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1.
PLoS One ; 16(1): e0245085, 2021.
Artículo en Inglés | MEDLINE | ID: mdl-33444325

RESUMEN

INTRODUCTION: Maintaining virologic suppression of children and adolescents on ART in rural communities in sub-Saharan Africa is challenging. We explored switching drug regimens to protease inhibitor (PI) based treatment and reducing nevirapine and zidovudine use in a differentiated community service delivery model in rural Zimbabwe. METHODS: From 2016 through 2018, we followed 306 children and adolescents on ART in Hurungwe, Zimbabwe at Chidamoyo Christian Hospital, which provides compact ART regimens at 8 dispersed rural community outreach sites. Viral load testing was performed (2016) by Roche and at follow-up (2018) by a point of care viral load assay. Virologic failure was defined as viral load ≥1,000 copies/ml. A logistic regression model which included demographics, treatment regimens and caregiver's characteristics was used to assess risks for virologic failure and loss to follow-up (LTFU). RESULTS: At baseline in 2016, 296 of 306 children and adolescents (97%) were on first-line ART, and only 10 were receiving a PI-based regimen. The median age was 12 years (IQR 8-15) and 55% were female. Two hundred and nine (68%) had viral load suppression (<1,000 copies/ml) and 97(32%) were unsuppressed (viral load ≥1000). At follow-up in 2018, 42/306 (14%) were either transferred 23 (7%) or LTFU 17 (6%) and 2 had died. In 2018, of the 264 retained in care, 107/264 (41%), had been switched to second-line, ritonavir-boosted PI with abacavir as a new nucleotide analog reverse transcriptase inhibitor (NRTI). Overall viral load suppression increased from 68% in 2016 to 81% in 2018 (P<0.001). CONCLUSION: Viral load testing, and switching to second-line, ritonavir-boosted PI with abacavir significantly increased virologic suppression among HIV-infected children and adolescents in rural Zimbabwe.

2.
Artículo en Inglés | MEDLINE | ID: mdl-33430681

RESUMEN

Pretreatment drug resistance (PDR) can compromise antiretroviral therapy (ART) efficacy and undermine the WHO targets to end the AIDS epidemic as a public health threat by 2030. Thus, we examined the level of PDR in Harare, Zimbabwe. Eligible study participants were adults who were ART naive or individuals with previous ART exposure reinitiating treatment, recruited between October 2018 and February 2020 in a HIV ART treatment clinic, in Harare. HIV drug resistance tests were performed for all specimens with viral load ≥400 copies/mL and interpreted using the Stanford HIVDB Algorithm. Chi-square test or Fisher's exact test was used for comparison of proportions of PDR across ART-naive or prior ART-exposed participants. All statistical analyses were performed using Stata version 14. Overall, 120 samples were genotyped of whom 104 were ART naive and 16 reported previous ART exposure. The overall PDR frequency among all participants was 31% [95% confidence interval (CI): 22.5-39.6]. PDR to any non-nucleotide reverse transcriptase inhibitor (NNRTI) was reported in 29% (95% CI: 21.0-37.9). PDR to nucleotide reverse transcriptase inhibitors (NRTIs) and protease inhibitors were low, found in 3% (95% CI: 0.9-8.2) and 1% (95% CI: 0.02-4.52), respectively. PDR to NNRTIs [efavirenz/nevirapine (EFV/NVP)] was found in 17% (95% CI: 10.5-24.6) and was more than six times higher among people with previous ART exposure than ART-naive people: 63% versus 10%, p < .001. Our study shows that PDR to NNRTIs in Zimbabwe has remarkably increased from the 10.9% prevalence reported in the 2016 WHO survey. Addressing PDR at a national level is a critical need and will be facilitated by fast-tracking the transition to dolutegravir in first-line ART regimens.

3.
JCO Glob Oncol ; 6: 1276-1281, 2020 08.
Artículo en Inglés | MEDLINE | ID: mdl-32783640

RESUMEN

PURPOSE: High-risk human papillomaviruses (hrHPV) are the primary cause of cervical cancer. Human papillomavirus (HPV) vaccination is expected to prevent cervical cancers caused by the HPV types included in vaccines and possibly by cross-protection from other types. This study sought to determine the hrHPV type distribution in women at a rural Zimbabwe hospital. METHODS: We implemented a cross-sectional study at the Karanda Mission Hospital. Using the Visual Inspection with Acetic Acid Cervicography technique, clinicians collected cervical swabs from 400 women presenting for screening for cervical cancer. Samples were initially analyzed by Cepheid GeneXpert; candidate hrHPV genotypes were further characterized using the Anyplex II HPV28 Detection Kit. RESULTS: Twenty-one percent of the 400 women were positive for a high-risk genotype when using the GeneXpert analyzer; 17% were positive when using the multiplex analysis. Almost two thirds of the hrHPV women had a single DNA type identified, whereas one third had multiple genotypes, ranging from 2 to 5. hrHPV was observed more frequently in HIV-positive than in HIV-negative women (27% v 15%). Of the 113 isolates obtained, 77% were hrHPV genotypes not included in the bivalent or quadrivalent vaccines, and 47% represented DNA types not covered in the nonavalent vaccine. Forty-seven percent of the women with hrHPV harbored a single genotype that was not covered by the nonavalent vaccine. CONCLUSION: A large fraction of hrHPV isolates from women participating in a cervical cancer screening program in northern Zimbabwe are DNA types not covered by the bivalent, quadrivalent, or nonavalent vaccines. These findings suggest the importance of characterizing the hrHPV DNA types isolated from cervical neoplasia in this population and determining whether cross-immunization against these genotypes develops after administration of the vaccines in current use.

4.
mSphere ; 5(4)2020 07 29.
Artículo en Inglés | MEDLINE | ID: mdl-32727861

RESUMEN

Coronavirus disease 2019 (COVID-19) has wreaked havoc across the globe; although the number of cases in Africa remains lower than in other regions, it is on a gradual upward trajectory. To date, COVID-19 cases have been reported in 54 out of 55 African countries. However, due to limited severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) real-time reverse transcription-PCR (rRT-PCR) testing capacity and scarcity of testing reagents, it is probable that the total number of cases could far exceed published statistics. In this viewpoint, using Ghana, Malawi, South Africa, and Zimbabwe as examples of countries that have implemented different testing strategies, we argue that the implementation of sample pooling for rRT-PCR over antibody rapid diagnostic testing could have a greater impact in assessing disease burden. Sample pooling offers huge advantages compared to single test rRT-PCR, as it reduces diagnostic costs, personnel time, burnout, and analytical run times. Africa is already strained in terms of testing resources for COVID-19; hence, cheaper alternative ways need to be implemented to conserve resources, maximize mass testing, and reduce transmission in the wider population.


Asunto(s)
Técnicas de Laboratorio Clínico/métodos , Infecciones por Coronavirus/diagnóstico , Inmunoensayo/métodos , Neumonía Viral/diagnóstico , Reacción en Cadena en Tiempo Real de la Polimerasa/métodos , Reacción en Cadena de la Polimerasa de Transcriptasa Inversa/métodos , Pruebas Serológicas/métodos , África , Países en Desarrollo , Costos de la Atención en Salud , Humanos , Pandemias , Manejo de Especímenes/métodos , Factores de Tiempo
5.
J Clin Microbiol ; 58(9)2020 Aug 24.
Artículo en Inglés | MEDLINE | ID: mdl-32522826

RESUMEN

HIV drug resistance (HIVDR) is a barrier to sustained virologic suppression in low- and middle-income countries (LMICs). Point mutation assays targeting priority drug resistance mutations (DRMs) are being evaluated to improve access to HIVDR testing. In a cross-sectional study (June 2018 to September 2019), we evaluated the diagnostic accuracy of a simple and rapid HIVDR assay (the pan-degenerate amplification and adaptation [PANDAA] assay targeting the mutations K65R, K103NS, M184VI, Y181C, and G190A) compared to Sanger sequencing and next-generation sequencing (NGS). Plasma samples from adolescents and young adults (aged 10 to 24 years) failing antiretroviral therapy (viral load, >1,000 copies/ml on 2 consecutive occasions 1 month apart) were analyzed. Sensitivity and specificity of the PANDAA assay were determined by a proprietary application designed by Aldatu Biosciences. Agreement between genotyping methods was evaluated using Cohen's kappa coefficient. One hundred fifty samples previously characterized by Sanger sequencing were evaluated using PANDAA. For all DRMs detected, PANDAA showed a sensitivity and specificity of 98% and 94%, respectively. For nucleotide reverse transcriptase inhibitor DRMs, sensitivity and specificity were 98% (95% confidence interval [CI], 92% to 100%) and 100% (94% to 100%), respectively. For non-nucleotide reverse transcriptase inhibitor DRMs, sensitivity and specificity were 100% (97% to 100%) and 76% (61% to 87%), respectively. PANDAA showed strong agreement with Sanger sequencing for K65R, K103NS, M184VI, and G190A (kappa > 0.85) and substantial agreement for Y181C (kappa = 0.720). Of the 21 false-positive samples genotyped by PANDAA, only 6 (29%) were identified as low-abundance variants by NGS. With the high sensitivity and specificity to detect major DRMs, PANDAA could represent a simple and rapid alternative HIVDR assay in LMICs.

6.
Mol Biol Rep ; 47(7): 4975-4987, 2020 Jul.
Artículo en Inglés | MEDLINE | ID: mdl-32533403

RESUMEN

The fresh water snail Biomphalaria pfeifferi is the intermediate host for Schistosoma mansoni, which causes human intestinal schistosomiasis in Zimbabwe. Despite the medical importance of this intermediate host, there are no current data on its molecular characterization in Zimbabwe. In 2016, human water contact sites were identified in four communities in Madziwa area, Shamva district, Zimbabwe. The survey sites were recorded and mapped using a global positioning system. A 655 bp region of the mitochondrial cytochrome oxidase subunit I gene was amplified in 70 B. pfeifferi snails. The sequence data were analysed to determine the relationships between the individual snails, their inter, intra population diversity and structure. Overall, four unique cox1 haplotypes, with a haplotype diversity of 0.608, were identified in the snails. One haplotype spanned across most of the sites. There was no clear geographical clustering of haplotypes. The mean diversity among the haplotypes was very low (0.009), while the net divergence among the collection sites ranged from 0.000 to 0.026. The diversity within and between the sites was 0.017 and 0.012 respectively. This data advances our knowledge of the understanding of the population structure of B. pfeifferi in Madziwa area, Zimbabwe, with the high occurrence of one haplotype indicating the possibility of a recent bottleneck followed by population expansion. The population genetic structure of B. pfeifferi snails described here has provided an opportunity to investigate the contribution of snail genetics to variation in disease burden; and development of control strategies that exploit genetic differences in susceptibility to parasites.

7.
AIDS Res Hum Retroviruses ; 36(7): 566-573, 2020 07.
Artículo en Inglés | MEDLINE | ID: mdl-32138527

RESUMEN

Barriers to sustainable virologic suppression (VS) of HIV-infected adolescents and young adults include drug resistance mutations (DRMs) and limited treatment options, which may impact the outcome of second-line antiretroviral therapy (ART). We sequenced plasma viral RNA from 74 adolescents and young adults (16-24 years) failing first-line ART at Newlands Clinic, Zimbabwe between October 2015 and December 2016. We evaluated first-line nucleoside reverse transcriptase inhibitor (NRTI) susceptibility scores to first- and second-line regimens. Boosted protease inhibitor (bPI)-based ART was provided and viral load (VL) monitored for ≥48 weeks. Fisher's exact test was used to evaluate factors associated with VS on second-line regimens, defined as VL <1,000 copies/mL (VS1,000) or <50 copies/mL (VS50). The 74 participants on first-line ART had a median [interquartile range (IQR)] age of 18 (16-21) years and 42 (57%) were female. The mean (±standard deviation) duration on ART was 5.5 (±3.06) years and the median (IQR) log10 VL was 4.26 (3.78-4.83) copies/mL. After switching to a second-line PI regimen, 88% suppressed to <1,000 copies/mL and 76% to <50 copies/mL at ≥48 weeks. A new NRTI was associated with increased VS50 (p = .031). These 74 adolescents and young adults failing first-line ART demonstrated high levels (97%) of DRMs, despite enhanced adherence counseling. Switching to new NRTIs in second-line improved VS. With the widespread adoption of generic dolutegravir, lamivudine and tenofovir combinations in Africa, genotyping to determine NRTI susceptibility, may be warranted.

8.
Parasit Vectors ; 13(1): 14, 2020 Jan 10.
Artículo en Inglés | MEDLINE | ID: mdl-31924254

RESUMEN

BACKGROUND: Bulinus species are freshwater snails that transmit the parasitic trematode Schistosoma haematobium. Despite their importance, the diversity of these intermediate host snails and their evolutionary history is still unclear in Zimbabwe. Bulinus globosus and B. truncatus collected from a urogenital schistosomiasis endemic region in the Madziwa area of Zimbabwe were characterized using molecular methods. METHODS: Malacological survey sites were mapped and snails were collected from water contact sites in four communities in the Madziwa area, Shamva district for a period of one year, at three-month intervals. Schistosoma haematobium infections in snails were determined by cercarial shedding and the partial mitochondrial cytochrome c oxidase subunit 1 gene (cox1) was used to investigate the phylogeny and genetic variability of the Bulinus spp. collected. RESULTS: Among the 1570 Bulinus spp. snails collected, 30 (1.9%) B. globosus were shedding morphologically identified schistosomes. None of the B. truncatus snails were shedding. The mitochondrial cox1 data from 166 and 16 samples for B. globosus and B. truncatus, respectively, showed genetically diverse populations within the two species. Twelve cox1 haplotypes were found from the 166 B. globosus samples and three from the 16 B. truncatus samples with phylogenetic analysis showing that the haplotypes fall into well-supported clusters within their species groups. Both B. truncatus and B. globosus clustered into two distinct lineages. Overall, significant negative values for both Tajima's D statistic and the Fu's Fs statistic were observed for B. globosus and B. truncatus. CONCLUSIONS: The study provided new insights into the levels of genetic diversity within B. globosus and additional information on B. truncatus collected from a small geographical area in Zimbabwe. Low prevalence levels of infection observed in the snails may reflect the low transmission level of urogenital schistosomiasis in the area. Our results contribute towards the understanding of the distribution and population genetic structure of Bulinus spp. supporting the mapping of the transmission or risk of transmission of urogenital schistosomiasis, particularly in Zimbabwe.


Asunto(s)
Bulinus/parasitología , Schistosoma haematobium/genética , Esquistosomiasis Urinaria/transmisión , Animales , Cercarias/aislamiento & purificación , Complejo IV de Transporte de Electrones/genética , Agua Dulce/parasitología , Variación Genética , Especificidad del Huésped , Filogenia , Prevalencia , Schistosoma haematobium/parasitología , Zimbabwe
9.
AIDS ; 33(11): 1729-1737, 2019 09 01.
Artículo en Inglés | MEDLINE | ID: mdl-31361272

RESUMEN

OBJECTIVES: The integrase strand inhibitor dolutegravir (DTG) combined with tenofovir and lamivudine (TLD) is a single tablet regimen recommended for 1st, 2nd and 3rd-line public health antiretroviral therapy (ART). We determined drug resistance mutations (DRMs) and evaluated the predictive efficacy of a TLD containing regimen for viremic adolescents and young adults in Harare, Zimbabwe. METHODS: We sequenced plasma viral RNA from HIV-1-infected adolescents and young adults on 1st and 2nd-line ART with confirmed virologic failure (viral load >1000 copies/ml) and calculated total genotypic susceptibility scores to current 2nd, 3rd line and DTG regimens. RESULTS: A total of 160 participants were genotyped; 112 (70%) on 1st line and 48 (30%) on 2nd line, median (interquartile range) age 18 (15-19) and duration of ART (interquartile range) was 6 (4-8) years. Major DRMs were present in 94 and 67% of 1st and 2nd-line failures, respectively (P < 0.001). Dual class resistance to nucleotide reverse transcriptase inhibitors and nonnucleotide reverse transcriptase inhibitors was detected in 96 (60%) of 1st-line failures; protease inhibitor DRMs were detected in a minority (10%) of 2nd-line failures. A total genotypic susceptibility score of 2 or less may risk protease inhibitor or DTG monotherapy in 11 and 42% of 1st-line failures switching to 2nd-line protease inhibitor and TLD respectively. CONCLUSION: Among adolescents and young adults, current protease inhibitor-based 2nd-line therapies are poorly tolerated, more expensive and adherence is poor. In 1st-line failure, implementation of TLD for many adolescents and young adults on long-term ART may require additional active drug(s). Drug resistance surveillance and susceptibility scores may inform strategies for the implementation of TLD.


Asunto(s)
Farmacorresistencia Viral/genética , Infecciones por VIH/tratamiento farmacológico , Inhibidores de Integrasa VIH/uso terapéutico , Compuestos Heterocíclicos con 3 Anillos/uso terapéutico , Adolescente , Estudios Transversales , Combinación de Medicamentos , Femenino , Genotipo , Infecciones por VIH/sangre , Inhibidores de la Proteasa del VIH , VIH-1/efectos de los fármacos , VIH-1/genética , Humanos , Lamivudine/uso terapéutico , Masculino , Cumplimiento de la Medicación , Oxazinas , Piperazinas , Piridonas , Tenofovir/uso terapéutico , Insuficiencia del Tratamiento , Carga Viral , Adulto Joven , Zimbabwe
10.
J Mol Diagn ; 21(4): 580-592, 2019 07.
Artículo en Inglés | MEDLINE | ID: mdl-31026601

RESUMEN

A point-of-care HIV-1 genotypic resistance assay that could be performed during a clinic visit would enable care providers to make informed treatment decisions for patients starting therapy or experiencing virologic failure on therapy. The main challenge for such an assay is the genetic variability at and surrounding each drug-resistance mutation (DRM). We analyzed a database of diverse global HIV sequences and used thermodynamic simulations to design an array of surface-bound oligonucleotide probe sets with each set sharing distinct 5' and 3' flanking sequences but having different centrally located nucleotides complementary to six codons at HIV-1 DRM reverse transcriptase position 103: AAA, AAC, AAG, AAT, AGA, and AGC. We then performed in vitro experiments using 80-mer oligonucleotides and PCR-amplified DNA from clinical plasma HIV-1 samples and culture supernatants that contained subtype A, B, C, D, CRF01_AE, and CRF02_AG viruses. Multiplexed solid-phase melt curve analysis discriminated perfectly among each of the six reported reverse transcriptase position 103 codons in both 80-mers and clinical samples. The sensitivity and specificity for detecting targets that contained AAC mixed with targets that contained AAA were >98% when AAC was present at a proportion of ≥10%. Multiplexed solid-phase melt curve analysis is a promising approach for developing point-of-care assays to distinguish between different codons in genetically variable regions such as those surrounding HIV-1 DRMs.


Asunto(s)
Farmacorresistencia Viral , Infecciones por VIH/virología , VIH-1/efectos de los fármacos , VIH-1/genética , Pruebas en el Punto de Atención , Bases de Datos Genéticas , Genotipo , Infecciones por VIH/diagnóstico , Infecciones por VIH/tratamiento farmacológico , Humanos , Mutación , ARN Viral
11.
Open Forum Infect Dis ; 6(3): ofz034, 2019 Mar.
Artículo en Inglés | MEDLINE | ID: mdl-30863788

RESUMEN

Background: Efavirenz (EFV)-based regimens select broad drug resistance to nonnucleoside reverse-transcriptase inhibitors (NNRTIs), limiting the effectiveness of EFV and other NNRTIs. The duration, persistence, and decay of drug resistance mutations (DRMs) in the proviral reservoir is not well defined. Methods: Participants with virologic failure of EFV-based regimens and drug-resistant viremia with the K103N mutation in plasma ribonucleic acid (RNA) were identified from AIDS Clinical Trials Group (ACTG) studies A364 and A5095. These individuals received a second-line, boosted protease inhibitor-based regimen with suppression of viremia for up to10 years during long-term follow-up (median = 3.6 years; interquartile range, 2.1-6.9 years). Proviral deoxyribonucleic acid (DNA) from cryopreserved peripheral blood mononuclear cells was sequenced to identify the persistence of DRM. Results: Twenty-eight participants from ACTG 364 and ACTG 5095 were evaluated. Sanger sequencing of proviral DNA detected K103N as well as additional reverse-transcriptase inhibitor (RTI) mutations. Ultradeep sequencing confirmed persistence of K103N in 71% of participants with minimal decay over time. In an adjusted model including years since suppression, persistent proviral K103N was 2.6 times more likely (95% confidence interval, 1.0-6.4) per log10 higher human immunodeficiency virus RNA at EFV failure. Conclusions: Persistence of RTI mutations in proviral DNA after virologic failure has implications for the effectiveness of future drug regimens and the recycling of RTI drugs.

12.
Int J Infect Dis ; 82: 21-29, 2019 May.
Artículo en Inglés | MEDLINE | ID: mdl-30807869

RESUMEN

OBJECTIVES: High-risk human papilloma viruses (hrHPV) are the causative agents of cervical cancer, the leading cause of cancer deaths among Zimbabwean women. The objective of this study was to describe the hrHPV types found in Zimbabwe for consideration in cervical cancer screening and vaccination efforts. DESIGN AND METHODS: To determine hrHPV prevalence and type distribution in Zimbabwe we implemented a community-based cross-sectional study of self-collected cervicovaginal samples with hrHPV screening using near-point-of-care Cepheid GeneXpert HPV. RESULTS: The hrHPV prevalence was 17% (112/643); 33% (41/123) vs. 14% (71/520) among HIV-1-positive and -negative participants, respectively (p=2.3E-07). Typing via Xpert HPV showed very good overall agreement (77.2%, kappa=0.698) with the Seegene Anyplex II HPV HR Detection kit. The most common types were HPV16, HPV18, HPV35, HPV52, HPV58, HPV68, HPV18, and HPV51, each of which appeared in 14-20% of infections. 37% (28/76) of women with positive cytology results (ASCUS+) had a type not included in the basic vaccine and 25% (19/76) had a type not currently in the nine-valent vaccine. CONCLUSIONS: hrHPV type distribution includes less common high-risk types in rural Zimbabwe. The distribution and carcinogenicity of hrHPV type distribution should be considered during screening assay design, program development, as well as vaccine distribution and design.


Asunto(s)
Papillomaviridae/inmunología , Infecciones por Papillomavirus/epidemiología , Sistemas de Atención de Punto , Neoplasias del Cuello Uterino/epidemiología , Vacunación , Adulto , Anciano , Estudios Transversales , Detección Precoz del Cáncer , Femenino , Humanos , Tamizaje Masivo , Persona de Mediana Edad , Papillomaviridae/clasificación , Infecciones por Papillomavirus/prevención & control , Infecciones por Papillomavirus/virología , Prevalencia , Manejo de Especímenes , Neoplasias del Cuello Uterino/prevención & control , Neoplasias del Cuello Uterino/virología , Zimbabwe/epidemiología
13.
J Public Health Afr ; 10(2): 1081, 2019 Dec 31.
Artículo en Inglés | MEDLINE | ID: mdl-32257079

RESUMEN

Low-and-middle-income countries (LMICs) have high disease burdens, necessitating increased research. However, LMIC research output constitutes only 2% of global total. To increase output, researchers must be capacitated. The University of Zimbabwe (UZ) and the University at Buffalo (UB), developed and implemented the AIDS International Research Training Program (AITRP), in 2008, that focused on graduate scholars. The subsequent HIV Research Training Program (HRTP), begun in 2016, and piloted post-doctoral training to enhance research productivity at UZ. This report discusses the collaboration. As of 2016, prospective candidates applied by submitting letters of intent, research proposals, curriculum vitae and biographical sketches. The scholars research training included hypothesis and project development, completion of grant applications, research project budgets, research presentations to diverse audiences and the application of advanced statistics to research data. The first cohort of five postdoctoral scholars were trained at UZ and UB, between 2016 and 2019. Through the formalized postdoctoral training approach, scholars identified areas of focus. In 2017, one of the scholars obtained a National Institutes of Health (NIH) Emerging Global Leader Award and is now a highly-rated researcher based in South Africa. A second scholar made NIH D43 and K43 grant applications, while the remaining three are academicians and early researchers at UZ. Although research output in Africa and many LMICs is low, it can be built through cooperation similar to the UZ-UB HRTP. This manuscript reports on an effort aimed at building individual and institutional research capacity in Zimbabwe. This can serve as a model for building other similar training programs.

14.
AIDS Res Hum Retroviruses ; 35(2): 129-138, 2019 02.
Artículo en Inglés | MEDLINE | ID: mdl-30430843

RESUMEN

There is evidence of increasing levels of pretreatment HIV drug resistance (PDR) in Southern Africa. We used data from two large population-based HIV surveillance studies to estimate prevalence of PDR in KwaZulu-Natal, the province with the highest HIV prevalence in South Africa. Sanger sequencing was performed on samples obtained from a longitudinal HIV surveillance program (study A, 2013-2014) and the HIV Incidence Provincial Surveillance System (study B, 2014-2015). Sequences were included for adult HIV positive participants (age ≥15 years for study A, age 15-49 years for study B) with no documented prior exposure to antiretroviral therapy (ART). Overall and drug class-specific PDR was estimated using the World Health Organization 2009 surveillance drug resistance mutation (SDRM) list, and phylogenetic analysis was performed to establish evidence of drug resistance transmission linkage. A total of 1,845 sequences were analyzed (611 study A; 1,234 study B). An overall PDR prevalence of 9.2% [95% confidence interval (CI) 7.0-11.7] was observed for study A and 11.0% (95% CI 8.9-13.2) for study B. In study B, the prevalence of non-nucleoside reverse-transcriptase inhibitor (NNRTI) PDR exceeded 10% for sequences collected in 2014 (10.2%, 95% CI 7.5-12.9). The most prevalent SDRMs were K103NS (7.5%), M184VI (2.4%), and V106AM (1.4%). There was no evidence of large transmission chains of drug-resistant virus. High level NNRTI PDR (>10%) suggests a need to modify the standard first-line ART regimen and to focus attention on improving the quality of HIV prevention, treatment, and care.


Asunto(s)
Farmacorresistencia Viral , Infecciones por VIH/epidemiología , Infecciones por VIH/virología , VIH-1/genética , Mutación , Adolescente , Adulto , Monitoreo Epidemiológico , Femenino , Genotipo , Infecciones por VIH/transmisión , Proteasa del VIH/genética , Transcriptasa Inversa del VIH/genética , VIH-1/efectos de los fármacos , Humanos , Estudios Longitudinales , Masculino , Persona de Mediana Edad , Prevalencia , ARN Viral/genética , Sudáfrica/epidemiología , Adulto Joven
16.
Sci Data ; 5: 180147, 2018 07 24.
Artículo en Inglés | MEDLINE | ID: mdl-30040081

RESUMEN

Most HIV-1-infected individuals with virological failure on a pharmacologically-boosted protease inhibitor (PI) regimen do not develop PI-resistance protease mutations. One proposed explanation is that HIV-1 gag or gp41 cytoplasmic domain mutations might also reduce PI susceptibility. In a recent study of paired gag and gp41 sequences from individuals with virological failure on a PI regimen, we did not identify PI-selected mutations and concluded that if such mutations existed, larger numbers of paired sequences from multiple studies would be needed for their identification. In this study, we generated site-specific amino acid profiles using gag and gp41 published sequences from 5,338 and 4,242 ART-naïve individuals, respectively, to assist researchers identify unusual mutations arising during therapy and to provide scripts for performing established and novel maximal likelihood estimates of dN/dS substitution rates in paired sequences. The pipelines used to generate the curated sequences, amino acid profiles, and dN/dS analyses will facilitate the application of consistent methods to paired gag and gp41 sequence datasets and expedite the identification of potential sites under PI-selection pressure.


Asunto(s)
Fármacos Anti-VIH/uso terapéutico , Proteína gp41 de Envoltorio del VIH/genética , Infecciones por VIH/terapia , Infecciones por VIH/virología , VIH-1/genética , Productos del Gen gag del Virus de la Inmunodeficiencia Humana/genética , VIH-1/efectos de los fármacos , Humanos , Mutación , Análisis de Secuencia de Proteína , Análisis de Secuencia de ARN
17.
Sci Rep ; 7(1): 11559, 2017 09 14.
Artículo en Inglés | MEDLINE | ID: mdl-28912582

RESUMEN

Several groups have proposed that genotypic determinants in gag and the gp41 cytoplasmic domain (gp41-CD) reduce protease inhibitor (PI) susceptibility without PI-resistance mutations in protease. However, no gag and gp41-CD mutations definitively responsible for reduced PI susceptibility have been identified in individuals with virological failure (VF) while receiving a boosted PI (PI/r)-containing regimen. To identify gag and gp41 mutations under selective PI pressure, we sequenced gag and/or gp41 in 61 individuals with VF on a PI/r (n = 40) or NNRTI (n = 20) containing regimen. We quantified nonsynonymous and synonymous changes in both genes and identified sites exhibiting signal for directional or diversifying selection. We also used published gag and gp41 polymorphism data to highlight mutations displaying a high selection index, defined as changing from a conserved to an uncommon amino acid. Many amino acid mutations developed in gag and in gp41-CD in both the PI- and NNRTI-treated groups. However, in neither gene, were there discernable differences between the two groups in overall numbers of mutations, mutations displaying evidence of diversifying or directional selection, or mutations with a high selection index. If gag and/or gp41 encode PI-resistance mutations, they may not be confined to consistent mutations at a few sites.


Asunto(s)
Evolución Molecular , Proteína gp41 de Envoltorio del VIH/genética , Infecciones por VIH/tratamiento farmacológico , Inhibidores de la Proteasa del VIH/uso terapéutico , VIH-1/aislamiento & purificación , Ritonavir/uso terapéutico , Productos del Gen gag del Virus de la Inmunodeficiencia Humana/genética , Adulto , Femenino , Genotipo , Infecciones por VIH/virología , VIH-1/genética , Humanos , Masculino , Persona de Mediana Edad , Mutación , Selección Genética , Análisis de Secuencia de ADN , Adulto Joven
18.
AIDS Res Hum Retroviruses ; 33(12): 1185-1191, 2017 12.
Artículo en Inglés | MEDLINE | ID: mdl-28899102

RESUMEN

Treatment of HIV has reduced HIV/AIDS-related mortality. Sustaining >90% virologic suppression in sub-Saharan Africa requires decentralized care and prevention services to rural communities. In Zimbabwe, the number of people receiving antiretroviral treatment (ART) has increased rapidly. However, access to treatment monitoring tools such as viral load and drug resistance testing is limited. We assessed virologic treatment outcomes among ART recipients in Nyamutora, a rural community receiving bimonthly ART and prevention services. We enrolled all ART recipients (143) at 6-monthly visits in the Nyamutora community in 2014 and 2015. Whole blood samples were collected in K-EDTA tubes, transported to Harare for CD4 counts and viral load testing, and genotype was obtained in participants with viral loads >1,000 copies/ml. Ages ranged from 2 to 75 years (median 43 years) with a median 42 months on ART at follow-up. Eight of 143 (6%) had viral loads >1,000 copies/ml at one of the 3 visits, 7 on first-line nevirapine (NVP)-based ART and 1 on second-line LPV/r-based ART. Seven participants had sequence data available, and five had drug resistance mutations, K65R, T69N, K101E, K103N, Y181C/I, M184V, and G190A. Virologic failure (p = .001) and drug resistance mutations (p = .01) on first-line NVP-based ART were associated with younger age by univariate exact logistic regression. The participants had high viral suppression (94%) despite less than optimal (NVP based) ART regimens without laboratory monitoring. Virologic failure and drug resistance were higher among children and adolescents. Effective ART delivery to the community achieved high rates of virologic suppression and minimal drug resistance.


Asunto(s)
Síndrome de Inmunodeficiencia Adquirida/tratamiento farmacológico , Fármacos Anti-VIH/uso terapéutico , Terapia Antirretroviral Altamente Activa , Centros Comunitarios de Salud , Síndrome de Inmunodeficiencia Adquirida/mortalidad , Síndrome de Inmunodeficiencia Adquirida/virología , Adolescente , Adulto , Anciano , Recuento de Linfocito CD4 , Niño , Preescolar , Estudios Transversales , Didanosina/uso terapéutico , Didesoxinucleósidos/uso terapéutico , Farmacorresistencia Viral/fisiología , Femenino , VIH-1/efectos de los fármacos , VIH-1/genética , Humanos , Lopinavir/uso terapéutico , Masculino , Persona de Mediana Edad , Nevirapina/uso terapéutico , Ritonavir/uso terapéutico , Población Rural , Insuficiencia del Tratamiento , Carga Viral , Adulto Joven , Zimbabwe
19.
AIDS Res Hum Retroviruses ; 33(11): 1083-1098, 2017 11.
Artículo en Inglés | MEDLINE | ID: mdl-28540766

RESUMEN

To characterize HIV-1 transmission dynamics in regions where the burden of HIV-1 is greatest, the 'Phylogenetics and Networks for Generalised HIV Epidemics in Africa' consortium (PANGEA-HIV) is sequencing full-genome viral isolates from across sub-Saharan Africa. We report the first 3,985 PANGEA-HIV consensus sequences from four cohort sites (Rakai Community Cohort Study, n=2,833; MRC/UVRI Uganda, n=701; Mochudi Prevention Project, n=359; Africa Health Research Institute Resistance Cohort, n=92). Next-generation sequencing success rates varied: more than 80% of the viral genome from the gag to the nef genes could be determined for all sequences from South Africa, 75% of sequences from Mochudi, 60% of sequences from MRC/UVRI Uganda, and 22% of sequences from Rakai. Partial sequencing failure was primarily associated with low viral load, increased for amplicons closer to the 3' end of the genome, was not associated with subtype diversity except HIV-1 subtype D, and remained significantly associated with sampling location after controlling for other factors. We assessed the impact of the missing data patterns in PANGEA-HIV sequences on phylogeny reconstruction in simulations. We found a threshold in terms of taxon sampling below which the patchy distribution of missing characters in next-generation sequences has an excess negative impact on the accuracy of HIV-1 phylogeny reconstruction, which is attributable to tree reconstruction artifacts that accumulate when branches in viral trees are long. The large number of PANGEA-HIV sequences provides unprecedented opportunities for evaluating HIV-1 transmission dynamics across sub-Saharan Africa and identifying prevention opportunities. Molecular epidemiological analyses of these data must proceed cautiously because sequence sampling remains below the identified threshold and a considerable negative impact of missing characters on phylogeny reconstruction is expected.

20.
J Virol Methods ; 243: 151-157, 2017 05.
Artículo en Inglés | MEDLINE | ID: mdl-27894862

RESUMEN

INTRODUCTION: HIV genotyping is often unavailable in low and middle-income countries due to infrastructure requirements and cost. We compared genotype resistance testing in patients with virologic failure, by amplification of HIV pol gene, followed by "in-house" sequencing and commercial sequencing. METHODS: Remnant plasma samples from adults and children failing second-line ART were amplified and sequenced using in-house and commercial di-deoxysequencing, and analyzed in Harare, Zimbabwe and at Stanford, U.S.A, respectively. HIV drug resistance mutations were determined using the Stanford HIV drug resistance database. RESULTS: Twenty-six of 28 samples were amplified and 25 were successfully genotyped. Comparison of average percent nucleotide and amino acid identities between 23 pairs sequenced in both laboratories were 99.51 (±0.56) and 99.11 (±0.95), respectively. All pairs clustered together in phylogenetic analysis. Sequencing analysis identified 6/23 pairs with mutation discordances resulting in differences in phenotype, but these did not impact future regimens. CONCLUSIONS: The results demonstrate our ability to produce good quality drug resistance data in-house. Despite discordant mutations in some sequence pairs, the phenotypic predictions were not clinically significant.


Asunto(s)
Antirretrovirales/uso terapéutico , Técnicas de Genotipaje/métodos , Infecciones por VIH/tratamiento farmacológico , Infecciones por VIH/virología , VIH/efectos de los fármacos , Análisis de Secuencia de ADN/métodos , Antirretrovirales/farmacología , Terapia Antirretroviral Altamente Activa , Farmacorresistencia Viral , VIH/genética , VIH/aislamiento & purificación , Humanos , Pruebas de Sensibilidad Microbiana/métodos , Insuficiencia del Tratamiento , Estados Unidos , Zimbabwe
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