Resistance is common in paediatric patients failing ART in South Africa.

BACKGROUND: Minimal data exist on HIV drug resistance patterns and prevalence among paediatric patients failing ART in resource-limited settings. We assessed levels of HIV drug resistance in children with virological failure. METHODS: This cross-sectional study, performed from March 2017 to March 2019 in South Africa, enrolled HIV-positive children aged ≤19 years, receiving ART through public health facilities with recent evidence suggestive of virological failure (at least one viral load ≥1000 copies/mL), across 45 randomly selected high-volume clinics from all nine provinces. Resistance genotyping was performed using next-generation sequencing technologies. Descriptive analysis taking into account survey design was used to determine outcomes. RESULTS: Among 899 participants enrolled, the adjusted proportion of HIV drug resistance among children with virological failure was 87.5% (95% CI 83.0%-90.9%). Resistance to NNRTIs was detected in 77.4% (95% CI 72.5%-81.7%) of participants, and resistance to NRTIs in 69.5% (95% CI 62.9%-75.4%) of participants. Overall, resistance to PIs was detected in 7.7% (95% CI 4.4%-13.0%) of children. CONCLUSIONS: HIV drug resistance was highly prevalent in paediatric patients failing ART in South Africa, with 9 in 10 patients harbouring resistance to NNRTIs and/or NRTIs. PI-based regimens are predicted to be highly efficacious in achieving virological suppression amongst patients failing NNRTI-based regimens. Scaling up resistance testing amongst patients would facilitate access to second- and third-line regimens in South Africa.

Low-Abundance Drug-Resistant HIV-1 Variants in Antiretroviral Drug-Naive Individuals: A Systematic Review of Detection Methods, Prevalence, and Clinical Impact.

BACKGROUND: The presence of high-abundance drug-resistant HIV-1 jeopardizes success of antiretroviral therapy (ART). Despite numerous investigations, the clinical impact of low-abundance drug-resistant HIV-1 variants (LA-DRVs) at levels <15%-25% of the virus population in antiretroviral (ARV) drug-naive individuals remains controversial. METHODS: We systematically reviewed 103 studies assessing prevalence, detection methods, technical and clinical detection cutoffs, and clinical significance of LA-DRVs in antiretroviral drug-naive adults. RESULTS: In total, 14 919 ARV drug-naive individuals were included. Prevalence of LA-DRVs (ie, proportion of individuals harboring LA-DRVs) was 0%-100%. Technical detection cutoffs showed a 4 log range (0.001%-10%); 42/103 (40.8%) studies investigating the impact of LA-DRVs on ART; 25 studies included only individuals on first-line nonnucleoside reverse transcriptase inhibitor-based ART regimens. Eleven of those 25 studies (44.0%) reported a significantly association between preexisting LA-DRVs and risk of virological failure whereas 14/25 (56.0%) did not. CONCLUSIONS: Comparability of the 103 studies is hampered by high heterogeneity of the studies' designs and use of different methods to detect LA-DRVs. Thus, evaluating clinical impact of LA-DRVs on first-line ART remains challenging. We, the WHO HIVResNet working group, defined central areas of future investigations to guide further efforts to implement ultrasensitive resistance testing in routine settings.

The role of drug resistance in poor viral suppression in rural South Africa: findings from a population-based study.

BACKGROUND: Understanding factors driving virological failure, including the contribution of HIV drug resistance mutations (DRM), is critical to ensuring HIV treatment remains effective. We examine the contribution of drug resistance mutations for low viral suppression in HIV-positive participants in a population-based sero-prevalence survey in rural South Africa. METHODS: We conducted HIV drug resistance genotyping and ART analyte testing on dried blood spots (DBS) from HIV-positive adults participating in a 2014 survey in North West Province. Among those with virologic failure (> 5000 copies/mL), we describe frequency of DRM to protease inhibitors (PI), nucleoside reverse transcriptase inhibitors (NRTI), and non-nucleoside reverse transcriptase inhibitors (NNRTI), report association of resistance with antiretroviral therapy (ART) status, and assess resistance to first and second line therapy. Analyses are weighted to account for sampling design. RESULTS: Overall 170 DBS samples were assayed for viral load and ART analytes; 78.4% of men and 50.0% of women had evidence of virologic failure and were assessed for drug resistance, with successful sequencing of 76/107 samples. We found ≥1 DRM in 22% of participants; 47% were from samples with detectable analyte (efavirenz, nevirapine or lopinavir). Of those with DRM and detectable analyte, 60% showed high-level resistance and reduced predicted virologic response to ≥1 NRTI/NNRTI typically used in first and second-line regimens. CONCLUSIONS: DRM and predicted reduced susceptibility to first and second-line regimens were common among adults with ART exposure in a rural South African population-based sample. Results underscore the importance of ongoing virologic monitoring, regimen optimization and adherence counseling to optimize durable virologic suppression.

Prevalence of HIV-1 drug resistance amongst newly diagnosed HIV-infected infants age 4-8 weeks, enrolled in three nationally representative PMTCT effectiveness surveys, South Africa: 2010, 2011-12 and 2012-13.

BACKGROUND: South Africa (SA) has expanded efforts to reduce mother-to-child transmission of HIV (MTCT) to less than 2% at six weeks after birth and to less than 5% at 18 months postpartum by 2016. Despite improved antiretroviral regimens and coverage between 2001 and 2016, there is little data on infant HIV drug resistance. This paper tracks the prevalence of HIV drug resistance patterns amongst HIV infected infants from three nationally representative studies that assessed the effectiveness of national programs to prevent MTCT (PMTCT). The first study was conducted in 2010 (under the dual therapy PMTCT policy), the second from 2011 to 12 (PMTCT Option A policy) and the third from 2012 to 13 (PMTCT Option A policy). From 2010 to 2013, infant non-nucleoside reverse transcriptase inhibitor (NNRTI) exposure increased from single dose to daily throughout breastfeeding; maternal nucleoside reverse transcriptase inhibitor (NRTI) and NNRTI exposure increased with initiation of NNRTI-and NRTI- containing triple antiretroviral therapy (ART) earlier in gestation and at higher CD4 cell counts. METHODS: Three nationally representative surveys were conducted in 2010, 2011-12 and 2012-13. During the surveys, mothers with known, unknown, or no exposure to antiretrovirals for PMTCT and their infants were included, and MTCT was measured. For this paper, infant dried blood spots (iDBS) from HIV PCR positive infants aged 4-8 weeks, with consent for additional iDBS testing, were analysed for HIV drug resistance at the National Institute of Communicable Diseases (NICD), SA, using an in-house assay validated by the Centers for Disease Control and Prevention (CDC). Total viral nucleic acid was extracted from 2 spots and amplified by nested PCR to generate a ~ 1 kb amplicon that was sequenced using Sanger sequencing technologies. Sequence assembly and editing was performed using RECall v3. RESULTS: Overall, HIV-1 drug resistance was detected in 51% (95% Confidence interval (CI) [45-58%]) of HIV PCR positive infants, 37% (95% CI [28-47%]) in 2010, 64% (95% CI [53-74%]) in 2011 and 63% (95% CI [47-77%]) in 2012 (p < 0.0001), particularly to the NNRTI drug class. Pooled analyses across all three surveys demonstrated that infants whose mothers received ART showed the highest prevalence of resistance (74%); 26% (21/82) of HIV PCR positive infants with no or undocumented antiretroviral drug (ARV) exposure harboured NNRTI resistance. CONCLUSIONS: These data demonstrate increasing NNRTI resistance amongst newly-diagnosed infants in a high HIV prevalence setting where maternal ART coverage increased across the years, starting earlier in gestation and at higher CD4 cell counts. This is worrying as lifelong maternal ART coverage for HIV positive pregnant and lactating women is increasing. Also of concern is that resistant virus was detected in HIV positive infants whose mothers were not exposed to ARVs, raising questions about circulating resistant virus. Numbers in this group were too small to assess trends over the three years.

Walking and living independently with spina bifida: a 50-year prospective cohort study.

AIM: To describe trends in walking and living independently in a cohort of consecutive cases of spina bifida, followed-up over 50 years. METHOD: From 1972 to 2017, a cohort of 117 (born 1963-1971, 50 males, 67 females) survivors and/or carers was surveyed approximately every 5 years by clinical examination and/or postal questionnaire/telephone interview. The Office for National Statistics provided details of deaths. RESULTS: The follow-up in 2016 and 2017 was 99% (116/117). There were 37 survivors (17 males, 20 females) aged 46 to 53 years and 79 deaths (50y survival, 32%). The percentage of survivors who could walk more than 50m at the mean ages of 9 years, 18 years, 25 years, 30 years, 35 years, 40 years, 45 years, and 50 years was 51% (38/75), 50% (34/68), 33% (20/61), 30% (17/57), 30% (16/54), 30% (14/46), 31% (12/39), and 27% (10/37) respectively. However, the percentage living independently in the community after age 25 years increased over time: 23% (14/61); 37% (21/57); 41% (22/54); 39% (18/46); 56% (22/39); and 54% (20/37). Living independently at age 50 years was more common in survivors without a history of raised intracranial pressure or cerebrospinal fluid shunt revisions. INTERPRETATION: In this unselected cohort, mobility declined with age, possibly because of increasing obesity and deteriorating health. By contrast, partly because survival was better in those least disabled, the percentage living independently increased. WHAT THIS PAPER ADDS: By age 50 years, the percentage of patients who could walk more than 50m had declined to 27%. By age 50 years, the percentage living independently had doubled to over 50%. Survivors without a history of raised intracranial pressure or cerebrospinal fluid shunt revision are more likely to live independently.

CAMINAR Y VIVIR DE MANERA INDEPENDIENTE CUANDO SE TIENE UN DIAGNÓSTICO DE ESPINA BÍFIDA: UN ESTUDIO PROSPECTIVO DE COHORTE DE 50 AÑOS: OBJETIVO: Describir las tendencias para caminar y vivir de forma independiente en una cohorte de casos consecutivos de espina bífida, seguidos durante 50 años. MÉTODO: Desde 1.972 hasta 2.017, una cohorte de 117 (nacidos entre 1.963-1.971, 50 varones, 67 mujeres) sobrevivientes y/o cuidadores fueron encuestados aproximadamente cada 5 años mediante examen clínico y/o cuestionario postal/entrevista telefónica. La Oficina de Estadísticas Nacionales proporcionó detalles de las muertes. RESULTADOS: El seguimiento en 2.016 y 2.017 fue del 99% (116/117). Hubo 37 sobrevivientes (17 varones, 20 mujeres) de 46 a 53 años y 79 muertes (50 años de supervivencia, 32%). El porcentaje de sobrevivientes que pudieron caminar más de 50 metros en las edades medias de 9, 18, 25, 30, 35, 40, 45 y 50 años fue del 51% (38/75), 50% (34/68), 33% (20/61), 30% (17/57), 30% (16/54), 30% (14/46), 31% (12/39) y 27% (10/37) respectivamente. Sin embargo, el porcentaje de vida independiente en la comunidad después de los 25 años aumentó con el tiempo: 23% (14/61); 37% (21/57); 41% (22/54); 39% (18/46); 56% (22/39); y 54% (20/37). Vivir de forma independiente a los 50 años de edad fue más común en los sobrevivientes sin antecedentes de aumento de la presión intracraneal o revisiones de derivación del líquido cefalorraquídeo. INTERPRETACIÓN: En esta cohorte no seleccionada, la movilidad disminuyó con la edad, posiblemente debido al aumento de la obesidad y al deterioro de la salud. Por el contrario, en parte porque la supervivencia fue mejor en los individuos con menos desafíos fisicos, el porcentaje de vida independiente aumentó.

CAMINHANDO E VIVENDO COM INDEPENDÊNCIA TENDO ESPINHA BÍFIDA: UM ESTUDO DE COORTE PROSPECTIVO DE 50 ANOS: OBJETIVO: Descrever tendências no caminhar e viver com independência em uma coorte de casos consecutivos de espinha bífida, acompanhados por 50 anos. MÉTODO: De 1972 a 2017, uma coorte de 117 (nascidos 1963-1971, 50 do sexo masculino, 67 do sexo feminino) sobreviventes e/ou cuidadores foi avaliada aproximadamente a cada 5 anos por exame clínico e/ou entrevista por telefone ou correios. O Escritório de Estatística Nacional forneceu detalhes sobre óbitos. RESULTADOS: O acompanhamento em 2016 e 2017 foi 99% (116/117). Houve 37 sobreviventes (17 do sexo masculino, 20 do sexo feminino) com idades de 46 to 53 anos e 79 óbitos (sobrevivência em 50a, 32%). A porcentagem de sobreviventes que podiam andar mais de 50m nas idades médias de 9, 18, 25, 30, 35, 40, 45, e 50 foi 51% (38/75), 50% (34/68), 33% (20/61), 30% (17/57), 30% (16/54), 30% (14/46), 31% (12/39), and 27% (10/37) respectivamente. No entanto, a porcentagem vivendo independentemente na comunidade após a idade de 25 anos aumentou com o tempo: 23% (14/61); 37% (21/57); 41% (22/54); 39% (18/46); 56% (22/39); e 54% (20/37). Viver com independência na idade de 50 anos foi mais comum em sobreviventes sem história de aumento de pressão intra-craniana ou revisões da válvula de líquido cérebro-espinhal. INTERPRETAÇÃO: Nesta coorte não selecionada, a mobilidade diminuiu com a idade, possivelmente por causa do aumento da obesidade e deterioração das condições de saúde. Em contraste, em parte porque a sobrevivência foi melhor naqueles com menos incapacidades, a porcentagem dos que viviam com independência aumentou.

Switching to Efavirenz Versus Remaining on Ritonavir-boosted Lopinavir in Human Immunodeficiency Virus-infected Children Exposed to Nevirapine: Long-term Outcomes of a Randomized Trial.

BACKGROUND: We previously demonstrated the noninferiority of switching to efavirenz (EFV) versus remaining on ritonavir-boosted lopinavir (LPV/r) for virologic control in children infected with human immunodeficiency virus (HIV) and exposed to nevirapine (NVP) for prevention of mother-to-child transmission. Here we assess outcomes up to 4 years post-randomization. METHODS: From 2010-2013, 298 NVP-exposed HIV-infected children ≥3 years of age were randomized to switch to EFV or remain on LPV/r in Johannesburg, South Africa (Clinicaltrials.gov NCT01146873). After trial completion, participants were invited to enroll into observational follow-up. We compared HIV RNA levels, CD4 counts and percentages, lipids, and growth across groups through four years post-randomization. RESULTS: HIV RNA levels 51-1000 copies/mL were less frequently observed in the EFV group than the LPV/r group (odds ratio [OR] 0.67, 95% confidence interval [CI]: 0.51-0.88, P = .004), as was HIV RNA >1000 copies/mL (OR 0.52 95% CI: 0.28-0.98, P = .04). The probability of confirmed HIV RNA >1000 copies/mL by 48 months was 0.07 and 0.12 in the EFV and LPV/r groups, respectively (P = .21). Children randomized to EFV had a reduced risk of elevated total cholesterol (OR 0.45 95% CI: 0.27-0.75, P = .002) and a reduced risk of abnormal triglycerides (OR 0.42, 95% CI 0.29-0.62, P < .001). CONCLUSIONS: Our results indicate that the benefits of switching virologically suppressed NVP-exposed HIV-infected children ≥3 years of age from LPV/r to EFV are sustained long-term. This approach has several advantages, including improved palatability, reduced metabolic toxicity, simplified cotreatment for tuberculosis, and preservation of second line options. CLINICAL TRIALS REGISTRATION: NCT01146873.

Human Immunodeficiency Virus (HIV) Drug Resistance in African Infants and Young Children Newly Diagnosed With HIV: A Multicountry Analysis.

BACKGROUND: Programs for the prevention of mother-to-child transmission (PMTCT) of human immunodeficiency virus (HIV) have been scaled up in many low- and middle-income countries. However, HIV drug resistance (HIVDR) data among HIV-1-infected young children remain limited. METHODS: Surveys of pretreatment HIVDR among children aged <18 months who were diagnosed with HIV through early infant diagnosis were conducted in 5 sub-Saharan African countries (Mozambique, Swaziland, South Africa, Uganda, and Zimbabwe) between 2011 and 2014 following World Health Organization (WHO) guidance. Deidentified demographic and clinical data were used to explore risk factors associated with nonnucleoside reverse transcriptase inhibitor (NNRTI) resistance. RESULTS: Among the 1450 genotypes analyzed, 1048 had accompanying demographic and clinical data. The median age of children was 4 months; 50.4% were female. HIV from 54.1% showed resistance to 1 or more antiretroviral (ARV) drugs, with 53.0% and 8.8% having resistance to 1 or more NNRTI or nucleoside reverse transcriptase inhibitors, respectively. NNRTI resistance was particularly high in children exposed to ARV drugs through PMTCT; adjusted odds ratios were 1.8 (95% confidence interval [CI], 1.3-2.6) for maternal exposure only and 2.4 (CI, 1.6-3.6) for neonatal exposure only. CONCLUSIONS: Protease inhibitor-based regimens in children aged <3 years are currently recommended by WHO, but the implementation of this recommendation is suboptimal. These results reinforce the urgent need to overcome barriers to scaling up pediatric protease inhibitor-based regimens in sub-Saharan Africa and underscore the need to accelerate the study and approval of integrase inhibitors for use in young children.

Rapid Detection of Common HIV-1 Drug Resistance Mutations by Use of High-Resolution Melting Analysis and Unlabeled Probes.

HIV rapidly accumulates resistance mutations following exposure to subtherapeutic concentrations of antiretroviral drugs that reduces treatment efficacy. High-resolution melting analysis (HRMA) has been used to successfully identify single nucleotide polymorphisms (SNPs) and to genotype viral and bacterial species. Here, we tested the ability of HRMA incorporating short unlabeled probes to accurately assign drug susceptibilities at the 103, 181, and 184 codons of the HIV-1 reverse transcriptase gene. The analytical sensitivities of the HRMA assays were 5% of mixed species for K103N and Y181C and 20% for M184V. When applied to 153 HIV-1 patient specimens previously genotyped by Sanger population sequencing, HRMA correctly assigned drug sensitivity or resistance profiles to 80% of the samples at codon 103 (K103K/N) (Cohen's kappa coefficient [κ] > 0.6; P < 0.05), 90% at 181 (Y181Y/C) (κ > 0.74, P < 0.05), and 80% at 184 (M184M/V) (κ > 0.62; P < 0.05). The frequency of incorrect genotypes was very low (≤1 to 2%) for each assay, which in most cases was due to the higher sensitivity of the HRMA assay. Specimens for which drug resistance profiles could not be assigned (9 to 20%) often had polymorphisms in probe binding regions. Thus, HRMA is a rapid, inexpensive, and sensitive method for the determination of drug sensitivities caused by major HIV-1 drug resistance mutations and, after further development to minimize the melting effects of nontargeted polymorphisms, may be suitable for surveillance purposes.

Rates of virological suppression and drug resistance in adult HIV-1-positive patients attending primary healthcare facilities in KwaZulu-Natal, South Africa.

BACKGROUND: KwaZulu-Natal (KZN) Province in South Africa has the highest HIV disease burden in the country, with an estimated population prevalence of 24.7%. A pilot sentinel surveillance project was undertaken in KZN to classify the proportion of adult patients failing first-line ART and to describe the patterns of drug resistance mutations (DRMs) in patients with virological failure (VF). METHODS: Cross-sectional surveillance of acquired HIV drug resistance was conducted in 15 sentinel ART clinics between August and November 2013. Two population groups were surveyed: on ART for 12-15 months (Cohort A) or 24-36 months (Cohort B). Plasma specimens with viral load ≥1000 copies/mL were defined as VF and genotyped for DRMs. RESULTS: A total of 1299 adults were included in the analysis. The prevalence of VF was 4.0% (95% CI 1.8-8.8) among 540 adults in Cohort A and 7.7% (95% CI 4.4-13.0) of 759 adults in Cohort B. Treatment with efavirenz was more likely to suppress viral load in Cohort A (P = 0.005). Independent predictors of VF for Cohort B included male gender, advanced WHO stage at ART initiation and treatment with stavudine or zidovudine compared with tenofovir. DRMs were detected in 89% of 123 specimens with VF, including M184I/V, K103N/S, K65N/R, V106A/M and Y181C. CONCLUSIONS: VF in adults in KZN was <8% up to 3 years post-ART initiation but was associated with a high frequency of DRMs. These data identify key groups for intensified adherence counselling and highlight the need to optimize first-line regimens to maintain viral suppression.

Contribution of Gag and Protease to HIV-1 Phenotypic Drug Resistance in Pediatric Patients Failing Protease Inhibitor-Based Therapy.

Protease inhibitors (PIs) are used as a first-line regimen in HIV-1-infected children. Here we investigated the phenotypic consequences of amino acid changes in Gag and protease on lopinavir (LPV) and ritonavir (RTV) susceptibility among pediatric patients failing PI therapy. The Gag-protease from isolates from 20 HIV-1 subtype C-infected pediatric patients failing an LPV and/or RTV-based regimen was phenotyped using a nonreplicativein vitroassay. Changes in sensitivity to LPV and RTV relative to that of the matched baseline (pretherapy) sample were calculated. Gag and protease amino acid substitutions associated with PI failure were created in a reference clone by site-directed mutagenesis and assessed. Predicted phenotypes were determined using the Stanford drug resistance algorithm. Phenotypic resistance or reduced susceptibility to RTV and/or LPV was observed in isolates from 10 (50%) patients, all of whom had been treated with RTV. In most cases, this was associated with protease resistance mutations, but substitutions at Gag cleavage and noncleavage sites were also detected. Gag amino acid substitutions were also found in isolates from three patients with reduced drug susceptibilities who had wild-type protease. Site-directed mutagenesis confirmed that some amino acid changes in Gag contributed to PI resistance but only in the presence of major protease resistance-associated substitutions. The isolates from all patients who received LPV exclusively were phenotypically susceptible. Baseline isolates from the 20 patients showed a large (47-fold) range in the 50% effective concentration of LPV, which accounted for most of the discordance seen between the experimentally determined and the predicted phenotypes. Overall, the inclusion of thegaggene and the use of matched baseline samples provided a more comprehensive assessment of the effect of PI-induced amino acid changes on PI resistance. The lack of phenotypic resistance to LPV supports the continued use of this drug in pediatric patients.

Geographic and temporal trends in the molecular epidemiology and genetic mechanisms of transmitted HIV-1 drug resistance: an individual-patient- and sequence-level meta-analysis.

BACKGROUND: Regional and subtype-specific mutational patterns of HIV-1 transmitted drug resistance (TDR) are essential for informing first-line antiretroviral (ARV) therapy guidelines and designing diagnostic assays for use in regions where standard genotypic resistance testing is not affordable. We sought to understand the molecular epidemiology of TDR and to identify the HIV-1 drug-resistance mutations responsible for TDR in different regions and virus subtypes. METHODS AND FINDINGS: We reviewed all GenBank submissions of HIV-1 reverse transcriptase sequences with or without protease and identified 287 studies published between March 1, 2000, and December 31, 2013, with more than 25 recently or chronically infected ARV-naïve individuals. These studies comprised 50,870 individuals from 111 countries. Each set of study sequences was analyzed for phylogenetic clustering and the presence of 93 surveillance drug-resistance mutations (SDRMs). The median overall TDR prevalence in sub-Saharan Africa (SSA), south/southeast Asia (SSEA), upper-income Asian countries, Latin America/Caribbean, Europe, and North America was 2.8%, 2.9%, 5.6%, 7.6%, 9.4%, and 11.5%, respectively. In SSA, there was a yearly 1.09-fold (95% CI: 1.05-1.14) increase in odds of TDR since national ARV scale-up attributable to an increase in non-nucleoside reverse transcriptase inhibitor (NNRTI) resistance. The odds of NNRTI-associated TDR also increased in Latin America/Caribbean (odds ratio [OR] = 1.16; 95% CI: 1.06-1.25), North America (OR = 1.19; 95% CI: 1.12-1.26), Europe (OR = 1.07; 95% CI: 1.01-1.13), and upper-income Asian countries (OR = 1.33; 95% CI: 1.12-1.55). In SSEA, there was no significant change in the odds of TDR since national ARV scale-up (OR = 0.97; 95% CI: 0.92-1.02). An analysis limited to sequences with mixtures at less than 0.5% of their nucleotide positions­a proxy for recent infection­yielded trends comparable to those obtained using the complete dataset. Four NNRTI SDRMs­K101E, K103N, Y181C, and G190A­accounted for >80% of NNRTI-associated TDR in all regions and subtypes. Sixteen nucleoside reverse transcriptase inhibitor (NRTI) SDRMs accounted for >69% of NRTI-associated TDR in all regions and subtypes. In SSA and SSEA, 89% of NNRTI SDRMs were associated with high-level resistance to nevirapine or efavirenz, whereas only 27% of NRTI SDRMs were associated with high-level resistance to zidovudine, lamivudine, tenofovir, or abacavir. Of 763 viruses with TDR in SSA and SSEA, 725 (95%) were genetically dissimilar; 38 (5%) formed 19 sequence pairs. Inherent limitations of this study are that some cohorts may not represent the broader regional population and that studies were heterogeneous with respect to duration of infection prior to sampling. CONCLUSIONS: Most TDR strains in SSA and SSEA arose independently, suggesting that ARV regimens with a high genetic barrier to resistance combined with improved patient adherence may mitigate TDR increases by reducing the generation of new ARV-resistant strains. A small number of NNRTI-resistance mutations were responsible for most cases of high-level resistance, suggesting that inexpensive point-mutation assays to detect these mutations may be useful for pre-therapy screening in regions with high levels of TDR. In the context of a public health approach to ARV therapy, a reliable point-of-care genotypic resistance test could identify which patients should receive standard first-line therapy and which should receive a protease-inhibitor-containing regimen.

Neurological level at birth predicts survival to the mid-40s and urological deaths in open spina bifida: a complete prospective cohort study.

AIM: To conduct a 50-year complete, community-based, prospective cohort study to investigate long-term survival, causes of death, and influence of level of the lesion in treated open spina bifida. METHOD: The cohort comprised 117 consecutive cases whose backs were closed non-selectively at birth between 1963 and 1971 in Cambridge, UK. In 2013 we surveyed the survivors (n=39, 18 males, 21 females; mean age 46y, range 43-49y) by postal questionnaire and telephone interview. We compared outcomes in those born with a neurological deficit in terms of sensory and motor levels of L1 and above versus L2 and below. RESULTS: Two-thirds of the cohort (78/117) had died. Causes of death were cardiorespiratory (n=26), neurological (n=24), urological (n=22), or other (n=6). Only the urological deaths were related to level of the lesion: there were none in those with a sensory level of L2 or below (p<0.001). Birth findings also predicted survival: of the 57 infants with a neurological level of L1 or above, only 12% (n=7) survived compared with 55% (30/55) of the remainder (p<0.001). INTERPRETATION: The increased mortality in those born with an extensive neurological deficit was mainly due to urological deaths. Neurological level, particularly the sensory level, is the best predictor of long-term outcome and should be assessed routinely at birth.

Efavirenz-Based Antiretroviral Therapy Among Nevirapine-Exposed HIV-Infected Children in South Africa: A Randomized Clinical Trial.

IMPORTANCE: Advantages of using efavirenz as part of treatment for children infected with human immunodeficiency virus (HIV) include once-daily dosing, simplification of co-treatment for tuberculosis, preservation of ritonavir-boosted lopinavir for second-line treatment, and harmonization of adult and pediatric treatment regimens. However, there have been concerns about possible reduced viral efficacy of efavirenz in children exposed to nevirapine for prevention of mother-to-child transmission. OBJECTIVE: To evaluate whether nevirapine-exposed children achieving initial viral suppression with ritonavir-boosted lopinavir-based therapy can transition to efavirenz-based therapy without risk of viral failure. DESIGN, SETTING, AND PARTICIPANTS: Randomized, open-label noninferiority trial conducted at Rahima Moosa Mother and Child Hospital, Johannesburg, South Africa, from June 2010 to December 2013, enrolling 300 HIV-infected children exposed to nevirapine for prevention of mother-to-child transmission who were aged 3 years or older and had plasma HIV RNA of less than 50 copies/mL during ritonavir-boosted lopinavir-based therapy; 298 were randomized and 292 (98%) were followed up to 48 weeks after randomization. INTERVENTIONS: Participants were randomly assigned to switch to efavirenz-based therapy (n = 150) or continue ritonavir-boosted lopinavir-based therapy (n = 148). MAIN OUTCOMES AND MEASURES: Risk difference between groups in (1) viral rebound (ie, ≥1 HIV RNA measurement of >50 copies/mL) and (2) viral failure (ie, confirmed HIV RNA >1000 copies/mL) with a noninferiority bound of -0.10. Immunologic and clinical responses were secondary end points. RESULTS: The Kaplan-Meier probability of viral rebound by 48 weeks was 0.176 (n = 26) in the efavirenz group and 0.284 (n = 42) in the ritonavir-boosted lopinavir group. Probabilities of viral failure were 0.027 (n = 4) in the efavirenz group and 0.020 (n = 3) in the ritonavir-boosted lopinavir group. The risk difference for viral rebound was 0.107 (1-sided 95% CI, 0.028 to ∞) and for viral failure was -0.007 (1-sided 95% CI, -0.036 to ∞). We rejected the null hypothesis that efavirenz is inferior to ritonavir-boosted lopinavir (P < .001) for both end points. By 48 weeks, CD4 cell percentage was 2.88% (95% CI, 1.26%-4.49%) higher in the efavirenz group than in the ritonavir-boosted lopinavir group. CONCLUSIONS AND RELEVANCE: Among HIV-infected children exposed to nevirapine for prevention of mother-to-child transmission and with initial viral suppression with ritonavir-boosted lopinavir-based therapy, switching to efavirenz-based therapy compared with continuing ritonavir-boosted lopinavir-based therapy did not result in significantly higher rates of viral rebound or viral failure. This therapeutic approach may offer advantages in children such as these. TRIAL REGISTRATION: clinicaltrials.gov Identifier: NCT01146873.

Sensitive tenofovir resistance screening of HIV-1 from the genital and blood compartments of women with breakthrough infections in the CAPRISA 004 tenofovir gel trial.

The Centre for the AIDS Programme of Research in South Africa 004 (CAPRISA 004) study demonstrated that vaginally applied tenofovir gel is a promising intervention for protecting women from sexually acquiring human immunodeficiency virus (HIV). However, the potential for emergence of tenofovir resistance remains a concern in women who seroconvert while using the gel despite the lack of plasma virus resistance as assessed by population sequencing during the trial. We applied highly sensitive polymerase chain reaction-based assays to screen for tenofovir resistance in plasma and vaginal swab specimens. The absence of mutation detection suggested little immediate risk of tenofovir-resistant HIV-1 emergence and forward transmission in settings in which gel users are closely monitored for HIV seroconversion.

Patient evaluation of early discharge after hip arthroplasty: development of a measure and comparison of three centres with differing durations of stay.

OBJECTIVE: We compared patients' evaluation of care between a surgical unit with a rapid discharge policy and two comparison units to test the hypothesis that the centre with rapid discharge has outcomes that are not inferior to those of the comparison sites. DESIGN: Cross-sectional cohort study. SUBJECTS: Consecutive consenting patients undergoing primary hip arthroplasty during 12 months in: a unit that had reduced postoperative stay to median three days; a specialised orthopaedic surgery treatment centre with median stay of five days; a traditional unit with median stay of six days (N = 316, 125, 119, respectively). METHODS: Six weeks postoperatively, patients completed a specially developed questionnaire measuring their evaluation of care and recovery, together with measures of function and quality of life for validation purposes. RESULTS: Factor analysis of questionnaire responses identified two independent components of patients' evaluation: problems in staff care and problems in physical recovery. Neither component was impaired in the unit with rapid discharge: similar proportions of patients reported recovery problems in each site (odds radios (ORs) for the two comparators versus unit with rapid discharge: 0.96, 1.18); and more patients reported care problems in the two comparator sites (ORs 2.97, 2.16). CONCLUSION: Duration of stay after primary hip arthroplasty can be reduced to three days without intensive pre- or postoperative care, without detriment to patient evaluation.

Pretreatment Human Immunodeficiency Virus (HIV) Drug Resistance Among Treatment-Naive Infants Newly Diagnosed With HIV in 2016 in Namibia: Results of a Nationally Representative Study.

Background: The World Health Organization (WHO) recommends routine surveillance of pretreatment human immunodeficiency virus (HIV) drug resistance (HIVDR) in children <18 months of age diagnosed with HIV through early infant diagnosis (EID). In 2016, 262 children <18 months of age were diagnosed with HIV in Namibia through EID. Levels of HIVDR in this population are unknown. Methods: In 2016, Namibia surveyed pretreatment HIVDR among children aged <18 months following WHO guidance. Reverse transcriptase, protease, and integrase regions of HIV-1 were genotyped from remnant dried blood spot specimens from all infants diagnosed with HIV in Namibia in 2016. HIVDR was predicted using the Stanford HIVdb algorithm. Results: Of 262 specimens genotyped, 198 HIV-1 protease and reverse transcriptase sequences and 118 HIV-1 integrase sequences were successfully amplified and analyzed. The prevalence of efavirenz/nevirapine (EFV/NVP), abacavir (ABC), zidovudine, lamivudine/emtricitabine (3TC/FTC), and tenofovir (TDF) resistance was 62.6%, 17.7%, 5.6%, 15.7%, and 10.1%, respectively. No integrase inhibitor resistance was detected. Conclusions: The high level of EFV/NVP resistance is unsurprising; however, levels of ABC and TDF resistance are among the highest observed to date in infants in sub-Saharan Africa. The absence of resistance to dolutegravir (DTG) is reassuring but underscores the need to further study the impact of ABC and 3TC/FTC resistance on pediatric protease inhibitor- and DTG-based regimens and accelerate access to other antiretroviral drugs. Results underscore the need for antiretroviral therapy optimization and prompt management of high viral loads in infants and pregnant and breastfeeding women.

Epidemiology of SARS-CoV-2 infection and SARS-CoV-2 positive hospital admissions among children in South Africa.

INTRODUCTION: We describe epidemiology and outcomes of confirmed SARS-CoV-2 infection and positive admissions among children <18 years in South Africa, an upper-middle income setting with high inequality. METHODS: Laboratory and hospital COVID-19 surveillance data, 28 January - 19 September 2020 was used. Testing rates were calculated as number of tested for SARS-CoV-2 divided by population at risk; test positivity rates were calculated as positive tests divided by total number of tests. In-hospital case fatality ratio (CFR) was calculated based on hospitalized positive admissions with outcome data who died in-hospital and whose death was judged SARS-CoV-2 related by attending physician. FINDINGS: 315 570 children aged <18 years were tested for SARS-CoV-2; representing 8.9% of all 3 548 738 tests and 1.6% of all children in the country. Of children tested, 46 137 (14.6%) were positive. Children made up 2.9% (n = 2007) of all SARS-CoV-2 positive admissions to sentinel hospitals. Among children, 47 died (2.6% case-fatality). In-hospital deaths were associated with male sex [adjusted odds ratio (aOR) 2.18 (95% confidence intervals [CI] 1.08-4.40)] vs female; age <1 year [aOR 4.11 (95% CI 1.08-15.54)], age 10-14 years [aOR 4.20 (95% CI1.07-16.44)], age 15-17 years [aOR 4.86 (95% 1.28-18.51)] vs age 1-4 years; admission to a public hospital [aOR 5.07(95% 2.01-12.76)] vs private hospital and ≥1 underlying conditions [aOR 12.09 (95% CI 4.19-34.89)] vs none. CONCLUSIONS: Children with underlying conditions were at greater risk of severe SARS-CoV-2 outcomes. Children > 10 years, those in certain provinces and those with underlying conditions should be considered for increased testing and vaccination.

Community-led cross-sectional study of social and employment circumstances, HIV and associated factors amongst female sex workers in South Africa: study protocol.

BACKGROUND: In South Africa, female sex workers (FSWs) are perceived to play a pivotal role in the country's HIV epidemic. Understanding their health status and risk factors for adverse health outcomes is foundational for developing evidence-based health care for this population. OBJECTIVE: Describe the methodology used to successfully implement a community-led study of social and employment circumstances, HIV and associated factors amongst FSWs in South Africa. METHOD: A community-centric, cross-sectional, survey of 3,005 adult FSWs was conducted (January-July 2019) on 12 Sex Work (SW) programme sites across nine provinces of South Africa. Sites had existing SW networks and support programmes providing peer education and HIV services. FSWs were involved in the study design, questionnaire development, and data collection. Questions included: demographic, sexual behaviour, HIV testing and treatment/PrEP history, and violence exposure. HIV rapid testing, viral load, CD4 count, HIV recency, and HIV drug resistance genotypic testing were undertaken. Partner organisations provided follow-up services. RESULTS: HIV Prevalence was 61.96%, the median length of selling sex was 6 years, and inconsistent condom use was reported by 81.6% of participants, 88.4% reported childhood trauma, 46.2% reported physical or sexual abuse by an intimate partner and 57.4% by a client. More than half of participants had depression and post-traumatic stress disorder (52.7% and 54.1%, respectively). CONCLUSION: This is the first national survey of HIV prevalence amongst FSWs in programmes in South Africa. The data highlight the vulnerability of this population to HIV, violence and mental ill health, suggesting the need for urgent law reform. Based on the unique methodology and the successful implementation alongside study partners, the outcomes will inform tailored interventions. Our rapid rate of enrolment, low rate of screening failure and low proportion of missing data showed the feasibility and importance of community-centric research with marginalised, highly vulnerable populations.