HIV-1 Dual Infection Research Articles

Triple HIV-1 Infection Is Associated With Faster CD4+ T-Cell Decline.

HIV-1 dual infection occurs when an individual is simultaneously or sequentially infected with two or more genetically distinct HIV-1 strains. According to the number of infected strains, HIV-1 dual infection can be divided in double infection and triple infection and so on. Currently, the majority of dual infection cases have been reported to be double infections which can result in detrimental clinical outcomes. The high incidence of double infection among specific high-risk populations increases the likelihood of triple infection, which has been sporadically described. There is no doubt that we are concerned about the association between triple infection and disease progression. However, this relationship is still unclear on the population level. In this study, 70 individuals from the Beijing PRIMO cohort were longitudinally followed up with a median time of 15.75 months for the purpose of investigating the incidence of dual infection. Phylogenetic analyses using bulk and single-genome sequences showed that nine individuals acquired double infection, with the incidence of 9.21 per 100 person-years, and three individuals with triple infection were identified, with the incidence of 3.07 per 100 person-years. The further survival analysis demonstrated that the triple infection group exhibited faster CD4+ T-cell decline. In summary, these results demonstrate for the first time that the triple HIV-1 infection might reduce CD4+ T-cell counts, which would predict a more rapid disease progression.

Frequency of occurrence of HIV-1 dual infection in a Belgian MSM population.

IntroductionHIV-1 dual infection is a condition that results from infection with at least two HIV-1 variants from different sources. The scarceness of information on this condition is partly due to the fact that its detection is technically challenging. Using next-generation sequencing we defined the extent of HIV-1 dual infection in a cohort of men who have sex with men (MSM).Material & methodsEighty-six MSM, diagnosed with HIV-1 subtype B infection between 2008 and 2013 were selected for next-generation sequencing of the HIV-1 envelope V3. Sequencing was performed on 2 plasma samples collected with an interval of > 6 months before the initiation of antiretroviral therapy. Maximum likelihood phylogenetic trees were inspected for dual infection, defined as the presence of two or more monophyletic clusters with ≥ 90% bootstrap support and a mean between-cluster genetic distance of ≥ 10%. To confirm dual infection, deep V3 sequencing of intermediate samples was performed as well as clonal sequencing of the HIV-1 protease-reverse transcriptase gene.ResultsFive of the 74 patients (6.8%) for whom deep sequencing was successful, showed clear evidence of dual infection. In 4 of them, the second strain was absent in the first sample but occurred in subsequent samples. This was highly suggestive for superinfection. In 3 patients both virus variants were of subtype B, in 2 patients at least one of the variants was a subtype B/non-B recombinant virus.ConclusionsDual infection was confirmed in 6.8% of MSM diagnosed with HIV-1 in Belgium. This prevalence is probably an underestimation, because stringent criteria were used to classify viral variants as originating from a new infection event.

NGS combined with phylogenetic analysis to detect HIV-1 dual infection in Romanian people who inject drugs

Dual HIV infections are possible and likely in people who inject drugs (PWID). Thirty-eight newly diagnosed patients, 19 PWID and 19 heterosexually HIV infected were analyzed. V2V3 loop of HIV-1 env gene was sequenced on the NGS platform 454 GSJunior (Roche). HIV-1 dual/multiple infections were identified in five PWID. For three of these patients, the reconstructed variants belonged to pure F1 subtype and CRF14_BG strains according to phylogenetic analysis. New recombinant forms between these parental strains were identified in two PWID samples. NGS data can provide, with the help of phylogenetic analysis, important insights about the intra-host sub-population structure.

Dual Infection Contributes to Rapid Disease Progression in Men Who Have Sex With Men in China.

Considerable numbers of HIV-1-infected men who have sex with men (MSM) show a relatively rapid disease progression in China; however, the cause remains elusive. HIV-1 dual infection was reported to occur commonly among the MSM population, and its contribution to clinical prognosis remains controversial. We investigated the occurrence and impact on disease progression of dual infection in a prospective MSM cohort in China. Sixty-four HIV-1 early-infected participants were longitudinally followed up for 2 years. Deep sequencing was used as dual-infection screening. CD4 T-cell counts and HIV-1 viral load were compared between coinfection and single-infection participants and pre- versus post-superinfection. Eight coinfected participants and 10 superinfected participants were identified, including 9 participants with intersubtype and 9 with intrasubtype dual infections. The prevalence of coinfection was 13.1%, with a superinfection incidence of 15.6%. Coinfection participants showed lower CD4 T-cell counts at 120 days after infection (P = 0.042) and a higher viral set point tendency (P = 0.053) as compared with single-infection participants. Kaplan-Meier analysis showed that the time for the viral load to increase to above 4 log10 copies per milliliter was shorter in coinfection participants than in single-infection participants (P < 0.001). After superinfection, the median CD4 T-cell count decreased from 635 to 481 cells/μL (P = 0.027). The occurrence of dual infection among Chinese MSM is relatively high, and HIV-1 dual infection might contribute to rapid disease progression seen in the MSM population.

HIV-associated neurocognitive disorder is associated with HIV-1 dual infection.

Compared with HIV monoinfection, HIV dual infection has been associated with decreased CD4 T-cell counts and increased viral loads. The same markers are also associated with the development of HIV-associated neurocognitive disorder (HAND), which continues to be a prevalent problem in the era of combination antiretroviral therapy (ART). We sought to determine the relationship between dual infection and HAND. Participants on ART (N = 38) underwent deep sequencing of four PCR-amplified HIV coding regions derived from peripheral blood mononuclear cell DNA samples. Phylogenetic analyses were performed to evaluate whether two distinct viral lineages, that is, dual infection, were present in the same individual. All study participants underwent neurocognitive, substance use, and neuromedical assessments at each study visit. Of 38 participants, nine (23.7%) had evidence of dual infection. Using clinical ratings, global neurocognitive impairment was identified in 21 (55%) participants, and multivariate analysis demonstrated a significant association between dual infection and impairment; odds ratio (95% confidence interval) = 18.3 (1.9, 414.2), P = 0.028. Neurocognitive impairment was also associated with lower current (P = 0.028) and nadir (P = 0.043) CD4 T-cell counts. Deep sequencing of HIV DNA populations in blood mononuclear cell identified dual infection in nearly a quarter of HIV-infected adults receiving ART, and dual infection was associated with HAND. Dual infection may contribute to the development of HAND, perhaps because of increased viral diversity. Further investigation is needed to determine how dual infection results in worse neurocognitive performance.

HIV-1 Clade B pol Evolution following Primary Infection

ObjectiveCharacterize intra-individual HIV-1 subtype B pol evolution in antiretroviral naive individuals.DesignLongitudinal cohort study of individuals enrolled during primary infection.MethodsEligible individuals were antiretroviral naïve participants enrolled in the cohort from December 1997-December 2005 and having at least two blood samples available with the first one collected within a year of their estimated date of infection. Population-based pol sequences were generated from collected blood samples and analyzed for genetic divergence over time in respect to dual infection status, HLA, CD4 count and viral load.Results93 participants were observed for a median of 1.8 years (Mean = 2.2 years, SD = 1.9 years). All participants classified as mono-infected had less than 0.7% divergence between any two of their pol sequences using the Tamura-Nei model (TN93), while individuals with dual infection had up to 7.0% divergence. The global substitution rates (substitutions/nucleotide/year) for mono and dually infected individuals were significantly different (p<0.001); however, substitution rates were not associated with HLA haplotype, CD4 or viral load.ConclusionsEven after a maximum of almost 9 years of follow-up, all mono-infected participants had less than 1% divergence between baseline and longitudinal sequences, while participants with dual infection had 10 times greater divergence. These data support the use of HIV-1 pol sequence data to evaluate transmission events, networks and HIV-1 dual infection.

Using Ultradeep Pyrosequencing to Study HIV-1 Coreceptor Usage in Primary and Dual Infection

HIV-1 dual infection (DI) and CXCR4 (X4) coreceptor usage are associated with accelerated disease progression but frequency and dynamics of coreceptor usage during DI is unknown. Ultradeep sequencing was used to interrogate for DI and infer coreceptor usage in longitudinal blood samples of 102 subjects. At baseline, X4 usage was high (23 subjects harbored X4 variants) and was not associated with infection duration or DI. Coreceptor usage changed over time in 12 of 47 participants, and X4 usage emerged in 4 of 41 monoinfections vs 2 of 5 superinfections (P = .12), suggesting a weak statistical trend toward occurrence of superinfection and acquiring X4 usage.

HIV-1 Dual Infection Is Associated With Faster CD4+ T-Cell Decline in a Cohort of Men With Primary HIV Infection

HIV-1 Dual Infection Is Associated With Faster CD4+ T-Cell Decline in a Cohort of Men With Primary HIV Infection

British HIV Association guidelines for antiretroviral treatment of HIV‐2‐positive individuals 2010

British HIV Association guidelines for antiretroviral treatment of HIV‐2‐positive individuals 2010

Short Communication: HIV Type 1 Genetic Diversity among Tea Plantation Workers in Kericho, Kenya

In preparation for HIV-1 vaccine trials in Kenya, 2801 study volunteers, from a tea plantation in Kericho, were recruited as part of a prospective vaccine cohort development study. Cryopreserved plasma was available from 401 HIV-positive volunteers, and was the source of viral RNA for genotyping by the multiregion hybridization assay (MHA). Logistic regression was performed to determine association of risk factors and HIV-1 recombinant and dual infections. At baseline, HIV-1 subtype A was the dominant circulating pure subtype (56%), followed by subtype D (10%) and C (5%). Recombinant HIV-1 strains accounted for almost one-third of all infections (29%), with 7% infected with a dual strain of the HIV-1 variants described. A higher number of HIV-1 recombinant and dual infections was observed among volunteers who were 18-24 and 25-29 years of age, affiliated with the Luo tribe, had been married two or more times, reported not being circumcised, and had STI symptoms in the past 6 months. Adjusted odds ratios (AOR) significantly associated with HIV-1 recombinant and dual infection were age difference from current spouse (5-9 years; AOR = 2.5, 95% CI = 1.2-5.3 and > or = 10 years; AOR = 3.1, 95% CI = 1.5-6.4) and reported STI symptoms in the past 6 months (AOR = 4.8, 95% CI = 2.0-11.6), respectively. In conclusion, our results suggest that there is considerable heterogeneity with respect to HIV-1 subtype diversity in this population that should be considered in the planning for future vaccine trials in the region.

P.027 No changing incidence in HIV-1 dual infections in Amsterdam, The Netherlands, from 2003–2007

Purpose: The occurrence of HIV-1 dual infections in Amsterdam, The Netherlands, was examined from 2003–2007 to investigate whether or not HIV-1 dual infections are increasing as the number of HIV-1 infected individuals increased here over this time period. Methods: All first HIV-1 genotyping sequences determined between 2003 and 2007 were retrieved and examined for the number of degenerate base codes in the RT fragment. From a total of 73 patients with a degenerate base code count of > 33, a fragment of the V3-V4 region of the env gene was amplified, cloned and sequenced to verify the presence of a HIV-1 dual infection. Dual infections were counted for each year investigated. Results: No significant change in incidence of dual infections was seen in our patient population selected upon the degenerate base count in the HIV-1 genotyping sequence from 2003 till 2007. The frequency of HIV-1 dual infections varied between 1.0%–2.8%/year, with no significant trend in time (p = 0.49). Based upon the number of patients with a high degenerate base code count, an increase in dual infections was expected in 2006 and 2007, but this was not observed. HIV-1 dual infections were similar to HIV-1 single infections in The Netherlands in distribution by risk group, gender and subtype. Conclusion: HIV-1 dual infections in The Netherlands are not increasing from 2003 to 2007 although the HIV-1 infected population is expanding in this period.

P.029 Two decades of hepatitis B infections among drug users in Amsterdam: are they still a high-risk group?

Purpose: The occurrence of HIV-1 dual infections in Amsterdam, The Netherlands, was examined from 2003–2007 to investigate whether or not HIV-1 dual infections are increasing as the number of HIV-1 infected individuals increased here over this time period. Methods: All first HIV-1 genotyping sequences determined between 2003 and 2007 were retrieved and examined for the number of degenerate base codes in the RT fragment. From a total of 73 patients with a degenerate base code count of > 33, a fragment of the V3-V4 region of the env gene was amplified, cloned and sequenced to verify the presence of a HIV-1 dual infection. Dual infections were counted for each year investigated. Results: No significant change in incidence of dual infections was seen in our patient population selected upon the degenerate base count in the HIV-1 genotyping sequence from 2003 till 2007. The frequency of HIV-1 dual infections varied between 1.0%–2.8%/year, with no significant trend in time (p = 0.49). Based upon the number of patients with a high degenerate base code count, an increase in dual infections was expected in 2006 and 2007, but this was not observed. HIV-1 dual infections were similar to HIV-1 single infections in The Netherlands in distribution by risk group, gender and subtype. Conclusion: HIV-1 dual infections in The Netherlands are not increasing from 2003 to 2007 although the HIV-1 infected population is expanding in this period.

P.028 The utility of vomit as a specimen in the investigation of norovirus outbreaks

Purpose: The occurrence of HIV-1 dual infections in Amsterdam, The Netherlands, was examined from 2003–2007 to investigate whether or not HIV-1 dual infections are increasing as the number of HIV-1 infected individuals increased here over this time period. Methods: All first HIV-1 genotyping sequences determined between 2003 and 2007 were retrieved and examined for the number of degenerate base codes in the RT fragment. From a total of 73 patients with a degenerate base code count of > 33, a fragment of the V3-V4 region of the env gene was amplified, cloned and sequenced to verify the presence of a HIV-1 dual infection. Dual infections were counted for each year investigated. Results: No significant change in incidence of dual infections was seen in our patient population selected upon the degenerate base count in the HIV-1 genotyping sequence from 2003 till 2007. The frequency of HIV-1 dual infections varied between 1.0%–2.8%/year, with no significant trend in time (p = 0.49). Based upon the number of patients with a high degenerate base code count, an increase in dual infections was expected in 2006 and 2007, but this was not observed. HIV-1 dual infections were similar to HIV-1 single infections in The Netherlands in distribution by risk group, gender and subtype. Conclusion: HIV-1 dual infections in The Netherlands are not increasing from 2003 to 2007 although the HIV-1 infected population is expanding in this period.

Routine HIV-1 genotyping as a tool to identify dual infections

The incidence of HIV-1 dual infections is generally thought to be low, but as dual infections have been associated with accelerated disease progression, its recognition is clinically important. Methods to identify HIV-1 dual infections are time consuming and are not routinely performed. Genotyping of the HIV-1 protease and reverse transcriptase (prot/RT) genes is commonly performed in the western world to detect drug-resistance mutations in clinical isolates. In our hospital, prot/RT baseline sequencing is part of the patient care for all newly infected patients in the Amsterdam region since 2003. We reasoned that degenerate base codes in this sequence could indicate either extensive viral evolution or infection with multiple HIV-1 strains. We amplified, cloned and sequenced multiple HIV-1 envelope (env)-V3 and gag sequences from patients with 34 or more (range 34-99) degenerate base codes in the ViroSeq genotyping RT sequence (37 out of 1661 available records) to estimate the number of HIV-1 dual infections in this group. Of the 37 patients included in this study, 16 (43.2%, equal to 1% of the 1661 total records) had an HIV-1 dual infection based on phylogenetic analysis of env-V3/gag sequences. If only sequences with 45 or more degenerate base codes were taken into account, 73.3% of patients showed evidence of a dual infection. We describe an additional use of routinely performed HIV-1 genotyping. In patients with a high number of degenerate bases (> or = 34) in RT it is important to consider the possibility of a dual HIV-1 infection.

HIV-1 diversity and prevalence differ between urban and rural areas in the Mbeya region of Tanzania

To characterize HIV-1 strains in a potential vaccine trial cohort (CODE) in the Mbeya region of southwest Tanzania. Study volunteers (n = 3096) were recruited from urban areas in Mbeya Town, using two different recruitment strategies, and in a nearby rural village. Cryopreserved plasma from 507 HIV-1 prevalent cases was the source of viral RNA for HIV-1 genotyping by the Multi-region Hybridization Assay, the MHA(acd), and selected strains were confirmed by complete genome sequencing. The overall HIV-1 prevalence was 16.6% [95% confidence interval (CI), 15.3-17.9] within the cohort. HIV-1 prevalence was higher among women, and in urban areas. Recruitment through advertisement targeted a high-risk urban male population for HIV-1 infection [adjusted odds ratio (adj. OR), 1.68; 95% CI, 1.13-2.51] when compared with men recruited door-to-door. The complexity of the HIV-1 epidemic was also higher in urban areas evidenced by the high-risk of HIV-1 infection with a recombinant strain (adj. OR, 2.69; 95% CI, 1.08-6.69) and HIV-1 dual infection (adj. OR, 5.16; 95% CI, 1.07-24.9), mainly driven by urban men recruited through advertisement. Overall the urban epidemic was more genetically complex, with higher prevalence and more recombinants and dual infections. Vaccine trials in Mbeya region can assess a complex HIV-1 population dynamic and determine vaccine efficacy in relationship to the genetic diversity of HIV-1 strains that challenge vaccines.

High concordance between polymerase chain reaction and antibody testing of specimens from individuals dually infected with HIV types 1 and 2 in Guinea-Bissau, West Africa.

In this study we have evaluated the concordance between serology, using five commercially available antibody assays designed to discriminate between HIV-1 and HIV-2, and the polymerase chain reaction (PCR) for the detection of HIV-1 and HIV-2 dual infection. Thirty-seven HIV-1 and HIV-2 dually reactive serum samples from individuals in Guinea-Bissau with total CD4+ T lymphocyte counts ranging from 9 to 948 x 10(6)/liter were included in the study. All samples were tested by Multispot, Pepti-LAV, and Immunocomb HIV-1 and HIV-2 discriminatory antibody assays. Thirty-two of the 37 samples were also tested by a combination of two HIV type-specific antibody enzyme-linked immunosorbent assays (ELISA; Wellcozyme HIV-1 and Murex HIV-2). Each sample showed dual reactivity in all or any of these assays. A nested PCR based on primer systems in the vif and pol regions of HIV-1 and in the gag and LTR regions of HIV-2 was used to evaluate the serological results. Thirty samples from HIV-1 antibody-positive individuals and 30 samples from HIV-2 antibody-positive individuals were all PCR positive with their corresponding primer systems. The type specificity was 100% for all of the primer systems. The concordance between dual HIV-1 and HIV-2 reactivity on the serological assays and PCR was 77.7% for Multispot, 80% for Pepti-LAV, 81.8% for Immunocomb, and 85.7% for the two ELISAs used in combination. Thus the majority of individuals included in this study appeared to be truly dually infected. The study shows that it is possible, through a careful selection of assays, to reach a high concordance between serological assays and PCR in studying HIV-1 and HIV-2 dual infections.

HIV-1 and HIV-2 dual infection: lack of HIV-2 provirus correlates with low CD4+ lymphocyte counts.

We conducted this study to genetically characterize dual infection in individuals demonstrating a dual serological profile. All subjects were first evaluated by immunoblot for antibody reactivity to the major viral antigens for HIV-1 and HIV-2. Sera were judged to be dual-seropositive if they reacted with strong and equal intensity with the envelope antigens of both HIV-1 and HIV-2 and were confirmed with type-specific recombinant env peptides. We used nested polymerase chain reaction (PCR) to amplify proviral gag and env sequence from peripheral blood mononuclear cell (PBMC) DNA from HIV-1- and HIV-2-infected individuals. Positive amplification was detected after Southern blot hybridization. Plasmid dilution and mixing showed equivalent sensitivity of HIV-1 and HIV-2 primers that was not altered by heterologous target sequences. The DNA PCR showed 100% sensitivity and specificity for detection of monotypic HIV infection. Serologically defined HIV-dual reactives were evaluated by this assay, with 100% detection in female sex workers (21 out of 21), but only 38.5% detection (five out of 13) in hospitalized patients; all being HIV-1 positive only. The lack of HIV-2 proviral signal was significantly correlated with low CD4+ lymphocyte counts (Pvalue = 0.04). The results suggest that HIV dual infection may not be a static condition. Levels of HIV-2 may decrease with disease progression or sequester in tissue reservoirs; our results may also suggest that HIV-1 effectively overgrows HIV-2 in the dually exposed host individual.