Current and historic HIV-1 molecular epidemiology in paediatric and adult population from Kinshasa in the Democratic Republic of Congo

Rubio-Garrido, Marina; González-Alba, José Marı́a; Reina, Gabriel; Ndarabu, Adolphe; Barquín, David; Carlos, Silvia; Galán, Juan Carlos; Holguín, África

doi:10.1038/s41598-020-74558-z

Cited by 12 publications

(12 citation statements)

References 70 publications

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“…The majority of patients, enrolled in the study, were women (64%); mean age of participants was 41. 4 Diagnostic accuracy of the HIV serological screening assays and the total adjusted sensitivity and specificity of both immunoassays were close to 100%. However, specificity of Elecsys® HIV combi PT (Roche) was lower (98.9%) due to a false positive result.…”

Section: Resultsmentioning

confidence: 84%

“…The UNAIDS 95-95-95 targets to end the AIDS epidemic propose that 95% of all people living with HIV should know their HIV status by 2030, 95% of those diagnosed should receive antiretroviral therapy (ART), and 95% of them should be virally suppressed (1,2). Differences in treatment algorithms and prevention strategies between different SSA regions and risk groups lead to a variable global and regional HIV incidence and prevalence (3)(4)(5). Currently, 93% of people infected with HIV live in low-income countries (6,7), almost 70% in Sub-Saharan Africa (SSA).…”

Section: Introductionmentioning

confidence: 99%

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HIV-1 diagnosis using dried blood spots from patients in Kinshasa, DRC: a tool to detect misdiagnosis and achieve World Health Organization 2030 targets

Barquín

Ndarabu

Carlos

et al. 2021

International Journal of Infectious Diseases

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Section: Resultsmentioning

confidence: 84%

Section: Introductionmentioning

confidence: 99%

HIV-1 diagnosis using dried blood spots from patients in Kinshasa, DRC: a tool to detect misdiagnosis and achieve World Health Organization 2030 targets

Barquín

Ndarabu

Carlos

et al. 2021

International Journal of Infectious Diseases

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“…Previous studies have proposed re-classifying some of the defined HIV-1 subtypes and circulating recombinant forms. In some cases, this was motivated by the availability of new genomic data [59,60].…”

Section: Discussionmentioning

confidence: 99%

Revisiting the recombinant history of HIV-1 group M with dynamic network community detection

Olabode

Wade

et al. 2021

Preprint

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In previous work, we used a comprehensive sliding-window molecular clock analysis of near full length HIV-1 genomes to find that different regions of the virus genome yield significantly different estimates of the time to the most recent common ancestor. This finding, together with other evidence of the deep recombinant history of SIV and HIV, is not consistent with the standard model of the evolutionary history of HIV-1/M where non-recombinant subtypes are globally distributed through founder effects, followed by occasional inter-subtype recombination. We propose to re-examine the history of HIV-1/M using recombination detection methods that do not rely on predefined non-recombinant genomes. Here we describe an unsupervised non-parametric clustering approach to this problem by adapting a community detection method developed for the analysis of dynamic social networks. We compared our method to other reference-free recombination detection programs, namely GARD (HyPhy) and RDP (versions 4 and 5). We simulated recombination events by swapping randomly sampled branches in a time-scaled tree, which we reconstructed from subtype reference sequences in BEAST. Extant sequences were simulated for each tree using INDELible, and concatenated segments delimited by randomly sampled breakpoints from the resulting alignments to form the recombinant sequences. We show that our community detection method outperforms GARD, RDP4 and RDP5 in detecting recombinant breakpoints in simulated data, with a significantly lower mean error rate (Wilcoxon test, P < 0:05). Our method groups HIV-1 into 25 communities and detects evidence of inter-subtype recombination in pure subtype reference genomes obtained from Los Alamos HIV sequence database. For instance, we estimate that sub-subtypes A1 and A2 may contain large fragments from subtype C, while subtype C seems to contain fragments from subtype G. Our method provides a new reference-free framework for detecting recombination in viral genomes, and network communities may provide an alternative framework for HIV-1 classification.

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“…This study has several limitations. Firstly, plasma was only available in 42 of 143 subjects under study since we used retrospective and remaining samples from other studies in paediatric population in Kinshasa [20,[37][38][39]. Furthermore, data related to immunization status and number of received doses per participant was not reported in the clinical les, preventing distinguish the children and adolescents with protective IgG due to vaccination or due to infection.…”

Section: Discussionmentioning

confidence: 99%

Protection to Six Vaccinable Pathogens in Paired Plasma/DBS and HIV Impact in Infected and Uninfected Children From Kinshasa

Rodríguez-Galet

Rubio-Garrido

Ana

et al. 2021

Preprint

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Child vaccination reduces infant mortality rates. HIV-infected children present higher risk of diseases than non-infected. We report the protection coverage rates to 6 vaccine-preventable diseases in a paediatric population from the Democratic Republic of the Congo (DRC) and the impact of HIV infection, providing the first data on the validity of dried blood samples (DBS) to monitor the immune protection. During 2016-2018 DBS from 143 children/adolescents were collected in Kinshasa (DRC), being 52 HIV-infected. Forty-two had a paired plasma sample. Protective IgG was quantified (VirClia®IgG,Vircell) to obtain the optimal cut-off in IgG detection in DBS. ROC curves were generated with R software and statistical analyses with Stata. Protective IgG levels varied across pathogens, not reaching the herd immunity. HIV-infected presented lower vaccine protection than uninfected for all analysed pathogens, except rubella, with statistically significant differences for measles (30.8% vs. 53.8%;p=0.008) and tetanus (3.8% vs. 22%;p=0.004). New cut-offs were calculated when using DBS to improve test performance. We reinforce the necessity to increase pediatric vaccination coverage in Kinshasa, specially in HIV seropositive, with less capacity to maintain adequate antibody levels. DBS were useful to monitor vaccination coverage in seroprevalence studies in resource-limited settings, after optimizing the cut-off value for each pathogen.

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Current and historic HIV-1 molecular epidemiology in paediatric and adult population from Kinshasa in the Democratic Republic of Congo

Cited by 12 publications

References 70 publications

HIV-1 diagnosis using dried blood spots from patients in Kinshasa, DRC: a tool to detect misdiagnosis and achieve World Health Organization 2030 targets

HIV-1 diagnosis using dried blood spots from patients in Kinshasa, DRC: a tool to detect misdiagnosis and achieve World Health Organization 2030 targets

Revisiting the recombinant history of HIV-1 group M with dynamic network community detection

Protection to Six Vaccinable Pathogens in Paired Plasma/DBS and HIV Impact in Infected and Uninfected Children From Kinshasa

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