Acquisition of HIV by African-born residents of Victoria, Australia : insights from molecular epidemiology

African-born Australians are a recognised "priority population" in Australia's Sixth National HIV/AIDS Strategy. We compared exposure location and route for African-born people living with HIV (PLHIV) in Victoria, Australia, with HIV-1 pol subtype from drug resistance assays and geographical origin suggested by phylogenetic analysis of env gene. Twenty adult HIV positive African-born Victorian residents were recruited via treating doctors. HIV exposure details were obtained from interviews and case notes. Viral RNA was extracted from participant stored plasma or whole blood. The env V3 region was sequenced and compared to globally representative reference HIV-1 sequences in the Los Alamos National Library HIV Database. Twelve participants reported exposure via heterosexual sex and two via iatrogenic blood exposures; four were men having sex with men (MSM); two were exposed via unknown routes. Eight participants reported exposure in their countries of birth, seven in Australia, three in other countries and two in unknown locations. Genotype results (pol) were available for ten participants. HIV env amplification was successful in eighteen cases. HIV-1 subtype was identified in all participants: eight both pol and env; ten env alone and two pol alone. Twelve were subtype C, four subtype B, three subtype A and one subtype CRF02-AG. Reported exposure location was consistent with the phylogenetic clustering of env sequences. African Australians are members of multiple transnational social and sexual networks influencing their exposure to HIV. Phylogenetic analysis may complement traditional surveillance to discern patterns of HIV exposure, providing focus for HIV prevention programs in mobile populations

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Tuberculosis incidence rates in Kiribati are among the highest in the Western Pacific Region, however the genetic diversity of circulating Mycobacterium tuberculosis complex strains (MTBC) and transmission dynamics are unknown. Here, we analysed MTBC strains isolated from culture positive pulmonary tuberculosis (TB) cases from the main TB referral centre between November 2007 and October 2009. Strain genotyping (IS6110 typing, spoligotyping, 24-loci MIRU-VNTR and SNP typing) was performed and demographic information collected. Among 73 MTBC strains analysed, we identified seven phylogenetic lineages, dominated by Beijing strains (49%). Beijing strains were further differentiated in two main branches, Beijing-A (n = 8) and -B (n = 28), that show distinct genotyping patterns and are characterized by specific deletion profiles (Beijing A: only RD105, RD207 deleted; Beijing B: RD150 and RD181 additionally deleted). Many Kiribati strains (59% based on IS6110 typing of all strains) occurred in clusters, suggesting ongoing local transmission. Beijing-B strains and over-crowded living conditions were associated with strain clustering (likely recent transmission), however little evidence of anti-tuberculous drug resistance was observed. We suggest enhanced case finding amongst close contacts and continued supervised treatment of all identified cases using standard first-line drugs to reduce TB burden in Kiribati. Beijing strains can be subdivided in different principle branches that might be associated with differential spreading patterns in the population

African-born Victorian residents with HIV: participant characteristics, HIV testing history, exposure and HIV-1 subtype.

<p>[1] <i>pol</i> subtype from antiretroviral susceptibility genotype assay; <i>env</i> subtype from sequencing and phylogenetic analysis of V3 (see Methods).</p

African-born Victorian residents with HIV: stage at diagnosis.

<p>Non-AIDS defining condition.</p><p>Condition fitting definition of acquired immune deficiency syndrome used in national HIV/AIDS surveillance (Kaldor J & McDonald A. JAIDS. 2003;32 Suppl 1).</p><p>CD4 count at HIV diagnosis not recorded.</p><p>Late HIV diagnosis: CD4 count <350 cells/µL at HIV diagnosis, including “advanced HIV disease”.</p><p>Advanced HIV disease: CD4 count <200 cell/µL at diagnosis or AIDS at HIV diagnosis.</p><p><i>Pneumocystis jiroveci</i> pneumonia.</p><p>Cytomegalovirus retinitis or disease other than liver, spleen or nodes.</p

IS<i>6110</i> clustering patterns, DNA fingerprinting pattern and MTBC 15-9 classification of Kiribati isolated Beijing strains.

<p>The classification of Beijing strains in two major branches is further supported by completely different IS<i>6110</i> fingerprint patterns showing a higher copy number for Beijing-B isolates (&gt;17 bands) compared Beijing-A isolates (&lt;13 bands).</p

Neighbour joining tree combining 24 loci MIRU-VNTR and spoligotyping data.

<p>Neighbour joining tree (left panel) based on the copy numbers of 24 loci MIRU-VNTR (right panel, spoligotyping results whereby a repeat region's presence or absence is indicated by a black box or white box respectively) of the 73 strains investigated. The tree was calculated using the MIRU-VNTR<i>plus</i> server (Distance Measure: Dc: Cavalli-Sforza and Edwards, 1967: Dc <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0055423#pone.0055423-CavalliSforza1" target="_blank">[15]</a>). Seven lineages were identified including 71 out of the 73 strains (97%), while two strains could not be allocated to a strain family. Classification of the strains into the different phylogenetic lineages is visualized by color coding, key on <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0055423#pone-0055423-g002" target="_blank">Figure 2</a>.</p

Minimum Spanning Tree of 24 loci MIRU-VNTR data.

<p>Minimum Spanning Tree, based on the 24 loci MIRU-VNTR typing data of 73 analysed Kiribati strains. The size of each circle is proportional with the number of MIRU-VNTR types belonging to a particular complex. Classification of the strains into the different phylogenetic lineages is visualized by color coding.</p

Factors associated with sputum sample being culture positive.

1<p>Chi square test.</p>2<p>Wilcoxon Rank Sum test.</p

Demographic details of study participants.

1<p>Chi square test.</p>2<p>Wilcoxon Rank Sum test.</p>3<p>Fisher's Exact test.</p>4<p>All available HIV serology was negative. In Kiribati, HIV testing is generally performed using the Determine HIV1/2 kit as an initial screening assay (Alere, Queensland, Australia).</p

Demographic characteristics of survey participants.

<p>Demographic characteristics of survey participants.</p