title: Subtype assignment and phylogenetic analysis of HIV type 1 strains in patients from Swaziland.
abstract: Aim of this study was to assess HIV-1 subtype distribution and prevalence of transmitted mutations related to antiretroviral drugs in Swaziland. According to the WHO guidelines, 47 plasma samples from naive patients stored at HIV/AIDS National Reference Laboratory in Mbabane between 2002 and 2003, before the introduction of antiretroviral therapy in the country, were studied. HIV-1 RNA was extracted from the plasma samples, RT and protease regions of pol gene were amplified and sequenced. The mutations associated to drug resistance were defined as major or minor on the basis of the recommendations of the International AIDS Society-USA panel. A mutation associated to non nucleoside inhibitors (Y181I) was found in one case showing a prevalence of transmitted drug resistance <5% in Swaziland. No major mutations conferring resistance to protease and nucleoside RT inhibitors were found. Clade assignment was performed by phylogenetic analysis of pol gene. The general time-reversible model of substitution was used to study the phylogenetic relationships between sequences obtained from Swazi patients and sequences from neighbor countries. All patients were found to carry a C subtype. No phylogenetic relationships were detected within Swazi sequences, indicating the absence of epidemiological relationships among patients in study. Although local variants of subtype C have been recently recognized, phylogenetic analysis did not reveal the presence of significant cluster of Swaziland sequences within African variants. This finding may be explained by multiple introduction of C strains.
authors.affiliation: Department of Clinical Sciences, Infection Diseases Section, "Luigi Sacco" Hospital, University of Milan, Milan, Italy. lorenzo.deho@unimi.it
authors.forename: Lorenzo
authors.initials: L
authors.lastname: Dehò
authors.forename: Richard
authors.initials: R
authors.lastname: Walwema
authors.forename: Anna
authors.initials: A
authors.lastname: Cappelletti
authors.forename: Hosea
authors.initials: H
authors.lastname: Sukati
authors.forename: Dumile
authors.initials: D
authors.lastname: Sibandze
authors.forename: Mauro
authors.initials: M
authors.lastname: Almaviva
authors.forename: Stefano
authors.initials: S
authors.lastname: Buttò
authors.forename: Barbara
authors.initials: B
authors.lastname: Ensoli
authors.forename: Massimo
authors.initials: M
authors.lastname: Galli
authors.forename: Claudia
authors.initials: C
authors.lastname: Balotta
mesh_terms: D000328:Adult; D019943:Amino Acid Substitution / Q000235:genetics; D016000:Cluster Analysis; D024882:Drug Resistance, Viral; D013541:Eswatini / Q000453:epidemiology; D005260:Female; D015658:HIV Infections / Q000453:epidemiology / Q000821:virology*; D016333:HIV Protease / Q000235:genetics; D054303:HIV Reverse Transcriptase / Q000235:genetics; D015497:HIV-1 / Q000145:classification* / Q000235:genetics* / Q000302:isolation & purification; D006801:Humans; D008297:Male; D017720:Molecular Epidemiology; D010802:Phylogeny; D017422:Sequence Analysis, DNA; D017386:Sequence Homology, Amino Acid
chemical_list: C514824:reverse transcriptase, Human immunodeficiency virus 1; D054303:HIV Reverse Transcriptase; D016333:HIV Protease; C514803:p16 protease, Human immunodeficiency virus 1