Evidence for onward transmission of HIV-1 non-B subtype strains in the United Kingdom

Post-migration HIV acquisition: A systematic review and meta-analysis

Migrants in Europe face a disproportionate burden of HIV infection; however, it remains unclear if this can be prevented through public health interventions in host countries. We undertake a systematic review and meta-analysis to estimate post-migration HIV acquisition (PMHA) as a proportion of all HIV cases in European migrants. MEDLINE, EMBASE, Global Health, HMIC, and Cochrane Library were searched with terms capturing 'HIV', 'migration', and 'Europe'. Data relating to the proportion of HIV acquired following migration were extracted and random-effects model (REM) meta-analysis was undertaken to calculate a pooled estimate for the proportion of PMHA in European countries. Subgroup meta-analysis was undertaken for PMHA by migrant demographic characteristics and host country. Fifteen articles were included for systematic review following retrieval and screening of 2,320 articles. A total of 47,182 migrants in 11 European countries were included in REM meta-analysis, showing an overall PMHA proportion of 0.30 (95% CI: 0.23-0.38). Subgroup analysis showed no significant difference in PMHA between host country and migrant demographic characteristics. This work illustrates that migrants continue to be at high risk of HIV acquisition in Europe. This indicates the need for targeted screening and HIV prevention interventions, ensuring resources are appropriately directed to combat the spread of HIV.

Post-migration HIV acquisition among african immigrants in the U.S

BACKGROUND

African immigrants in the U.S. are more likely to have a late HIV diagnosis than U.S.-born people, potentially leading to onward transmission. We sought to determine the proportion of African-born people living with HIV (APLWH) who (1) had tested HIV negative prior to diagnosis, and (2) likely acquired HIV in the U.S.

METHODS

We interviewed APLWH from 2014 to 2017 and estimated the proportion with post-migration HIV acquisition based on clinical data, HIV testing history, immigration date, and behavioral data.

RESULTS

Of 179 participants, 113 (63%) were women. Less than half (44%) reported a negative HIV test prior to diagnosis. Among 142 (79%) participants with sufficient data to evaluate post-migration HIV acquisition, we estimate that 29% acquired HIV post-migration. Most APLWH acquire HIV prior to immigration.

DISCUSSION

Approximately one-quarter of APLWH acquire HIV post-migration and HIV testing is infrequent, highlighting the need for prevention efforts for African immigrants in the U.S.

Non-B variants of HIV-1 in San Francisco, California

The HIV-1 epidemic in the US has historically been dominated by subtype B. HIV subtype diversity has not been extensively examined in most US cities to determine whether non-B variants have become established, as has been observed in many other global regions. We describe the diversity of non-B variants and present evidence of local transmission of non-B HIV in San Francisco. Viral sequences collected from patients between 2000 and 2016 were matched to the San Francisco HIV/AIDS case registry. HIV subtype was determined using COMET. Phylogenies were reconstructed using the pol region of subtypes A, C, D, G, CRF01_AE, CRF02_AG, and CRF07_BC, with reference sequences from the LANL HIV database. Associations of non-B subtypes and circulating recombinant forms (CRFs) with patient characteristics were assessed using multivariable logistic regression. Out of 11,381 sequences, 10,669 were from 7235 registry cases, of which 141 (2%) had non-B subtypes and CRFs and 72 (1%) had unique recombinant forms. CRF01_AE (0.8%) and subtype C (0.5%) were the most prevalent non-B forms. The frequency of non-B subtypes and CRFs increased in San Francisco during years 2000-2016. Out of 146 transmission events involving non-B study sequences, 18% indicated local transmission within the study population and 74% appeared to be inward migration of the virus. Compared to 7016 cases with only subtype B, 141 cases with non-B sequences were more likely to be of non-US country of birth (aOR = 11.02; p < 0.001), of Asian/Pacific-Islander race/ethnicity (aOR = 3.17; p < 0.001), and diagnosed after 2009 (aOR = 4.81; p < 0.001). Results suggest that most non-B infections were likely acquired outside the US and that local transmission of non-B forms has occurred but so far has not produced extensive transmission networks. Thus, non-B variants were not widely established in San Francisco, an observation that differs from cities worldwide with more diverse epidemics.

Brief Report: Onward Transmission of Multiple HIV-1 Unique Recombinant Forms Among Men Who Have Sex With Men in Beijing, China

BACKGROUND

Unique recombinant forms (URFs) were generated in dually infected or multiply infected individuals, and some of URFs can be transmitted to many people resulting in the emergence of circulating recombinant forms (CRFs). We examined whether there was evidence for onward transmission of multiple URFs among men who have sex with men (MSM) in Beijing.

METHODS

A total of 146 MSM subjects with acute/early HIV-1 infection were recruited from the Beijing PRIMO clinical cohort between September 2010 and July 2012. HIV-1 full-length gag and partial pol, env genes were amplified and sequenced separately. Phylogenetic analysis and recombination analysis were performed to determine the viral genotypes. Single genome amplification and direct sequencing were used to confirm onward transmission of URFs.

RESULTS

CRF01_AE was the most common genotype (51.9%), followed by CRF07_BC (23.0%), subtype B (14.8%), URFs (7.4%), CRF65_cpx (2.2%), and CRF55_01B (0.7%). Multiple forms of URFs were identified, including CRF01_AE/BC, CRF01_AE/B, and CRF01_AE/C. Nine of the 10 individuals harboring URFs were infected by onward transmission of URFs. The remaining one individual was coinfected with CRF01_AE and CRF07_BC variants.

CONCLUSIONS

We introduced a new method to provide evidence for onward transmission of URF strains by examining the absence of intersubtype coinfection among early infected individuals. Onward transmission of multiple URFs was found among MSM in Beijing, China. Our findings call for a program of continuous molecular surveillance and have implications to prevention programs among MSM in China.

Evidence of Local HIV Transmission in the African Community of King County, Washington

Little is known about the frequency of ongoing HIV transmission within U.S. African immigrant communities. We used HIV surveillance and partner services data to describe African-born persons newly reported with HIV infection in King County (KC), WA from 1/1/2010 to 12/31/2013. We performed phylogenetic clustering analysis of HIV-1 pol to identify putative transmission events within this population. From 2010 to 2013, 1148 KC adults were reported with HIV, including 102 (9 %) born in Africa. Forty-one African-born cases were interviewed and reported diagnosis after arrival in the U.S. Fourteen (34 %) reported ≥1 negative test prior to diagnosis, and 9 (26 %) reported ≥1 negative test after U.S. arrival. Pol genotypes were available for seven of these nine. For two of these seven, a KC case was the nearest phylogenetic neighbor; two others were infected with subtype B virus. We found substantial evidence of ongoing HIV transmission in the African community of KC.

Correlates of Sexual Risk among Recent Gay and Bisexual Immigrants from Western and Eastern Africa to the USA

We examined correlates of sexual risk among gay and bisexual men, who recently migrated from western and eastern African countries to the USA and lived in New York City and who are HIV negative or of unknown status. These men migrate from countries where same-sex sexuality is socially rejected and mostly illegal contributing to the motivation to migrate. Their background might predispose these men to engagement in sexual risk practices, while they are not specifically addressed in HIV prevention programming. Participants (N = 62) reported in face-to-face interviews on pre- and postmigration experiences, psychosocial determinants of sexual risk, and current sexual practices. Operationalization of sexual risk was based on the number of men with whom they had condomless receptive and/or insertive anal sex. Over a third of the men reported always having used condoms in the past year; among the other men, sexual risk varied. Multivariate analyses showed that sexual risk was lower among men with a stronger motivation to avoid HIV infection and higher among men who currently engaged in transactional sex. Further analyses indicated that housing instability was independently associated with reduced motivation to avoid HIV infection and with engagement in transactional sex in the USA. In recent western and eastern African gay and bisexual immigrants to the USA, structural factors, including housing instability, are strongly associated with sexual risk.

A Direct Comparison of Two Densely Sampled HIV Epidemics: The UK and Switzerland

Phylogenetic clustering approaches can elucidate HIV transmission dynamics. Comparisons across countries are essential for evaluating public health policies. Here, we used a standardised approach to compare the UK HIV Drug Resistance Database and the Swiss HIV Cohort Study while maintaining data-protection requirements. Clusters were identified in subtype A1, B and C pol phylogenies. We generated degree distributions for each risk group and compared distributions between countries using Kolmogorov-Smirnov (KS) tests, Degree Distribution Quantification and Comparison (DDQC) and bootstrapping. We used logistic regression to predict cluster membership based on country, sampling date, risk group, ethnicity and sex. We analysed >8,000 Swiss and >30,000 UK subtype B sequences. At 4.5% genetic distance, the UK was more clustered and MSM and heterosexual degree distributions differed significantly by the KS test. The KS test is sensitive to variation in network scale, and jackknifing the UK MSM dataset to the size of the Swiss dataset removed the difference. Only heterosexuals varied based on the DDQC, due to UK male heterosexuals who clustered exclusively with MSM. Their removal eliminated this difference. In conclusion, the UK and Swiss HIV epidemics have similar underlying dynamics and observed differences in clustering are mainly due to different population sizes.

The International Dimension of the U.S. HIV Transmission Network and Onward Transmission of HIV Recently Imported into the United States

The majority of HIV infections in the United States can be traced back to a single introduction in late 1960s or early 1970s. However, it remains unclear whether subsequent introductions of HIV into the United States have given rise to onward transmission. Genetic transmission networks can aid in understanding HIV transmission. We constructed a genetic distance-based transmission network using HIV-1 pol sequences reported to the U.S. National HIV Surveillance System (n = 41,539) and all publicly available non-U.S. HIV-1 pol sequences (n = 86,215). Of the 13,145 U.S. persons clustered in the network, 457 (3.5%) were genetically linked to a potential transmission partner outside the United States. For internationally connected persons residing in but born outside the United States, 61% had a connection to their country of birth or to another country that shared a language with their country of birth. Bayesian molecular clock phylogenetic analyses indicate that introduced nonsubtype B infections have resulted in onward transmission within the United States.

Transmission of Non-B HIV Subtypes in the United Kingdom Is Increasingly Driven by Large Non-Heterosexual Transmission Clusters

Background. The United Kingdom human immunodeficiency virus (HIV) epidemic was historically dominated by HIV subtype B transmission among men who have sex with men (MSM). Now 50% of diagnoses and prevalent infections are among heterosexual individuals and mainly involve non-B subtypes. Between 2002 and 2010, the prevalence of non-B diagnoses among MSM increased from 5.4% to 17%, and this study focused on the drivers of this change.

Methods. Growth between 2007 and 2009 in transmission clusters among 14 000 subtype A1, C, D, and G sequences from the United Kingdom HIV Drug Resistance Database was analysed by risk group.

Results. Of 1148 clusters containing at least 2 sequences in 2007, >75% were pairs and >90% were heterosexual. Most clusters (71.4%) did not grow during the study period. Growth was significantly lower for small clusters and higher for clusters of ≥7 sequences, with the highest growth observed for clusters comprising sequences from MSM and people who inject drugs (PWID). Risk group (P < .0001), cluster size (P < .0001), and subtype (P < .01) were predictive of growth in a generalized linear model.

Discussion. Despite the increase in non-B subtypes associated with heterosexual transmission, MSM and PWID are at risk for non-B infections. Crossover of subtype C from heterosexuals to MSM has led to the expansion of this subtype within the United Kingdom.

Characteristics and spread to the native population of HIV-1 non-B subtypes in two European countries with high migration rate

Background

Non-B subtypes account for at least 50 % of HIV-1 infections diagnosed in Belgium and Luxembourg. They are considered to be acquired through heterosexual contacts and infect primarily individuals of foreign origin. Information on the extent to which non-B subtypes spread to the local population is incomplete.

Methods

Pol and env gene sequences were collected from 410 non-subtype B infections. Profound subtyping was performed using 5 subtyping tools and sequences of both pol and env. Demographic information, disease markers (viral load, CD4 count) and viral characteristics (co-receptor tropism) were compared between subtypes. Maximum likelihood phylogenetic trees were constructed and examined for clustering.

Results

The majority of non-B infections were diagnosed in patients originating from Africa (55.8 %), individuals born in Western Europe represented 30.5 %. Heterosexual transmission was the most frequently reported transmission route (79.9 %), MSM transmission accounted for 12.2 % and was significantly more frequently reported for Western Europeans (25.7 % versus 4.3 % for individuals originating from other regions; p < 0.001). Subtypes A and C and the circulating recombinant forms CRF01_AE and CRF02_AG were the most represented and were included in the comparative analysis. Native Western Europeans were underrepresented for subtype A (14.5 %) and overrepresented for CRF01_AE (38.6 %). The frequency of MSM transmission was the highest for CRF01_AE (18.2 %) and the lowest for subtype A (0 %). No differences in age, gender, viral load or CD4 count were observed. Prevalence of CXCR4-use differed between subtypes but largely depended on the tropism prediction algorithm applied. Indications for novel intersubtype recombinants were found in 20 patients (6.3 %). Phylogenetic analysis revealed only few and small clusters of local transmission but could document one cluster of CRF02_AG transmission among Belgian MSM.

Conclusions

The extent to which non-B subtypes spread in the native Belgian-Luxembourg population is higher than expected, with 30.5 % of the non-B infections diagnosed in native Western Europeans. These infections resulted from hetero- as well as homosexual transmission. Introduction of non-B variants in the local high at risk population of MSM may lead to new sub-epidemics and/or increased genetic variability and is an evolution that needs to be closely monitored.

A systematic review of post-migration acquisition of HIV among migrants from countries with generalised HIV epidemics living in Europe: mplications for effectively managing HIV prevention programmes and policy

Background

Migrant populations from countries with generalised HIV epidemics make up a significant proportion of all HIV/AIDS cases in many European Union and European Economic Area (EU/EEA) countries, with heterosexual transmission the predominant mode of HIV acquisition. While most of these infections are diagnosed for the first time in Europe, acquisition is believed to have predominantly occurred in the home country. A proportion of HIV transmission is believed to be occurring post-migration, and many countries may underestimate the degree to which this is occurring. Our objectives were to review the literature estimating the proportion of migrants believed to have acquired their HIV post-migration and examine which EU member states are able to provide estimates of probable country of HIV acquisition through current surveillance systems.

Methods

A systematic review was undertaken to gather evidence of sexual transmission of HIV within Europe among populations from countries with a generalised epidemic. In addition, national surveillance focal points from 30 EU/EEA Member States were asked to complete a questionnaire about surveillance methods and monitoring of the likely place of HIV acquisition among migrants.

Results & discussion

Twenty-seven papers from seven countries were included in the review and 24 countries responded to the survey. Estimates of HIV acquisition post-migration ranged from as low as 2 % among sub Saharan Africans in Switzerland, to 62 % among black Caribbean men who have sex with men (MSM) in the UK. Surveillance methods for monitoring post-migration acquisition varied across the region; a range of methods are used to estimate country or region of HIV acquisition, including behavioural and clinical markers. There is little published evidence addressing this issue, although Member States highlight the importance of migrant populations in their epidemics.

Conclusions

There is post-migration HIV acquisition among migrants in European countries but this is difficult to quantify accurately with current data. Migrant MSM appear at particular risk of HIV acquisition post-migration. Countries that identify migrants as an important part of their HIV epidemic should focus on using an objective method for assigning probable country of HIV acquisition. Robust methods to measure HIV incidence should be considered in order to inform national prevention programming and resource allocation.

Phylogeographic analysis on the travel-related introduction of HIV-1 non-B subtypes to Northern Poland

Phylodynamic, sequence data based reconstructions for the surveillance of the geographic spatial spread are a powerful tool in molecular epidemiology. In this study region of origin for the set of 57 partial pol sequences derived from the patients the history of travel-related HIV transmission was analyzed using phylogeographic approach. Maximum likelihood trees based on the sets of country-annotated reference sequences were inferred for identified non-B variants. Region of sequence import was assigned using on the highest approximate likelihood ratios. Import of the A1 clades was traced to the Eastern Europe and associated with immigration from this region. Subtype C infections clustered most frequently with sequences of the South African origin while majority of subtype Ds were similar to the European clades. Subtype G sequences clustered with Portuguese lineage, CRF01_AE with Eastern or South-Eastern Asian. Eastern European, Middle African or Western African lineage was assigned for the CFR02_AG. Rare circulating recombinants originated either from Central Africa (CRF11_cpx - Democratic Republic of Congo, CRF13_cpx - Central African Republic, CRF37_cpx - Cameroon) or South America (CRF28_BF and CRF46_BF - Brazil). Import of the HIV-1 non-B variants, including recombinant forms previously rarely found in Poland and Europe is frequent among travelers. Observed founder events result in the heterosexually-driven introduction of the novel HIV-1 variants into the population.

Do HIV-1 non-B subtypes differentially impact resistance mutations and clinical disease progression in treated populations? Evidence from a systematic review

There are 31 million adults living with HIV-1 non-B subtypes globally, and about 10 million are on antiretroviral therapy (ART). Global evidence to guide clinical practice on ART response in HIV-1 non-B subtypes remains limited. We systematically searched 11 databases for the period 1996 to 2013 for evidence. Outcomes documented included time to development of AIDS and/or death, resistance mutations, opportunistic infections, and changes in CD4 cell counts and viral load. A lack of consistent reporting of all clinical end points precluded a meta-analysis. In sum, genetic diversity that precipitated differences in disease progression in ART-naïve populations was minimized in ART-experienced populations, although variability in resistance mutations persisted across non-B subtypes. To improve the quality of patient care in global settings, recording HIV genotypes at baseline and at virologic failure with targeted non-B subtype-based point-of-care resistance assays and timely phasing out of resistance-inducing ART regimens is recommended.

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.

Large-scale analysis of the prevalence and geographic distribution of HIV-1 non-B variants in the United States

The genetic diversity of human immunodeficiency virus type 1 (HIV-1) has significant implications for diagnosis, vaccine development, and clinical management of patients. Although HIV-1 subtype B is predominant in the United States, factors such as global travel, immigration, and military deployment have the potential to increase the proportion of non-subtype B infections. Limited data are available on the prevalence and distribution of non-B HIV-1 strains in the United States. We sought to retrospectively examine the prevalence, geographic distribution, diversity, and temporal trends of HIV-1 non-B infections in samples obtained by ARUP Laboratories, a national reference laboratory, from all regions of the United States. HIV-1 pol sequences from 24,386 specimens collected from 46 states between 2004 and September 2011 for drug resistance genotyping were analyzed using the REGA HIV-1 Subtyping Tool, version 2.0. Sequences refractory to subtype determination or reported as non-subtype B by this tool were analyzed by PHYLIP version 3.5 and Simplot version 3.5.1. Non-subtype B strains accounted for 3.27% (798/24,386) of specimens. The 798 non-B specimens were received from 37 states and included 5 subtypes, 23 different circulating recombinant forms (CRFs), and 39 unique recombinant forms (URFs). The non-subtype B prevalence varied from 0% in 2004 (0/54) to 4.12% in 2011 (201/4,884). This large-scale analysis reveals that the diversity of HIV-1 in the United States is high, with multiple subtypes, CRFs, and URFs circulating. Moreover, the geographic distribution of non-B variants is widespread. Data from HIV-1 drug resistance testing have the potential to significantly enhance the surveillance of HIV-1 variants in the United States.

Dynamics of HIV type 1 recombination following superinfection

There are currently few detailed studies describing HIV-1 recombination events or the potential impact of recombination on drug resistance. We describe here the viral recombination dynamics in a drug-naive patient initially infected with a circulating recombinant form 19 (CRF19) virus containing transmitted drug resistance mutations followed by superinfection with "wild-type" subtype B virus. Single genome analysis showed replacement of the primary CRF19 virus by recombinants of the CRF19 virus and the superinfecting subtype B virus. The CRF19/B recombinant virus dominating after superinfection had lost drug resistance mutations and at no time was the superinfecting subtype B variant found to be dominant in blood plasma. Furthermore, the detection of recombinant viruses in seminal plasma indicates the potential for onward transmission of these strains.

Ten years of external quality assessment of human immunodeficiency virus type 1 RNA quantification

Viral load testing is an essential parameter in guiding antiretroviral therapy for individuals infected with human immunodeficiency virus type 1 (HIV-1). An external quality assessment scheme for the molecular quantification of HIV-1 RNA was introduced by the United Kingdom National External Quality Assessment Service for Microbiology in 2000. Specimen pairs of freeze-dried plasma were distributed to a median of 141 participants three times a year. The aim of this study was to analyze the quantification of HIV-1 RNA results between 2000 and 2010. Overall variability, measured by the standard deviations of all viral load results for each specimen, was below 0.5 log copy/ml (n = 48). When we compared assay results, the medians of the viral load by assay were within a range of 0.25 to 1.08 log copies/ml, with the lowest median values being consistently reported with the Siemens branched-chain DNA assay. The spread of participant results and, hence, differences between assay medians were greater when quantifying non-B subtypes. Laboratories were scored on the proximity of their reported log difference for the specimen pair to the median log difference reported by all laboratories. The overall level of performance with the HIV-1 RNA specimens over the past 10 years has been consistently good, with more than 90% of the participants reporting in the accepted range (median difference, ±0.5 log unit). Future distributions may result in tightening the acceptance levels of quantification and the use of more challenging specimens, including a variety of subtypes, with developments focusing on maintaining the clinical relevance and educational value of the scheme.

Continuous spread of HIV-1 subtypes D and CRF01_AE in France from 2003 to 2009

Among 61 and 35 patients who were infected in France by viruses of the rare clades D and CRF01_AE, respectively, approximately half of them originated from areas where HIV-1 is endemic, but the data showed that both clades have spread in the French indigenous population, particularly in men having sex with men (MSM).

[New diagnosis of HIV infection in children]

INTRODUCTION

The number of children of immigrant origin in the last few years has increased the cohort of HIV-infected children in the Community of Madrid. The objectives of the study were to evaluate the epidemiological and clinical characteristics of the new diagnosed children and describe the different subtypes of HIV-1.

PATIENTS AND METHODS

The new diagnosed children were analysed from the year 1997, divided into 3 periods: P1 (1997-2000), P2 (2001-2004), P3 (2005-2009). The regions and countries of origin, the clinical, immune and viral characteristics, as well as the response to treatment were analysed. The subtypes of HIV-1 were evaluated by phylogenetic analysis of protease genes and reverse transcriptase.

RESULTS

We identified 141 new diagnoses of HIV infection, the percentage of immigrant origin in P1 was (22.5%), P2 (50%) and P3 (68%). The origin had changed from Latin America in P1 to sub-Saharan Africa in P3. There were no differences between Spanish and immigrant children in the age at diagnosis, the CDC clinical stage A/B/C, viral load, percentage of CD4 at diagnosis and actual. Better viral response was more likely in immigrants after the first regimen of HAART (Highly active antiretroviral treatment) independently of the treatment received. A total of 66 subtypes were obtained, 24% were subtypes non-B (56% recombinants forms). All subtypes of Spanish children (43) and Latin American (5) were subtypes B, and all the children from sub-Saharan Africa (14) were subtypes non-B.

CONCLUSION

There were no differences between immigrants and Spanish children infected by HIV, except the different subtypes of HIV-1.

Development of a United Kingdom National External Quality Assessment Scheme (UK NEQAS) for HIV point of care testing

The use of HIV point of care tests (POCTs) is increasing rapidly in both laboratory and other settings. These tests are often performed by non-laboratory trained staff. At the present time there are no external quality assessment (EQA) providers in the UK offering proficiency testing schemes for HIV point of care testing. The aim of this study is to develop such an EQA scheme. Firstly, a selection of the most widely used POCTs was selected and their performance assessed using existing HIV-positive serology EQA specimens. All assays produced the correct results however intensity of results observed for the same specimen differed greatly between POCT devices. In addition the effect of various sub-groups of HIV-1 serum samples on the HIV POCT assays was investigated and no difference between the results on the POCTs was observed. Ultimately four serum specimens, two HIV-1 and one HIV-2 positive, one HIV negative, were chosen and sent to NHS laboratories and sexual health clinics for testing as part of a pilot EQA scheme for HIV POCT. Results were excellent with 97% of participants reporting correct results (n= 20). The study highlighted a lack of awareness of EQA particularly in non-laboratory settings, although recommendations (ISO 22870:2006) are in place for the users of such devices. In conclusion, the need for EQA for providers of point of care testing is an integral part of ensuring reliability of results and quality of care for the patient.

HIV transmission patterns among The Netherlands, Suriname, and The Netherlands Antilles: a molecular epidemiological study

We aimed to study patterns of HIV transmission among Suriname, The Netherlands Antilles, and The Netherlands. Fragments of env, gag, and pol genes of 55 HIV-infected Surinamese, Antillean, and Dutch heterosexuals living in The Netherlands and 72 HIV-infected heterosexuals living in Suriname and the Antilles were amplified and sequenced. We included 145 pol sequences of HIV-infected Surinamese, Antillean, and Dutch heterosexuals living in The Netherlands from an observational cohort. All sequences were phylogenetically analyzed by neighbor-joining. Additionally, HIV-1 mobility among ethnic groups was estimated. A phylogenetic tree of all pol sequences showed two Surinamese and three Antillean clusters of related strains, but no clustering between ethnic groups. Clusters included sequences of individuals living in Suriname and the Antilles as well as those who have migrated to The Netherlands. Similar clustering patterns were observed in env and gag. Analysis of HIV mobility among ethnic groups showed significantly lower migration between groups than expected under the hypothesis of panmixis, apart from higher HIV migration between Antilleans in The Netherlands and all other groups. Our study shows that HIV transmission mainly occurs within the ethnic group. This suggests that cultural factors could have a larger impact on HIV mobility than geographic distance.

Epidemiology of non-B clade forms of HIV-1 in men who have sex with men in the UK

OBJECTIVES

To describe the frequency and risk factors of non-B HIV-1 subtypes in men who have sex with men (MSM) in the UK.

DESIGN

Observational study.

METHODS

MSM diagnosed with HIV-1 infection from 1980-2007, with HIV genotype held in the UK HIV Drug Resistance Database were identified. Protease and reverse transcriptase sequences were collected and viral clade determined using the REGA algorithm. Associations between demographic variables and subtype were analysed using logistic regression.

RESULTS

The prevalence of non-B HIV-1 infection amongst MSM in the UK was 5.4% (437/8058). In the UK this increased with year of diagnosis from pre1996 to 2002, and has subsequently remained relatively stable at around 7-9% after 2002, with a recent increase in 2007 to 13%. Multivariate analysis showed that acquisition of non-B HIV-1 infection was independently associated with later year of HIV diagnosis (P < 0.001), black ethnicity (P < 0.001) and non-European country of birth (P = 0.01). Age was also associated with subtype with individuals aged 25-39 years being less likely to have non-B virus than those aged less than 25 years (P = 0.01). Restricting the analysis to white men born in the UK, the association between subtype and year of diagnosis remained statistically significant (P < 0.001), as did the association with age (P < 0.001).

DISCUSSION

The number of MSM in the UK infected with non-B clade HIV-1 is increasing, suggesting that the sociodemographic boundaries between HIV-1 viral subtypes globally are diminishing. Should viral subtypes be relevant to clinical disease progression or vaccine design, the changing pattern of distribution will need to be taken into account.

Two independent epidemics of HIV in Maryland

BACKGROUND

HIV-1 subtype B virus is the predominant subtype in HIV-infected individuals in the United States. However, increasing evidence suggests that prevalence of non-B subtypes may be on the rise in the West, and this may have implications for HIV-1 disease surveillance and treatment. The state of Maryland currently has the fourth highest AIDS case report rate in the United States. The goal of this study was to evaluate the prevalence of HIV-1 non-B subtypes in Maryland. The study population included individuals diagnosed with HIV in 2007 through the voluntary counseling and testing sites at the Maryland Department of Health and Mental Hygiene and HIV-infected patients who had genotyping performed at the University of Maryland Medical Center.

RESULTS

At the Department of Health and Mental Hygiene sites, 47 unique non-B subtype strains were identified representing a non-B prevalence of 12.9%. These non-B subtypes included CRF02_AG (n = 20), C (n = 11), A (n = 7), G (n = 5), D (n = 1), and unique recombinant forms (n = 3). The non-B patients were predominantly non-Hispanic black (95.7%) with 63.8% female. Although the majority of the HIV subtype B cases (65.3%) were identified from the Baltimore metropolitan area, most (80.9%) of the non-B cases were from the Maryland suburbs of Washington, DC. Among University of Maryland Medical Center patients, there were 30 non-B subtypes, representing a non-B prevalence of 1.9%. The non-B subtypes detected were CRF02_AG (n = 14), C (n = 6), A (n = 6), G (n = 2), D (n = 1), and unique recombinant forms (n = 1). Phylogenetic analysis of the non-B subtypes revealed that viral sequences from both sources were intermixed, confirming that both sampling frames were drawing from the same overall population.

CONCLUSIONS

Multiple HIV-1 subtypes exist in the Baltimore-Washington metropolitan area with a significant non-B-infected population in the Maryland suburbs of Washington, DC, suggesting 2 independent epidemics of HIV in Maryland. Population-based surveillance inclusive of groups at higher risk of non-B strains is essential to monitor the prevalence and variations of HIV subtypes in Maryland and the United States.

Use of phylogenetics in the molecular epidemiology and evolutionary studies of viral infections

Since DNA sequencing techniques first became available almost 30 years ago, the amount of nucleic acid sequence data has increased enormously. Phylogenetics, which is widely applied to compare and analyze such data, is particularly useful for the analysis of genes from rapidly evolving viruses. It has been used extensively to describe the molecular epidemiology and transmission of the human immunodeficiency virus (HIV), the origins and subsequent evolution of the severe acute respiratory syndrome (SARS)-associated coronavirus (SCoV), and, more recently, the evolving epidemiology of avian influenza as well as seasonal and pandemic human influenza viruses. Recent advances in phylogenetic methods can infer more in-depth information about the patterns of virus emergence, adding to the conventional approaches in viral epidemiology. Examples of this information include estimations (with confidence limits) of the actual time of the origin of a new viral strain or its emergence in a new species, viral recombination and reassortment events, the rate of population size change in a viral epidemic, and how the virus spreads and evolves within a specific population and geographical region. Such sequence-derived information obtained from the phylogenetic tree can assist in the design and implementation of public health and therapeutic interventions. However, application of many of these advanced phylogenetic methods are currently limited to specialized phylogeneticists and statisticians, mainly because of their mathematical basis and their dependence on the use of a large number of computer programs. This review attempts to bridge this gap by presenting conceptual, technical, and practical aspects of applying phylogenetic methods in studies of influenza, HIV, and SCoV. It aims to provide, with minimal mathematics and statistics, a practical overview of how phylogenetic methods can be incorporated into virological studies by clinical and laboratory specialists.

Impact of HIV-1 viral subtype on disease progression and response to antiretroviral therapy

BACKGROUND

Our intention was to compare the rate of immunological progression prior to antiretroviral therapy (ART) and the virological response to ART in patients infected with subtype B and four non-B HIV-1 subtypes (A, C, D and the circulating recombinant form, CRF02-AG) in an ethnically diverse population of HIV-1-infected patients in south London.

METHODS

A random sample of 861 HIV-1-infected patients attending HIV clinics at King's and St Thomas' hospitals' were subtyped using an in-house enzyme-linked immunoassay and env sequencing. Subtypes were compared on the rate of CD4 cell decline using a multi-level random effects model. Virological response to ART was compared using the time to virological suppression (< 400 copies/ml) and rate of virological rebound (> 400 copies/ml) following initial suppression.

RESULTS

Complete subtype and epidemiological data were available for 679 patients, of whom 357 (52.6%) were white and 230 (33.9%) were black African. Subtype B (n = 394) accounted for the majority of infections, followed by subtypes C (n = 125), A (n = 84), D (n = 51) and CRF02-AG (n = 25). There were no significant differences in rate of CD4 cell decline, initial response to highly active antiretroviral therapy and subsequent rate of virological rebound for subtypes B, A, C and CRF02-AG. However, a statistically significant four-fold faster rate of CD4 decline (after adjustment for gender, ethnicity and baseline CD4 count) was observed for subtype D. In addition, subtype D infections showed a higher rate of virological rebound at six months (70%) compared with subtypes B (45%, p = 0.02), A (35%, p = 0.004) and C (34%, p = 0.01)

CONCLUSIONS

This is the first study from an industrialized country to show a faster CD4 cell decline and higher rate of subsequent virological failure with subtype D infection. Further studies are needed to identify the molecular mechanisms responsible for the greater virulence of subtype D.

African Australians living with HIV: a case series from Victoria

Background: This research aimed to describe the characteristics of African-born Victorians living with HIV, identify associations with delayed HIV diagnosis and describe their response to combination antiretroviral therapy (cART). Methods: A case series of African-born adults living with HIV in Victoria was conducted. Data was collected in interviews and reviews of case notes. Associations with delayed HIV diagnosis (CD4 below 200 cells µL–1 at diagnosis and/or AIDS within 3 months of HIV diagnosis) were explored using univariate regression. AIDS-defining illnesses and response to cART were described. Results: Fourteen males and six females were included. Ten were born in the Horn of Africa (nine in Ethiopia). Sixteen had sexual exposure (12 heterosexual; four male-to-male sex). Seven reported acquiring HIV in Australia. Median CD4 count at diagnosis was 145 cells µL–1. Ten had delayed HIV diagnosis, of whom eight were born in the Horn of Africa. Delayed HIV diagnosis was associated with birth in the Horn of Africa (odds ratio: 11.56). Nine had a diagnosis of AIDS, including three cases of tuberculosis, three of Pneumocystis jiroveci pneumonia and two of cerebral toxoplasmosis. Eighteen had received cART, of which 16 achieved virological suppression and 15 achieved a CD4 count above 200 cells µL–1. Clinical failure and virological failure occurred in seven and five cases, respectively. Conclusions: HIV prevention strategies for Victoria’s African communities should address HIV exposure in Australia. Ethiopian-born Victorians with HIV appear to be at particular risk of delayed diagnosis. Response to cART in this series was comparable to that observed in other industrialised countries.

Resistance and viral subtypes: how important are the differences and why do they occur?

PURPOSE OF REVIEW

The global HIV-1 pandemic has evolved to include 11 subtypes and 34 circulating recombinant forms. Our knowledge of HIV-1 response to antiretroviral drugs and emergent drug resistance has, however, been limited to subtype B infections circulating in Europe and North America, with little comparative information on non-B subtypes representing approximately 90% of worldwide epidemics. This review summarizes publications in the past year that highlight intersubtype differences influencing viral susceptibility to antiretroviral drugs and emergent drug resistance.

RECENT FINDINGS

Cumulative findings from clinical studies suggest that antiretroviral therapy will be of benefit in the overall treatment of non-B subtype infections, and result in drug-resistance profiles comparable to those observed for subtype B infections. Nevertheless, the 10-15% sequence diversity in the Pol region contributes to intersubtype differences in response to particular nucleoside and non-nucleoside analogues, as well as protease inhibitors. Distinct signature mutations and mutational pathways are identified for specific non-B subtypes. The implications of subtype on clinical outcome and interpretative algorithms are described.

SUMMARY

Understanding intersubtype differences in drug resistance is important in optimizing treatment strategies in resource-poor settings. Hopefully, this may assist in the design of prophylactic approaches to prevent HIV-1 horizontal and vertical HIV-1 transmission.

Characterization of genetically diverse HIV type 1 from a London cohort: near full-length genomic analysis of a subtype H strain

HIV-1 is characterized by an exceptional level of sequence diversity and a rapid rate of evolution. HIV diversity has implications for reliability of assays designed to detect and monitor infection, pathogenesis, disease progression, response to antiviral therapeutics, resistance pathways, and vaccine development. In the present study, HIV-1 strain diversity was assessed for a small clinical cohort (n = 15) from London, England at risk for infection with non-subtype B strains. Analysis of gag p24, pol IN, and env gp41 IDR revealed the presence of five subtypes (A, B, C, D, H), CRF02_AG, and four unique recombinant forms. Due to the paucity of complete subtype H genomes available, we performed near full-length genome sequence analysis on the candidate subtype H strain, designated as 00GB.AC4001. Phylogenetic analysis revealed that it formed a monophyletic cluster with the three available subtype H reference sequences. Bootscanning analysis confirmed that 00GB.AC4001 represents a new nonrecombinant subtype H genome.

Non-B HIV type 1 subtypes among men who have sex with men in Rome, Italy

An increase in the circulation of HIV-1 non-B subtypes has been observed in recent years in Western European countries. Due to the lack of data on the circulation of HIV-1 non-B subtypes among European HIV-1-infected men who have sex with men (MSM), a biomolecular study was conducted in Rome, Italy. HIV-1 partial pol gene sequences from 111 MSM individuals (76 drug naive and 35 drug experienced) were collected during the years 2004-2006. All these sequences were analyzed using the REGA HIV-1 Subtyping Tool, and aligned using CLUSTAL X followed by manual editing using the Bioedit software. A BLAST search for non-B subtype sequences was also performed. Twenty-six (23.4%) MSM were not Italians. Eight individuals (7.2%) were diagnosed as HIV infected before 1991, 20 (18.0%) between 1991 and 1999, and 83 (74.8%) from 2000 to 2006. Fifteen (15/111, 13.5%) individuals were infected with the non-B subtype. The percentage of infection with HIV-1 non-B subtypes was 8.2% (7/85) among Italian MSM and 30.8% (8/26) among the non-Italians (OR = 4.95 95% IC: 1.40-17.87). Individuals infected with the non-B subtype were significantly younger than those infected with the HIV-1 B subtype (28 years vs. 34 years, p = 0.003). The CRFs were more prevalent (8.1%) than pure subtypes (5.4%), which were distributed as follows: subtype C (2.6%), subtype A1 (1.7%), and subtype F1 (0.9%). Major mutations conferring resistance to antiretroviral drugs (ARV) were not found among HIV-1 non-B subtype drug-naive patients but were found in two ARV-experienced individuals. The data show that viral diversity is likely increasing in a population group that had been previously characterized by the circulation of HIV-1 subtype B.

Drug resistance differences among HIV types and subtypes: a growing problem

Although HIV-1 subtype B accounts for only 10% of worldwide HIV infections, almost all knowledge regarding antiretroviral (ARV) drug development and viral resistance is based on this subtype. More recently, an increasing body of evidence suggests that distinct HIV genetic variants possess different biological properties, including susceptibility and response to ARVs. In this review, we will summarize recent in vitro and in vivo studies reporting such differences. In general terms, infections with most HIV variants respond well to ARVs, but minor differences in susceptibility, in the emergence and selection of subtype-specific drug resistance mutations and in the acquisition of similar mutations over the period of ARV exposure have been reported. Such differences impact on drugresistance interpretation algorithms, which are mostly based on inference from sequence information. Despite the differences observed, clinical response to ARV therapy among subjects infected with distinct HIV variants is effective, and the dissemination of ARV access in developing countries where non-B subtypes prevail should not be delayed.

Reliability of rapid subtyping tools compared to that of phylogenetic analysis for characterization of human immunodeficiency virus type 1 non-B subtypes and recombinant forms

Human immunodeficiency virus type 1 (HIV-1) subtyping is often estimated on the basis of pol sequences by using online websites instead of phylogenetic analysis (phy). We evaluated the reliability of distinct rapid subtyping tools versus phy with a large panel of HIV-1 non-B subtypes and circulating recombinant forms (CRF). pol sequences (277 protease [PR] and 171 reverse transcriptase [RT] sequences) previously assigned by phy to eight distinct HIV-1 non-B subtypes were obtained from 277 HIV-infected patients. Phy was run again to identify CRF. Subtyping was then performed using three rapid tools (the Stanford, NCBI, and REGA online tools). Thirty-three additional clade B sequences were tested as controls. New phylogenetic analyses reclassified two-thirds of pol sequences previously assigned to HIV-1 non-B clades as CRF. CRF02_AG variants were correctly assigned by the Stanford and NCBI tools for 92 to 97% and 96 to 99% of PR-RT sequences, respectively, while they were correctly assigned by the REGA tool for only 18 to 32% of PR-RT sequences. The Stanford, NCBI, and REGA tools failed to assign pure non-B clades correctly for 24 to 33%, 35%, and 57 to 64% of PR-RT sequences, respectively. For PR-RT sequences from CRF other than CRF02_AG, discrepancies occurred in 98 to 100%, 18 to 43%, and 80 to 87% of sequences, respectively. The concordance between those tools and phy was almost complete for subtype B assignment. Rapid subtyping tools show relatively low agreement with phy in identifying HIV-1 non-B clades and CRF other than CRF02_AG. The Stanford tool shows the best concordance with phy for the assignment of pure non-B clades, while the NCBI tool performs better at identifying CRF. Before entering routine clinical use, rapid subtyping tools should be optimized and updated periodically. Larger numbers of different non-B subtypes and CRF sequences should be included.

Modelled in vivo HIV Fitness under drug Selective Pressure and Estimated Genetic Barrier Towards Resistance are Predictive for Virological Response

Background

A method has been developed to estimate a fitness landscape experienced by HIV-1 under treatment selective pressure as a function of the genotypic sequence thereby also estimating the genetic barrier to resistance.

Methods

We evaluated the performance of two estimated fitness landscapes (nelfinavir [NFV] and zidovudine [AZT] plus lamivudine [3TC]) to predict week 12 viral load (VL) change for 176 treatment change episodes (TCEs) and probability of week 48 virological failure for 90 TCEs, in treatment experienced patients starting these drugs in combination.

Results

A higher genetic barrier for AZT plus 3TC, (quantified per additional mutation required to develop resistance against these drugs) was associated with a 0.54 (95% confidence interval [CI] 0.30–0.77) larger log10 VL reduction at 12 weeks ( P<0.0001) and a 0.39 (95% CI 0.23–0.66) lower odds of virological failure at 48 weeks ( P=0.0005), in analyses adjusting for the pre-TCE VL and the exact time-lag between the TCE and the date of determining response VL. The strength of these associations was comparable with those seen with expert interpretation systems (Rega, ANRS and HIVDB). A higher genetic barrier to NFV resistance was the only genotypic predictor that tended to be associated with a 0.19 (95% CI 0–0.39) higher log10 VL reduction at 12 weeks ( P=0.05) and a 0.63 (95% CI 0.36–1.09) lower odds of virological failure at 48 weeks ( P=0.10) per additional mutation.

Conclusions

These results suggest that an estimated genetic barrier derived from fitness landscapes may contribute to an improvement of predicted treatment outcome for NFV and this approach should be explored for other drugs.

Clinical impact of HIV-1 subtype: are there important differences?

The enormous genetic diversity of HIV-1 is a major challenge to vaccine development and may have important clinical consequences. HIV-1 group M predominates globally, with nine subtypes, several sub-subtypes and over 30 circulating recombinant forms that may exhibit differences with respect to transmissibility, pathogenicity and development of antiretroviral resistance. Subtype D appears to be more virulent than other subtypes, in particular subtype A. Subtype C may be less virulent and more transmissible, although the evidence for this is inconclusive. All group M non-B subtypes appear to be equally susceptible to combination antiretroviral therapy, but development of resistance mutations may vary significantly between subtypes. Further research into the clinical implications of HIV-1 diversity is crucial for effective HIV-1 prevention and treatment.

Evaluation of performance across the dynamic range of the Abbott RealTime™ HIV-1 assay as compared to VERSANT HIV-1 RNA 3.0 and AMPLICOR HIV-1 MONITOR v1.5 using serial dilutions of 39 group M and O viruses

Performance of the Abbott m2000 instrument system and the Abbott RealTime HIV-1 assay was evaluated using a panel of 37 group M (subtypes A-D, F, G, CRF01_AE, CRF02_AG and unique recombinant forms) and 2 group O virus isolates. Testing was performed on 273 sample dilutions and compared to VERSANT HIV-1 RNA 3.0 (bDNA) and AMPLICOR HIV-1 MONITOR v1.5 (Monitor v1.5) test results. RealTime HIV-1, bDNA, and Monitor v1.5 tests quantified 87%, 78%, and 81% of samples, respectively. RealTime HIV-1 detected an additional 31 samples at < 40 copies/mL. For group M, RealTime HIV-1 dilution profiles and viral loads were highly correlated with bDNA and Monitor v1.5 values; 87% and 89% of values were within 0.5 log(10) copies/mL. In contrast, the group O viruses were not detected by Monitor v1.5 and were substantially underquantified by approximately 2 log(10) copies/mL in bDNA relative to the RealTime HIV-1 assay. Sequence analysis revealed that RealTime HIV-1 primer/probe binding sites are highly conserved and exhibit fewer nucleotide mismatches relative to Monitor v1.5. The automated m2000 system and RealTime HIV-1 assay offer the advantages of efficient sample processing and throughput with reduced "hands-on" time while providing improved sensitivity, expanded dynamic range and reliable quantification of genetically diverse HIV-1 strains.

Prevalence and predictors of antiretroviral drug resistance in newly diagnosed HIV-1 infection

OBJECTIVES

To determine prevalence and predictors of antiretroviral drug resistance in newly diagnosed individuals with HIV-1 infection, using a systematic approach to avoid selection bias.

METHODS

Plasma samples from all persons diagnosed HIV-1 seropositive at a large London centre between April 2004 and February 2006 underwent sequencing of HIV-1 reverse transcriptase (RT) and protease genes. Subtype was assigned by phylogenetic analysis. Resistance was scored according to the IAS-USA list (2005) modified to include T215revertants and exclude isolated E44D or V118I and minor protease mutations. Recent seroconversion was identified by HIV antibody avidity testing.

RESULTS

The cohort of 239 included 169 (70.7%) males, 126 (52.7%) homosexuals, 118 (49.5%) persons of white ethnicity and 144 (60.0%) persons born outside the UK. Subtypes included B 134 (56.1%), C 46 (19.2%), A 17 (7.1%), other non-B 42 (17.6%). The prevalence of resistance mutations was 17/239 (7.1%; 95% confidence interval 4.5-11.1%), comprising 10/239 (4.2%) nucleoside/nucleotide RT inhibitor (NRTI); 4/239 (1.7%) non-nucleoside RT inhibitor (NNRTI) and 4/239 (1.7%) protease inhibitor (PI) associated mutations. Dual-class (NRTI + PI) resistance mutations were detected in 1/239 (0.4%) person. The prevalence of resistance mutations was 7/85 (8.2%) and 10/154 (6.5%) in persons with recent and established infection, respectively. In multivariate analysis, having been born in the UK and high CD4 count, but not gender, age, risk group, ethnicity or subtype, were independent predictors of resistance.

CONCLUSIONS

In an unselected UK cohort, subtypes other than B accounted for 43.9% of new HIV-1 diagnoses. The prevalence of resistance mutations was 7.1% and highest in those born in the UK.

Performance of the automated Abbott RealTime™ HIV-1 assay on a genetically diverse panel of specimens from London: Comparison to VERSANT HIV-1 RNA 3.0, AMPLICOR HIV-1 MONITOR v1.5, and LCx® HIV RNA Quantitative assays

Automated RNA extraction and quantitation of HIV-1 by real-time PCR offer potential advantages of efficient sample processing, improved sensitivity, expanded dynamic range and reduced contamination risk. In this study, plasma was collected from 100 HIV-1 infected patients visiting The Courtyard Clinic of St. George's Hospital in London, United Kingdom (UK). Viral loads measured using the automated Abbott RealTime HIV-1 assay (m2000sp sample preparation and m2000rt amplification and detection instruments) were compared to results obtained with Versant HIV-1 RNA 3.0 (bDNA), AMPLICOR HIV-1 MONITOR v1.5 (Monitor v1.5) and LCx HIV RNA Quantitative (LCx HIV) assays. Based on gag p24, pol integrase, and env gp41 sequences, the panel included 26 subtype A, 20 B, 27 C, 10 D, 1 CRF01_AE, 3 CRF02_AG and 13 recombinant viruses. RealTime HIV-1, bDNA, Monitor v1.5 and LCx HIV quantitated 82, 74, 82, and 83% of samples, respectively, with 82, 71, 69 and 80 of the 100 samples measured within the dynamic ranges. Viral loads were highly correlated with 99% of values within 1 log(10) copies/ml between tests. The automated m2000 system and RealTime HIV-1 assay can increase laboratory throughput, enhance overall efficiency and reduce operator-associated errors while providing reliable quantitation of genetically diverse strains of HIV-1.