BackgroundOwing to high levels of resistance to previous first-line non-nucleoside reverse transc... more BackgroundOwing to high levels of resistance to previous first-line non-nucleoside reverse transcriptase inhibitors (NNRTI)-based antiretroviral therapy (ART), consolidated recommendations since 2019, from the WHO and others, have indicated that dolutegravir (DTG) is the preferred drug of choice for HIV treatment, globally. There is a paucity of resistance outcome data from non-B HIV subtypes circulating across West Africa.AimWe aimed to characterise the mutational profiles of HIV-positive patients from a small North-East Nigeria cohort, failing a DTG-based ART regimen.MethodsPlasma samples were collected and stored from 61 HIV-1 infected participants. Following failure of DTG-based ART, all samples were sequenced by Illumina whole-genome, ultra-deep sequencing. Sequencing was successful in (n=33) participants with median age of 40 years and median time on ART of 9 years. HIV-1 subtyping was performed using SNAPPy. Haplotype reconstruction and transmission were inferred using standa...
Human Immunodeficiency Virus (HIV) diagnosis remains the gateway to HIV care and treatment. Howev... more Human Immunodeficiency Virus (HIV) diagnosis remains the gateway to HIV care and treatment. However, due to changes in HIV prevalence and testing coverage across different geopolitical zones, it is crucial to evaluate the national HIV testing algorithm as false positivity due to low prevalence could be detrimental to both the client and the service delivery. Therefore, we evaluated the performance of the national HIV rapid testing algorithm using specimens collected from multiple HIV testing services (HTS) sites and compared the results from different HIV prevalence levels across the six geopolitical zones of Nigeria. The evaluation employed a dual approach, retrospective, and prospective. The retrospective evaluation focused on a desktop review of program data (n = 492,880) collated from patients attending routine HTS from six geopolitical zones of Nigeria between January 2017 and December 2019. The prospective component utilized samples (n = 2,895) collected from the field at the ...
In settings with high tuberculosis (TB) endemicity, various genotypes of the Mycobacterium tuberc... more In settings with high tuberculosis (TB) endemicity, various genotypes of the Mycobacterium tuberculosis complex (MTBC) often differ in prevalence. However, the factors leading to these differences remain poorly understood. Here we studied the MTBC population in Dar es Salaam, Tanzania over a six-year period, using 1,082 unique patient-derived MTBC whole-genome sequences (WGS) and associated clinical data. We show that the TB epidemic in Dar es Salaam is dominated by multiple genotypes introduced to Tanzania from different parts of the world during the last 300 years. The most common MTBC genotypes deriving from these introductions exhibited differences in transmission rates and in the duration of the infectious period, but little differences in overall fitness, as measured by the effective reproductive number. Moreover, measures of disease severity and bacterial load indicated no differences in virulence between these genotypes during active TB. Instead, the combination of an early ...
The World Health Organization recommends universal vaccination of medically stable infants with H... more The World Health Organization recommends universal vaccination of medically stable infants with Hepatitis B vaccine within 24 hours of birth to prevent mother-to-child transmission of Hepatitis B virus (HBV) infection. However, the proportion of infants who receive a timely birth dose is extremely low in Nigeria. We reviewed the implementation of an infant HBV vaccine schedule at a single center and identified factors affecting the receipt of a timely birth dose of HBV vaccine. We conducted a retrospective cohort study utilizing data from the INFANT study, a 2013–2017 prospective cohort study of pregnant women with and without HIV and their infants We utilized bivariate and multivariable logistic regression to assess if maternal characteristics, or the day of the week on which the infant was born were significantly associated with timely receipt of a birth dose of HBV vaccine. Receipt of HBV vaccine on the day of birth or the following calendar day were considered a timely birth dos...
Background Data on awareness of HIV status among people living with HIV (PLHIV) are critical to e... more Background Data on awareness of HIV status among people living with HIV (PLHIV) are critical to estimating progress toward epidemic control. To ascertain the accuracy of self-reported HIV status and antiretroviral drug (ARV) use in the Nigeria HIV/AIDS Indicator and Impact Survey (NAIIS), we compared self-reported HIV status with HIV rapid diagnostic test (RDT) results and self-reported ARV use with detectable blood ARV levels. Methods On the basis of responses and test results, participants were categorized by HIV status and ARV use. Self-reported HIV status and ARV use performance characteristics were determined by estimating sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV). Proportions and other analyses were weighted to account for complex survey design. Results During NAIIS, 186,405 participants consented for interview out of which 58,646 reported knowing their HIV status. Of the 959 (weighted, 1.5%) who self-reported being HIV-posi...
Background The Nigeria AIDS Indicator and Impact Survey (NAIIS), a cross-sectional household surv... more Background The Nigeria AIDS Indicator and Impact Survey (NAIIS), a cross-sectional household survey, was conducted in 2018 with primary objectives to estimate HIV prevalence, HIV-1 incidence, and status of UNAIDS 90-90-90 cascade. We conducted retrospective analysis of the performance of HIV rapid tests and the national HIV testing algorithm used in Nigeria. Methods The national algorithm included Determine HIV-1/2 as test 1 (T1), Unigold HIV-1/2 as test 2 (T2), and StatPak HIV-1/2 as the tie-breaker test (T3). Individuals reactive with T1 and either T2 or T3 were considered HIV-positive. HIV-positive specimens from the algorithm were further confirmed for the survey using supplemental test Geenius HIV-1/2. If Geenius did not confirm HIV-positive status, HIV-1 Western blot was performed. We calculated the concordance between tests and positive predictive value (PPV) of the algorithm on unweighted data. Results Of 204,930 participants (ages ≥18 months) 5,103 (2.5%) were reactive on T...
The observed epidemiology of SARS-CoV-2 in sub-Saharan Africa has varied greatly from that in Eur... more The observed epidemiology of SARS-CoV-2 in sub-Saharan Africa has varied greatly from that in Europe and the United States, with much lower reported incidence. Population-based studies are needed to estimate true cumulative incidence of SARS-CoV-2 to inform public health interventions. This study estimated SARS-CoV-2 seroprevalence in four selected states in Nigeria in October 2020. We implemented a two-stage cluster sample household survey in four Nigerian states (Enugu, Gombe, Lagos, and Nasarawa) to estimate age-stratified prevalence of SARS-CoV-2 antibodies. All individuals in sampled households were eligible for interview, blood draw, and nasal/oropharyngeal swab collection. We additionally tested participants for current/recent malaria infection. Seroprevalence estimates were calculated accounting for the complex survey design. Across all four states, 10,629 (96·5%) of 11,015 interviewed individuals provided blood samples. The seroprevalence of SARS-CoV-2 antibodies was 25·2% ...
BackgroundDrug-resistant Mycobacterium tuberculosis (Mtb) strains threaten tuberculosis (TB) cont... more BackgroundDrug-resistant Mycobacterium tuberculosis (Mtb) strains threaten tuberculosis (TB) control. We compared data on drug resistance obtained at clinics in seven high TB burden countries during routine care with whole-genome sequencing (WGS) carried out centrally.MethodsWe collected pulmonary Mtb isolates and clinical data from adult TB patients in Africa, Latin America, and Asia, stratified by HIV status and drug resistance, from 2013 to 2016. Participating sites performed drug susceptibility testing (DST) locally, using routinely available methods. WGS was done using Illumina HiSeq 2500 at laboratories in the USA and Switzerland. We used TBprofiler to analyse the genomes. We used multivariable logistic regression adjusted for sex, age, HIV-status, history of TB, sputum positivity, and Mtb-lineage to analyse mortality.FindingsWe included 582 TB patients. The median age was 32 years (interquartile range: 27-43 years), 225 (39%) were female, and 247 (42%) were HIV-positive. Base...
1Institute of Human Virology Nigeria, Maina Court, Plot 252, Herbert Macaulay Way, Central Busine... more 1Institute of Human Virology Nigeria, Maina Court, Plot 252, Herbert Macaulay Way, Central Business District, Abuja, Nigeria 2National TB and Leprosy Training Center, Saye Zaria Kaduna State, Nigeria 3Department of Medical Microbiology, University of Jos, Nigeria 4Jos University Teaching Hospital, Jos, Nigeria 5Institute of Human Virology at the University of Maryland School of Medicine Baltimore, Unites States
Multiplex assays for malaria antigen detection can gather data from large sample sets, but consid... more Multiplex assays for malaria antigen detection can gather data from large sample sets, but considerations for the consistency and quality assurance (QA) of mass testing lack evaluation. We present a QA framework for a study occurring November 2019 to March 2020 involving 504 assay plates detecting four Plasmodium antigens: pan-Plasmodium aldolase and lactate dehydrogenase (LDH), histidine-rich protein 2 (HRP2), P. vivax LDH (PvLDH). Controls on each plate included buffer blank, antigen negative blood, and 4-point positive dilution curve. The blank and negative blood provided consistently low signal for all targets except for pAldolase, which showed variability. Positive curve signals decreased throughout the 5-month study duration but retained a coefficient of variation (CV) of < 5%, with the exception of HRP2 in month 5 (CV of 11%). Regression fittings for inter-plate control signals provided mean and standard deviations (SDs), and of 504 assay plates, 6 (1.2%) violated the acce...
ObjectivesThis study evaluates the effect of Community Anti-retroviral Groups on Immunologic, Vir... more ObjectivesThis study evaluates the effect of Community Anti-retroviral Groups on Immunologic, Virologic and clinical outcomes of stable Antiretroviral Therapy patients in Nigeria.MethodA cohort of 251 eligible adults (≥18 years) on first-line ART for at least 6 months with CD4 counts >200 cells/mm3 and viral load <1000 c/ml were devolved from 10 healthcare facilities to 51 community antiretroviral therapy groups. Baseline immunologic, virologic and clinical parameters were collected and community antiretroviral therapy group patients were followed up for a year after which Human Immunodeficiency Virus treatment outcomes at the baseline and a year after follow-up were compared using paired sample t-test. All the analyses were performed in STATA version 14.ResultOut of the 251 stable antiretroviral therapy adults enrolled, 186 (75.3%) were female, 52 (22.7%) had attained post-secondary education and the mean age of participants was 38 years (SD: 9.5). Also, 66 (27.9%) were emplo...
Background: Hypertension is one of the common medical conditions observed among patients aged 50 ... more Background: Hypertension is one of the common medical conditions observed among patients aged 50 years and elder living with HIV (EPLWH) and to date no systematic review has estimated its global prevalence. Purpose: To conduct a systematic review to estimate the global prevalence of hypertension among EPLWH. Data Sources: PubMed/MEDLINE, Embase, the Cochrane Library, and Global Health databases for relevant publications up till May 25, 2018. Study Selection: Observational studies (cohort or cross-sectional studies) that estimated the prevalence of hypertension among EPLWH. Data Extraction: Required data were extracted independently by three reviewers and the main outcome was hypertension prevalence among EPLWH. Data Synthesis: The 24 (n = 29,987) eligible studies included were conducted in North America, Europe, Africa, and Asia. A low level bias threat to the estimated hypertension prevalence rates was observed. The global prevalence of hypertension among EPLWH was estimated at 42....
Background: The increasing prevalence of drug-resistant tuberculosis and the threat of extensivel... more Background: The increasing prevalence of drug-resistant tuberculosis and the threat of extensively-drug-resistant tuberculosis in HIV hotspots have made the detection and treatment of drug-resistant tuberculosis in the sub-Saharan Africa setting a global public health priority.Objective: We sought to examine the impact and challenges of tuberculosis diagnostic capacity development for the detection of drug-resistant tuberculosis and bio-surveillance using a modular biosafety level 3 (BSL-3) laboratory in Nigeria.Method: In 2010, the United States President’s Emergency Plan for AIDS Relief (PEPFAR) programme, through the Institute of Human Virology at the University of Maryland in Baltimore, Maryland, United States, deployed a modular, BSL-3 laboratory to support the national tuberculosis programme in drug-resistant tuberculosis detection and bio-surveillance for effective tuberculosis prevention and control.Results: From 2010 until present, sputum samples from 11 606 suspected cases...
BackgroundOwing to high levels of resistance to previous first-line non-nucleoside reverse transc... more BackgroundOwing to high levels of resistance to previous first-line non-nucleoside reverse transcriptase inhibitors (NNRTI)-based antiretroviral therapy (ART), consolidated recommendations since 2019, from the WHO and others, have indicated that dolutegravir (DTG) is the preferred drug of choice for HIV treatment, globally. There is a paucity of resistance outcome data from non-B HIV subtypes circulating across West Africa.AimWe aimed to characterise the mutational profiles of HIV-positive patients from a small North-East Nigeria cohort, failing a DTG-based ART regimen.MethodsPlasma samples were collected and stored from 61 HIV-1 infected participants. Following failure of DTG-based ART, all samples were sequenced by Illumina whole-genome, ultra-deep sequencing. Sequencing was successful in (n=33) participants with median age of 40 years and median time on ART of 9 years. HIV-1 subtyping was performed using SNAPPy. Haplotype reconstruction and transmission were inferred using standa...
Human Immunodeficiency Virus (HIV) diagnosis remains the gateway to HIV care and treatment. Howev... more Human Immunodeficiency Virus (HIV) diagnosis remains the gateway to HIV care and treatment. However, due to changes in HIV prevalence and testing coverage across different geopolitical zones, it is crucial to evaluate the national HIV testing algorithm as false positivity due to low prevalence could be detrimental to both the client and the service delivery. Therefore, we evaluated the performance of the national HIV rapid testing algorithm using specimens collected from multiple HIV testing services (HTS) sites and compared the results from different HIV prevalence levels across the six geopolitical zones of Nigeria. The evaluation employed a dual approach, retrospective, and prospective. The retrospective evaluation focused on a desktop review of program data (n = 492,880) collated from patients attending routine HTS from six geopolitical zones of Nigeria between January 2017 and December 2019. The prospective component utilized samples (n = 2,895) collected from the field at the ...
In settings with high tuberculosis (TB) endemicity, various genotypes of the Mycobacterium tuberc... more In settings with high tuberculosis (TB) endemicity, various genotypes of the Mycobacterium tuberculosis complex (MTBC) often differ in prevalence. However, the factors leading to these differences remain poorly understood. Here we studied the MTBC population in Dar es Salaam, Tanzania over a six-year period, using 1,082 unique patient-derived MTBC whole-genome sequences (WGS) and associated clinical data. We show that the TB epidemic in Dar es Salaam is dominated by multiple genotypes introduced to Tanzania from different parts of the world during the last 300 years. The most common MTBC genotypes deriving from these introductions exhibited differences in transmission rates and in the duration of the infectious period, but little differences in overall fitness, as measured by the effective reproductive number. Moreover, measures of disease severity and bacterial load indicated no differences in virulence between these genotypes during active TB. Instead, the combination of an early ...
The World Health Organization recommends universal vaccination of medically stable infants with H... more The World Health Organization recommends universal vaccination of medically stable infants with Hepatitis B vaccine within 24 hours of birth to prevent mother-to-child transmission of Hepatitis B virus (HBV) infection. However, the proportion of infants who receive a timely birth dose is extremely low in Nigeria. We reviewed the implementation of an infant HBV vaccine schedule at a single center and identified factors affecting the receipt of a timely birth dose of HBV vaccine. We conducted a retrospective cohort study utilizing data from the INFANT study, a 2013–2017 prospective cohort study of pregnant women with and without HIV and their infants We utilized bivariate and multivariable logistic regression to assess if maternal characteristics, or the day of the week on which the infant was born were significantly associated with timely receipt of a birth dose of HBV vaccine. Receipt of HBV vaccine on the day of birth or the following calendar day were considered a timely birth dos...
Background Data on awareness of HIV status among people living with HIV (PLHIV) are critical to e... more Background Data on awareness of HIV status among people living with HIV (PLHIV) are critical to estimating progress toward epidemic control. To ascertain the accuracy of self-reported HIV status and antiretroviral drug (ARV) use in the Nigeria HIV/AIDS Indicator and Impact Survey (NAIIS), we compared self-reported HIV status with HIV rapid diagnostic test (RDT) results and self-reported ARV use with detectable blood ARV levels. Methods On the basis of responses and test results, participants were categorized by HIV status and ARV use. Self-reported HIV status and ARV use performance characteristics were determined by estimating sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV). Proportions and other analyses were weighted to account for complex survey design. Results During NAIIS, 186,405 participants consented for interview out of which 58,646 reported knowing their HIV status. Of the 959 (weighted, 1.5%) who self-reported being HIV-posi...
Background The Nigeria AIDS Indicator and Impact Survey (NAIIS), a cross-sectional household surv... more Background The Nigeria AIDS Indicator and Impact Survey (NAIIS), a cross-sectional household survey, was conducted in 2018 with primary objectives to estimate HIV prevalence, HIV-1 incidence, and status of UNAIDS 90-90-90 cascade. We conducted retrospective analysis of the performance of HIV rapid tests and the national HIV testing algorithm used in Nigeria. Methods The national algorithm included Determine HIV-1/2 as test 1 (T1), Unigold HIV-1/2 as test 2 (T2), and StatPak HIV-1/2 as the tie-breaker test (T3). Individuals reactive with T1 and either T2 or T3 were considered HIV-positive. HIV-positive specimens from the algorithm were further confirmed for the survey using supplemental test Geenius HIV-1/2. If Geenius did not confirm HIV-positive status, HIV-1 Western blot was performed. We calculated the concordance between tests and positive predictive value (PPV) of the algorithm on unweighted data. Results Of 204,930 participants (ages ≥18 months) 5,103 (2.5%) were reactive on T...
The observed epidemiology of SARS-CoV-2 in sub-Saharan Africa has varied greatly from that in Eur... more The observed epidemiology of SARS-CoV-2 in sub-Saharan Africa has varied greatly from that in Europe and the United States, with much lower reported incidence. Population-based studies are needed to estimate true cumulative incidence of SARS-CoV-2 to inform public health interventions. This study estimated SARS-CoV-2 seroprevalence in four selected states in Nigeria in October 2020. We implemented a two-stage cluster sample household survey in four Nigerian states (Enugu, Gombe, Lagos, and Nasarawa) to estimate age-stratified prevalence of SARS-CoV-2 antibodies. All individuals in sampled households were eligible for interview, blood draw, and nasal/oropharyngeal swab collection. We additionally tested participants for current/recent malaria infection. Seroprevalence estimates were calculated accounting for the complex survey design. Across all four states, 10,629 (96·5%) of 11,015 interviewed individuals provided blood samples. The seroprevalence of SARS-CoV-2 antibodies was 25·2% ...
BackgroundDrug-resistant Mycobacterium tuberculosis (Mtb) strains threaten tuberculosis (TB) cont... more BackgroundDrug-resistant Mycobacterium tuberculosis (Mtb) strains threaten tuberculosis (TB) control. We compared data on drug resistance obtained at clinics in seven high TB burden countries during routine care with whole-genome sequencing (WGS) carried out centrally.MethodsWe collected pulmonary Mtb isolates and clinical data from adult TB patients in Africa, Latin America, and Asia, stratified by HIV status and drug resistance, from 2013 to 2016. Participating sites performed drug susceptibility testing (DST) locally, using routinely available methods. WGS was done using Illumina HiSeq 2500 at laboratories in the USA and Switzerland. We used TBprofiler to analyse the genomes. We used multivariable logistic regression adjusted for sex, age, HIV-status, history of TB, sputum positivity, and Mtb-lineage to analyse mortality.FindingsWe included 582 TB patients. The median age was 32 years (interquartile range: 27-43 years), 225 (39%) were female, and 247 (42%) were HIV-positive. Base...
1Institute of Human Virology Nigeria, Maina Court, Plot 252, Herbert Macaulay Way, Central Busine... more 1Institute of Human Virology Nigeria, Maina Court, Plot 252, Herbert Macaulay Way, Central Business District, Abuja, Nigeria 2National TB and Leprosy Training Center, Saye Zaria Kaduna State, Nigeria 3Department of Medical Microbiology, University of Jos, Nigeria 4Jos University Teaching Hospital, Jos, Nigeria 5Institute of Human Virology at the University of Maryland School of Medicine Baltimore, Unites States
Multiplex assays for malaria antigen detection can gather data from large sample sets, but consid... more Multiplex assays for malaria antigen detection can gather data from large sample sets, but considerations for the consistency and quality assurance (QA) of mass testing lack evaluation. We present a QA framework for a study occurring November 2019 to March 2020 involving 504 assay plates detecting four Plasmodium antigens: pan-Plasmodium aldolase and lactate dehydrogenase (LDH), histidine-rich protein 2 (HRP2), P. vivax LDH (PvLDH). Controls on each plate included buffer blank, antigen negative blood, and 4-point positive dilution curve. The blank and negative blood provided consistently low signal for all targets except for pAldolase, which showed variability. Positive curve signals decreased throughout the 5-month study duration but retained a coefficient of variation (CV) of < 5%, with the exception of HRP2 in month 5 (CV of 11%). Regression fittings for inter-plate control signals provided mean and standard deviations (SDs), and of 504 assay plates, 6 (1.2%) violated the acce...
ObjectivesThis study evaluates the effect of Community Anti-retroviral Groups on Immunologic, Vir... more ObjectivesThis study evaluates the effect of Community Anti-retroviral Groups on Immunologic, Virologic and clinical outcomes of stable Antiretroviral Therapy patients in Nigeria.MethodA cohort of 251 eligible adults (≥18 years) on first-line ART for at least 6 months with CD4 counts >200 cells/mm3 and viral load <1000 c/ml were devolved from 10 healthcare facilities to 51 community antiretroviral therapy groups. Baseline immunologic, virologic and clinical parameters were collected and community antiretroviral therapy group patients were followed up for a year after which Human Immunodeficiency Virus treatment outcomes at the baseline and a year after follow-up were compared using paired sample t-test. All the analyses were performed in STATA version 14.ResultOut of the 251 stable antiretroviral therapy adults enrolled, 186 (75.3%) were female, 52 (22.7%) had attained post-secondary education and the mean age of participants was 38 years (SD: 9.5). Also, 66 (27.9%) were emplo...
Background: Hypertension is one of the common medical conditions observed among patients aged 50 ... more Background: Hypertension is one of the common medical conditions observed among patients aged 50 years and elder living with HIV (EPLWH) and to date no systematic review has estimated its global prevalence. Purpose: To conduct a systematic review to estimate the global prevalence of hypertension among EPLWH. Data Sources: PubMed/MEDLINE, Embase, the Cochrane Library, and Global Health databases for relevant publications up till May 25, 2018. Study Selection: Observational studies (cohort or cross-sectional studies) that estimated the prevalence of hypertension among EPLWH. Data Extraction: Required data were extracted independently by three reviewers and the main outcome was hypertension prevalence among EPLWH. Data Synthesis: The 24 (n = 29,987) eligible studies included were conducted in North America, Europe, Africa, and Asia. A low level bias threat to the estimated hypertension prevalence rates was observed. The global prevalence of hypertension among EPLWH was estimated at 42....
Background: The increasing prevalence of drug-resistant tuberculosis and the threat of extensivel... more Background: The increasing prevalence of drug-resistant tuberculosis and the threat of extensively-drug-resistant tuberculosis in HIV hotspots have made the detection and treatment of drug-resistant tuberculosis in the sub-Saharan Africa setting a global public health priority.Objective: We sought to examine the impact and challenges of tuberculosis diagnostic capacity development for the detection of drug-resistant tuberculosis and bio-surveillance using a modular biosafety level 3 (BSL-3) laboratory in Nigeria.Method: In 2010, the United States President’s Emergency Plan for AIDS Relief (PEPFAR) programme, through the Institute of Human Virology at the University of Maryland in Baltimore, Maryland, United States, deployed a modular, BSL-3 laboratory to support the national tuberculosis programme in drug-resistant tuberculosis detection and bio-surveillance for effective tuberculosis prevention and control.Results: From 2010 until present, sputum samples from 11 606 suspected cases...
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