the global resistance surveillance and monitoring of HIV-1 where multiple subtypes and CRFs are found.
authors.affiliation: Division of Global AIDS, International Laboratory Branch, DGHA, NCHHSTP, CDC, Mail Stop A-11, 1600 Clifton Road, Atlanta, GA 30333, USA. cxy0@cdc.gov
authors.forename: Chunfu
authors.initials: C
authors.lastname: Yang
authors.forename: Amanda
authors.initials: A
authors.lastname: McNulty
authors.forename: Karidia
authors.initials: K
authors.lastname: Diallo
authors.forename: Jing
authors.initials: J
authors.lastname: Zhang
authors.forename: Boghuma
authors.initials: B
authors.lastname: Titanji
authors.forename: Sidibe
authors.initials: S
authors.lastname: Kassim
authors.forename: Nellie
authors.initials: N
authors.lastname: Wadonda-Kabondo
authors.forename: John
authors.initials: J
authors.lastname: Aberle-Grasse
authors.forename: Tabitha
authors.initials: T
authors.lastname: Kibuka
authors.forename: Peter M
authors.initials: PM
authors.lastname: Ndumbe
authors.forename: Shanmugam
authors.initials: S
authors.lastname: Vedapuri
authors.forename: Zhiyong
authors.initials: Z
authors.lastname: Zhou
authors.forename: Benson
authors.initials: B
authors.lastname: Chilima
authors.forename: John N
authors.initials: JN
authors.lastname: Nkengasong
mesh_terms: D001769:Blood / Q000821:virology*; D002163:Cameroon; D002681:China; D003890:Desiccation; D005838:Genotype; D015658:HIV Infections / Q000821:virology*; D015497:HIV-1 / Q000145:classification / Q000187:drug effects* / Q000235:genetics / Q000302:isolation & purification; D006801:Humans; D008295:Malawi; D008826:Microbial Sensitivity Tests / Q000379:methods; D008969:Molecular Sequence Data; D010802:Phylogeny; D017422:Sequence Analysis, DNA; D013048:Specimen Handling / Q000379:methods*; D013636:Tanzania