Prevalence of HIV drug resistance in Nigeria: results from a cross-sectional, population-based survey of Nigerian adults with unsuppressed viral load.

BACKGROUND: HIV drug resistance (HIVDR) surveillance is an important tool to monitor threats to progress towards epidemic control. The characterization of HIVDR in Nigeria at the national level is needed to inform both clinical decisions and population-level HIV policy strategies. This study uses data obtained from the Nigeria HIV/AIDS Indicator and Impact Survey (NAIIS) to describe the prevalence and distribution of HIVDR in Nigeria. METHODS: NAIIS was a cross-sectional, population-based survey of households throughout Nigeria in 2018. NAIIS was designed to provide estimates of HIV prevalence and related health indicators from a nationally representative sample. The study population included participants aged 15-64 years who tested positive for HIV, had a viral load at least 1000 copies/ml, and had available HIV drug resistance genotypes. HIV isolates were genotyped to detect drug resistance mutations. Individual characteristics of study participants associated with HIVDR were identified using a weighted multivariable logistic regression model. RESULTS: Of 1355 respondents with available HIV genotypes, 293 (19%) had evidence of drug-resistant mutations (DRMs) that conferred resistance to at least one antiretroviral drug. The majority of DRMs observed conferred resistance to NNRTIs (17.6%) and NRTIs (11.2%). HIVDR was associated with being ART-experienced, longer duration on ART, and lower CD4+ count but not sociodemographic characteristics. CONCLUSION: The population level DRM prevalence in Nigeria was consistent with what would be expected in a mature HIV treatment landscape. The continued roll out of dolutegravir-anchored regimens should mitigate the impact of NNRTI resistance on population viral load suppression and progress towards epidemic control.

Mortality from drug-resistant tuberculosis in high-burden countries comparing routine drug susceptibility testing with whole-genome sequencing: a multicentre cohort study.

BACKGROUND: Drug resistance threatens global tuberculosis control. We aimed to examine mortality in patients with tuberculosis from high-burden countries, according to concordance or discordance of results from drug susceptibility testing done locally and whole-genome sequencing (WGS). METHODS: In this multicentre cohort study, we collected pulmonary Mycobacterium tuberculosis isolates and clinical data from individuals with tuberculosis from antiretroviral therapy programmes and tuberculosis clinics in Côte d'Ivoire, Democratic Republic of the Congo, Kenya, Nigeria, Peru, South Africa, and Thailand, stratified by HIV status and drug resistance. Sites tested drug susceptibility using routinely available methods. WGS was done on Illumina HiSeq 2500 in the USA and Switzerland, and TBprofiler was used to analyse the genomes. We included individuals aged 16 years or older with pulmonary tuberculosis (bacteriologically confirmed or clinically diagnosed). We analysed mortality in multivariable logistic regression models adjusted for sex, age, HIV status, history of tuberculosis, and sputum positivity. FINDINGS: Between Sept 1, 2014, and July 4, 2016, of 634 patients included in our previous analysis, we included 582 patients with tuberculosis (median age 33 years [IQR 27-43], 225 [39%] women, and 247 [42%] HIV-positive). Based on WGS, 339 (58%) isolates were pan-susceptible, 35 (6%) monoresistant, 146 (25%) multidrug-resistant, and 24 (4%) pre-extensively drug-resistant (pre-XDR) or XDR. The analysis of mortality was based on 530 patients; 63 (12%) died and 77 (15%) patients received inappropriate treatment. Mortality ranged from 6% (18 of 310) in patients with pan-susceptible tuberculosis to 39% (nine of 23) in patients with pre-XDR or XDR tuberculosis. The adjusted odds ratio for mortality was 4·92 (95% CI 2·47-9·78) among undertreated patients, compared with appropriately treated patients. INTERPRETATION: In seven countries with a high burden of tuberculosis, we observed discrepancies between drug resistance patterns obtained locally and WGS. The underdiagnosis of drug resistance resulted in inappropriate treatment and higher mortality. WGS can provide accurate and detailed drug resistance information required to improve the outcomes of drug-resistant tuberculosis in high-burden settings. Our results support WHO's call for point-of-care tests based on WGS. FUNDING: National Institutes of Allergy and Infectious Diseases, Swiss National Science Foundation, and Swiss National Center for Mycobacteria.

Blueprint for building a biorepository in a resource-limited setting that follows international best practices.

BACKGROUND: Genetic diversity is abundant on the African continent. However, genomic research has been hampered by a lack of high quality and extensively annotated biospecimens and the necessary infrastructure to support such a technology-intensive effort. OBJECTIVE: The Institute of Human Virology Nigeria (IHVN) partnered with the H3Africa Consortium and the Coriell Institute for Medical Research to build an internationally recognised biorepository for the receipt, processing, storage and distribution of biospecimens for biomedical research. Here, the authors describe the procedures, challenges and results encountered. RESULTS: Key requirements for a high-quality biorepository were identified: (1) institutional support of infrastructure and services, (2) on-site trained staff with primary commitment to the biorepository, (3) reliance on best practices from globally recognised biorepository groups, (4) early implementation of a quality management system, (5) adoption of a laboratory information management system with demonstrated versatility in functions, (6) collaboration with external experts and sharing of experience through abstracts, newsletters, published manuscripts, and attendance at meetings and workshops, (7) strict adherence to local and national ethical standards and (8) a sustainability plan that is reviewed and updated annually. CONCLUSION: Utilising published best practices of globally recognised experts in the biorepository field as a benchmark, IHVN expanded and reorganised its existing laboratory facility and staff to take on this new purpose.

Drug susceptibility testing and mortality in patients treated for tuberculosis in high-burden countries: a multicentre cohort study.

BACKGROUND: Drug resistance is a challenge for the global control of tuberculosis. We examined mortality in patients with tuberculosis from high-burden countries, according to concordance or discordance of results from drug susceptibility testing done locally and in a reference laboratory. METHODS: This multicentre cohort study was done in Côte d'Ivoire, Democratic Republic of the Congo, Kenya, Nigeria, South Africa, Peru, and Thailand. We collected Mycobacterium tuberculosis isolates and clinical data from adult patients aged 16 years or older. Patients were stratified by HIV status and tuberculosis drug resistance. Molecular or phenotypic drug susceptibility testing was done locally and at the Swiss National Center for Mycobacteria, Zurich, Switzerland. We examined mortality during treatment according to drug susceptibility test results and treatment adequacy in multivariable logistic regression models adjusting for sex, age, sputum microscopy, and HIV status. FINDINGS: We obtained M tuberculosis isolates from 871 patients diagnosed between 2013 and 2016. After exclusion of 237 patients, 634 patients with tuberculosis were included in this analysis; the median age was 33·2 years (IQR 26·9-42·5), 239 (38%) were women, 272 (43%) were HIV-positive, and 69 (11%) patients died. Based on the reference laboratory drug susceptibility test, 394 (62%) strains were pan-susceptible, 45 (7%) monoresistant, 163 (26%) multidrug-resistant (MDR), and 30 (5%) had pre-extensively or extensively drug resistant (pre-XDR or XDR) tuberculosis. Results of reference and local laboratories were concordant for 513 (81%) of 634 patients and discordant for 121 (19%) of 634. Overall, sensitivity to detect any resistance was 90·8% (95% CI 86·5-94·2) and specificity 84·3% (80·3-87·7). Mortality ranged from 6% (20 of 336) in patients with pan-susceptible tuberculosis treated according to WHO guidelines to 57% (eight of 14) in patients with resistant strains who were under-treated. In logistic regression models, compared with concordant drug susceptibility test results, the adjusted odds ratio of death was 7·33 (95% CI 2·70-19·95) for patients with discordant results potentially leading to under-treatment. INTERPRETATION: Inaccurate drug susceptibility testing by comparison with a reference standard leads to under-treatment of drug-resistant tuberculosis and increased mortality. Rapid molecular drug susceptibility test of first-line and second-line drugs at diagnosis is required to improve outcomes in patients with MDR tuberculosis and pre-XDR or XDR tuberculosis. FUNDING: National Institutes of Allergy and Infectious Diseases, Swiss National Science Foundation, Swiss National Center for Mycobacteria.

Improved Performance of COBAS AmpliPrep/COBAS TaqMan Version 2.0 Assay Over Amplicor Monitor Version 1.5 in the Quantification of HIV-1 RNA Viral Load in Abuja, Nigeria.

BACKGROUND: Improved viral detections by the real time PCR over the manual assays have been reported by various manufacturers. However, discrepancies and discordance between different platforms targeting the same pathogen have also been observed at different settings. METHODS: We used an analytical study design to compare the performance of the Cobas Taqman /Cobas Ampliprep version 2.0 against the standard Amplicor Monitor 1.5 using 200 routine clinical samples, in Abuja- Nigeria. RESULTS: Taqman and Amplicor detected 118/200 (59%) and 83/200 (41.5%) samples respectively. Two of 83 samples (2.4%) undetectable by Cobas Taqman, were detectable by Roche Amplicor, while 5 of 37 samples (13.5%) which were undetectable by Amplicor using Taqman. Among the 81 detectable samples by both assays 4 samples (4.9%) had a log10 difference > 0.5 log copies, while 9 samples (11.1%) showed a wider discrepancy of >1 log10. Bland and Altman's comparison shows no significant difference between the two methods (p=0.2825) and CI-0.06171 to 0.2087. CONCLUSION: We observed a remarkable improvement in the performance of COBAS AmpliPrep/COBAS TaqMan version 2.0 Assay over Amplicor Monitor version 1.5 in the quantification of HIV1 RNA viral load. Discrepancies of clinical significance, in the viral load between the two platforms were also recorded. The implications of the inability of the automated Taqman 2.0 to detect 2.4% of samples detectable by the Amplicor need to be considered by programs, clinicians and the manufacturers. Periodic evaluation of platforms to detect new circulating HIV subtypes within each locality is also recommended.

Adherence to Anti-Retroviral Therapy in North Central Nigeria.

BACKGROUND: Nigeria bears nearly 10% of the global burden of HIV/AIDS. Most of the AIDS patients dwell in the part of Nigeria known as the "North Central" geopolitical region. Sustaining HIV patients in this high risk region is critical for the overall success of the ART program in Nigeria. We assessed the level of adherence to ART and adherence determinants among participants who had been on ART for an average of three and half years. METHODOLOGY: Eligible study participants initiated HAART between 2004 and 2010. HAART regimens contained AZT/3TC +NVP or EFV; AZT/3TC/NVP; 3TC/NVP/d4T; TDF/FTC +EFV or NVP and TDF+3TC+LPV/r. A composite adherence measure defined as not missing a dose and taking the correct dose and adhering to the correct frequency and correct schedule of drug administration was used to assess self-reported adherence over a period of three days. Selfreported adherence was validated with viral load test. Base line adherence was fixed at ≥95% adherence level. Significant test was fixed at p<0.05. RESULTS: We included 502 participants in the analysis. Median age for men was 42 years (IQR: 38 - 44 years) and women, 36 years (IQR: 30-40 years). Mean duration of therapy was 43 (16-70) months. Effective self-reported adherence was 97.3%. Only age and virologic suppression were significantly associated with adherence to ART. Forgetfullness (43%) was the major reason for non-adherence, while improvement in health condition (40%) was the main facilitator of adherence to the medications. CONCLUSION: Most participants achieved optimal adherence (≥95%) with high virologic suppression. Strategies to sustain optimal adherence, e.g., the use of fixed dose combinations (FDCs) and comprehensive adherence counselling should be maintained.

Experiences in establishing a PEPFAR-supported laboratory quality system in Nigeria.

The need to accurately diagnose HIV-infected persons and monitor their immune status and sequelae from increased access to antiretroviral therapy dictated the establishment of a quality assurance (QA) system supported by dedicated personnel, financial resources, and a close monitoring system. Assessment of laboratories and personnel in Nigeria revealed the need for improved laboratory infrastructure and training, including on-site didactic and wet workshops and the institution of a tiered QA unit of laboratory regional officers, focal persons, and site monitors who provided guidance and continuous monitoring. Quarterly assessments and generated reports guided corrective actions. A sustainable quality laboratory system was developed for the first time in Nigeria with funding from the US President's Emergency Plan for AIDS Relief. With expansion from 7 to 34 comprehensive treatment sites, a tiered laboratory organizational structure with regional and site-based Nigerian quality control officers was developed. Measured improvements included reduction in deficiencies from 13% to 2%.

Building laboratory infrastructure to support scale-up of HIV/AIDS treatment, care, and prevention: in-country experience.

An unprecedented influx of funds and support through large programs such as the Global Fund for AIDS, Malaria and Tuberculosis and the World Health Organization's and President's Emergency Plan for AIDS Relief (PEPFAR) has made it possible for more than 1 million persons in resource-limited settings to access AIDS treatment and several million more to be in care and prevention programs. Nevertheless, there remain major challenges that prevent AIDS drugs and care from reaching many more in need, especially in rural settings. The roll-out of a high-quality treatment, care, and prevention program depends on an effective and reliable laboratory infrastructure. This article presents a strategy used by the Institute of Human Virology (IHV)-University of Maryland and its affiliate IHV-Nigeria to establish a multifaceted, integrated tier laboratory program to support a PEPFAR-funded scale-up of its AIDS Care Treatment in Nigeria program, in collaboration with the Centers for Disease Control and Prevention and the Nigerian government, as a possible model for overcoming a key challenge that faces several resource-limited countries trying to roll out and scale-up their HIV/AIDS treatment, care, and prevention program.