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OBJECTIVE To describe the prevalence of HIV viral suppression and assess the factors associated with HIV viral suppression among persons receiving ART in Malawi in 2021. METHODS Implementation study using routinely collected patient-level HIV RNA-PCR test result data extracted from the national Laboratory Management Information System (LIMS) database managed by the Department of HIV/AIDS in 2021. We calculated frequencies, proportions and odds ratios (OR) of HIV viral suppression with their associated 95% confidence intervals (95%CI). We performed a random-effects logistic regression to determine the risk factors associated with HIV viral suppression amongst ART patients, controlling for the spatial autocorrelation between districts and adjusting for other variables. RESULTS We evaluated 515,797 adults and children receiving ART and having a viral load test in 2021. Of these, 92.8% had HIV viral suppression. ART patients living in urban areas had lower likelihood of HIV viral suppression than those living in rural areas (adjusted OR [aOR]=0.95, 95%CI: 0.92-0.99, P=0.01). There was an increasing trend in HIV viral suppression with increasing ART duration. Routine VL monitoring samples were 39% more likely to have suppressed VL values than confirmatory HIV VL monitoring samples (aOR=1.39; 95%CI:1.34-1.43, P

BackgroundLiterature Reviews (LRs) identify, evaluate, and synthesise relevant papers to a particular research question to advance understanding and support decision making. However, LRs, especially traditional systematic reviews are slow, resource intensive, and are outdated quickly.ObjectiveUsing recent Natural Language Processing (NLP) and Unsupervised Machine Learning (UML) methods, this paper presents a tool named LiteRev that supports researchers in conducting LRs.MethodsBased on the user’s query, LiteRev can perform an automated search on different open-access databases and retrieve relevant metadata on the resulting papers. Papers (abstracts or full texts) are text processed and represented as a Term Frequency-Inverse Document Frequency (TF-IDF) matrix. Using dimensionality reduction (PaCMAP) and clustering (HDBSCAN) techniques, the corpus is divided into different topics described by a list of keywords. The user can select one or several topics of interest, enter additional keywords to refine their search, or provide key papers to the research question. Based on these inputs, LiteRev performs an iterative nearest neighbours search, and suggests a list of potentially interesting papers. The user can tag the relevant ones and trigger a new search until no additional paper is suggested for screening. To assess the performance of LiteRev, we ran it in parallel to a manual LR on the burden and care for acute and early HIV infection in sub-Saharan Africa. We assessed the performance of LiteRev using True and False Predictive Values, recall and Work Saved over Sampling.ResultsWe extracted, text processed and represented into a TF-IDF matrix 631 unique papers from PubMed. The topic modelling module identified 5 main topics and 16 topics (ranging from 13 to 98 papers) and extracted the 10 most important keywords for each. Then, based on 18 key papers, we were able to identify 2 topics of interest with 7 key papers in each of them. Finally, we ran the k-nearest neighbours module and LiteRev suggested first a list of 110 papers for screening, among which 45 papers were confirmed as relevant. From these 45 papers, LiteRev suggested 26 additional papers, out of which 8 were confirmed as relevant. At the end of the iterative process (4 iterations), 193 papers out of 613 papers in total (31.5% of the whole corpus) were suggested by LiteRev. After title/abstract screening, LiteRev identified 64 out of the 87 relevant papers (i.e., recall of 73.6%). After full text screening, LiteRev identified 42 out of the 48 relevant papers (i.e., recall of 87.5%, and Work Saved over Sampling of 56.0%).ConclusionsWe presented LiteRev, an automation tool that uses NLP and UML methods to streamline and accelerate LRs and to support researchers in getting quick and in-depth overviews on any topic of interest.

BackgroundDespite the high availability of individual-level data of infants accessing HIV DNA polymerase chain reaction (DNA-PCR) testing service, there has been little in-depth analysis of such data. Therefore, we describe spatial and temporal trends in risk of HIV infection among Malawi’s HIV-exposed infants (HEI) with DNA-PCR HIV test result from 2013 to 2020.MethodsThis is an implementation study using routinely collected patient-level HIV DNA-PCR test result data extracted from the national Laboratory Management Information System database managed by the Department of HIV/AIDS between 1 January 2013 and 30 June 2020. We calculated frequencies, proportions and odds ratios (OR) with their associated 95% confidence intervals (95%CI). We performed a random-effects logistic regression to determine the risk factors associated with HIV infection in infants, controlling for the spatial autocorrelation between districts and adjusting for other variables.ResultsWe evaluated 255,229 HEI across 750 facilities in 28 districts. The overall risk of HIV infection among all tested HEI between 2013 and 2020 was 7.2% (95%CI: 7.1-7.3). We observed a decreasing trend in the proportion of HEI that tested HIV positive from 7.0% (95%CI: 6.6-7.4) in 2013 to 5.7% (95%CI: 5.4-5.9) in 2015 followed by an increase to 9.9% (95%CI: 9.6-10.2) in 2017 and then a decreasing trend to 4.2% (95%CI: 3.7-4.6) in 2020. The risk of HIV infection increased by age of the HEI. There was spatial heterogeneity of HIV prevalence between districts of Malawi.ConclusionWe summarised spatial and temporal trends of risk of HIV infection amongst HEI in Malawi between 2013 and 2020. There is need for further strengthening of EID program to ensure that all the HEI are enrolled in care by eight weeks of age in order to further reduce mother-to-child transmission of HIV.Key messageThere is need for further strengthening of the Malawi early infant diagnosis program to ensure that all the HIV-exposed infants are enrolled in care by eight weeks of age in order to eliminate mother-to-child transmission of HIV by 2030.What is known about the study?Malawi has implemented the Early Infant Diagnosis (EID) since 2009. Most of the studies on EID in Malawi have focused on just one or two health facilities.What the study adds?This is to our knowledge the first in-depth analysis of national routine data on HIV DNA-PCR tests among HIV-exposed infants with in Malawi. Our study has shown that there is spatial and temporal heterogeneity in risk of HIV infection amongst the HEI in Malawi between 2013 and 2020.

ObjectiveTo describe the trends in the incidence rate of HIV VL rebound and assess the factors associated with the incidence rate of HIV VL rebound among the persons receiving ART in Malawi between 2011 and 2020.MethodsWe analyzed routinely collected patient-level HIV VL data extracted from the Malawi Laboratory Management Information System (LIMS). We fitted a multivariable Cox regression model of having HIV VL rebound (>1000 copies/mL) using a forward step-wise selection method, with age and sex entered as a priori variables. We presented both crude and adjusted hazard ratios (aHR) of HIV VL rebound for the various independent variables. Statistical significance was set at PResultsWe evaluated 230,465 adults and children receiving ART and having at least one viral load test between 2011 and 2020. The median time between ART initiation and having a VL sample was 55 months (interquartile range: 25-92). The aHR for having HIV VL rebound were: 0.79 for females (95%CI:0.77-0.80, PConclusionThis is the first national analysis of Malawi HIV VL data from LIMS. Our findings show the need to take into account the geographic and demographic characteristics of the patients in order to persistently suppress HIV VL and consequently achieve 95% HIV VL suppression by 2030.

BackgroundAlthough the COVID-19 pandemic has resulted in lower reported number of cases and deaths within the paediatric population, indirect impacts on the health of children in Sub-Saharan Africa such as malnutrition are evident. Data on the socioeconomic factors affecting malnutrition in the under-age population of Sub-Saharan Africa brought by the COVID-19 pandemic remain limited. This paper assesses socioeconomic factors of malnutrition in relation with COVID-19 and potential mitigating measures.MethodsA scoping review of PubMed, Embase, and Web of Science from March 11, 2020, to May 1, 2021, was conducted. The included studies focused on COVID-19, children malnutrition, and Sub-Saharan Africa and adhered to the PRISMA guideline.ResultsAmong 73 total screened articles, 15 studies filled the inclusion criteria. The identified socioeconomic factors leading to malnutrition in children were reduction in average income or increase in unemployment rate, access to healthcare and food supplements, disrupted food supply chains and increased prices of food products, pauses in humanitarian responses, and reduced access to school-based meals. Potential mitigation measures were food subsidies, food price control measures, the identification of new vulnerable groups and the implementation of financial interventions.ConclusionMalnutrition amongst Sub-Saharan African children due to COVID-19 is a result of a combination of multiple socioeconomic factors. To stabilize household purchasing power and eventually malnutrition in children in SSA, a combined strategy of initial detection of newly developing vulnerable groups and efficient, rapid financial assistance through mobile phone transfers was suggested. These strategies were proposed in combination with other economical models.

The extent of SARS-CoV-2 circulation in many African countries remains unclear, underlining the need for antibody sero-surveys to assess the cumulative attack rate. Here, we present the results of a cross-sectional sero-survey of a random sample of residents of a health district in Yaoundé, Cameroon, conducted from October 14 to November 26, 2020. Among the 971 participants, the test-adjusted seroprevalence of anti-SARS-CoV-2 IgG antibodies was 29·2% (95%CI 24·3–34·1). This is about 323 times greater than the 0.09% nationwide attack rate implied by COVID-19 case counts at the time. Men, obese individuals and those living in large households were significantly more likely to be seropositive, and the majority (64·2% [58·7–69·4]) of seropositive individuals reported no symptoms. Despite the high seroprevalence, most of the population had not been infected with SARS-CoV-2, highlighting the importance of continued measures to control viral spread and quick vaccine deployment to protect the vulnerable.

The extent of SARS-CoV-2 circulation in many African countries remains unclear, underlining the need for antibody sero-surveys to assess the cumulative attack rate. Here, we present the results of a cross-sectional sero-survey of a random sample of residents of a health district in Yaounde, Cameroon, conducted from October 14 to November 26, 2020. Among the 971 participants, the test-adjusted seroprevalence of anti-SARS-CoV-2 IgG antibodies was 29·2% (95% CI 24·3–34·1). This is about 322 times greater than the 0.09% nationwide attack rate implied by COVID-19 case counts at the time. Men, obese individuals and those living in large households were significantly more likely to be seropositive, and the majority (64·2% [58·7–69·4]) of seropositive individuals reported no symptoms. Despite the high seroprevalence, most of the population had not been infected with SARS-CoV-2, highlighting the importance of continued measures to control viral spread and quick vaccine deployment to protect the vulnerable., Many African countries have reported relatively low numbers of COVID-19 cases but the true scale of the epidemic is unclear. Here, the authors conduct a population-based survey in a province of Cameroon and estimate 29% seroprevlance, >300 fold higher than the nationwide attack rate implied by case counts.

High yield HIV testing strategies are critical to reach epidemic control in high prevalence and low-resource settings such as East and Southern Africa. In this study, we aimed to predict the HIV status of individuals living in Angola, Burundi, Ethiopia, Lesotho, Malawi, Mozambique, Namibia, Rwanda, Zambia and Zimbabwe with the highest precision and sensitivity for different policy targets and constraints based on a minimal set of socio-behavioural characteristics.We analysed the most recent Demographic and Health Survey from these 10 countries to predict individual's HIV status using four different algorithms (a penalized logistic regression, a generalized additive model, a support vector machine, and a gradient boosting trees). The algorithms were trained and validated on 80% of the data, and tested on the remaining 20%. We compared the predictions based on the F1 score, the harmonic mean of sensitivity and positive predictive value (PPV), and we assessed the generalization of our models by testing them against an independent left-out country. The best performing algorithm was trained on a minimal subset of variables which were identified as the most predictive, and used to 1) identify 95% of people living with HIV (PLHIV) while maximising precision and 2) identify groups of individuals by adjusting the probability threshold of being HIV positive (90% in our scenario) for achieving specific testing strategies.Overall 55,151 males and 69,626 females were included in the analysis. The gradient boosting trees algorithm performed best in predicting HIV status with a mean F1 score of 76.8% [95% confidence interval (CI) 76.0%-77.6%] for males (vs [CI 67.8%-70.6%] for SVM) and 78.8% [CI 78.2%-79.4%] for females (vs [CI 73.4%-75.8%] for SVM). Among the ten most predictive variables for each sex, nine were identical: longitude, latitude and, altitude of place of residence, current age, age of most recent partner, total lifetime number of sexual partners, years lived in current place of residence, condom use during last intercourse and, wealth index. Only age at first sex for male (ranked 10th) and Rohrer's index for female (ranked 6th) were not similar for both sexes. Our large-scale scenario, which consisted in identifying 95% of all PLHIV, would have required testing 49.4% of males and 48.1% of females while achieving a precision of 15.4% for males and 22.7% for females. For the second scenario, only 4.6% of males and 6.0% of females would have had to be tested to find 55.7% of all males and 50.5% of all females living with HIV.We trained a gradient boosting trees algorithm to find 95% of PLHIV with a precision twice higher than with general population testing by using only a limited number of socio-behavioural characteristics. We also successfully identified people at high risk of infection who may be offered pre-exposure prophylaxis or voluntary medical male circumcision. These findings can inform the implementation of new high-yield HIV tests and help develop very precise strategies based on low-resource settings constraints.

This study analysed the reported incidence of COVID-19 and associated epidemiological and socio-economic factors in the WHO African region. Data from COVID-19 confirmed cases and SARS-CoV-2 tests reported to the WHO by Member States between 25 February and 31 December 2020 and publicly available health and socio-economic data were analysed using univariate and multivariate binomial regression models. The overall cumulative incidence was 1846 cases per million population. Cape Verde (21 350 per million), South Africa (18 060 per million), Namibia (9840 per million), Eswatini (8151 per million) and Botswana (6044 per million) recorded the highest cumulative incidence, while Benin (260 per million), Democratic Republic of Congo (203 per million), Niger (141 cases per million), Chad (133 per million) and Burundi (62 per million) recorded the lowest. Increasing percentage of urban population (β= −0.011,P= 0.04) was associated with low cumulative incidence, while increasing number of cumulative SARS-CoV-2 tests performed per 10 000 population (β= 0.0006,P= 0.006) and the proportion of population aged 15–64 years (adjustedβ= 0.174,P< 0.0001) were associated with high COVID-19 cumulative incidence. With limited testing capacities and overwhelmed health systems, these findings highlight the need for countries to increase and decentralise testing capacities and adjust testing strategies to target most at-risk populations.

BACKGROUND Demographic and sociobehavioral factors are strong drivers of HIV infection rates in sub-Saharan Africa. These factors are often studied in qualitative research but ignored in quantitative analyses. However, they provide in-depth insight into the local behavior and may help to improve HIV prevention. OBJECTIVE To obtain a comprehensive overview of the sociobehavioral factors influencing HIV prevalence and incidence in Malawi, we systematically reviewed the literature using a newly programmed tool for automatizing part of the systematic review process. METHODS Due to the choice of broad search terms (“HIV AND Malawi”), our preliminary search revealed many thousands of articles. We, therefore, developed a Python tool to automatically extract, process, and categorize open-access articles published from January 1, 1987 to October 1, 2019 in the PubMed, PubMed Central, JSTOR, Paperity, and arXiV databases. We then used a topic modelling algorithm to classify and identify publications of interest. RESULTS Our tool extracted 22,709 unique articles; 16,942 could be further processed. After topic modelling, 519 of these were clustered into relevant topics, of which 20 were kept after manual screening. We retrieved 7 more publications after examining the references so that 27 publications were finally included in the review. Reducing the 16,942 articles to 519 potentially relevant articles using the software took 5 days. Several factors contributing to the risk of HIV infection were identified, including religion, gender and relationship dynamics, beliefs, and sociobehavioral attitudes. CONCLUSIONS Our software does not replace traditional systematic reviews, but it returns useful results to broad queries of open-access literature in under a week, without a priori knowledge. This produces a “seed dataset” of relevance that could be further developed. It identified known factors and factors that may be specific to Malawi. In the future, we aim to expand the tool by adding more social science databases and applying it to other sub-Saharan African countries.

Background Demographic and sociobehavioral factors are strong drivers of HIV infection rates in sub-Saharan Africa. These factors are often studied in qualitative research but ignored in quantitative analyses. However, they provide in-depth insight into the local behavior and may help to improve HIV prevention. Objective To obtain a comprehensive overview of the sociobehavioral factors influencing HIV prevalence and incidence in Malawi, we systematically reviewed the literature using a newly programmed tool for automatizing part of the systematic review process. Methods Due to the choice of broad search terms (“HIV AND Malawi”), our preliminary search revealed many thousands of articles. We, therefore, developed a Python tool to automatically extract, process, and categorize open-access articles published from January 1, 1987 to October 1, 2019 in the PubMed, PubMed Central, JSTOR, Paperity, and arXiV databases. We then used a topic modelling algorithm to classify and identify publications of interest. Results Our tool extracted 22,709 unique articles; 16,942 could be further processed. After topic modelling, 519 of these were clustered into relevant topics, of which 20 were kept after manual screening. We retrieved 7 more publications after examining the references so that 27 publications were finally included in the review. Reducing the 16,942 articles to 519 potentially relevant articles using the software took 5 days. Several factors contributing to the risk of HIV infection were identified, including religion, gender and relationship dynamics, beliefs, and sociobehavioral attitudes. Conclusions Our software does not replace traditional systematic reviews, but it returns useful results to broad queries of open-access literature in under a week, without a priori knowledge. This produces a “seed dataset” of relevance that could be further developed. It identified known factors and factors that may be specific to Malawi. In the future, we aim to expand the tool by adding more social science databases and applying it to other sub-Saharan African countries.

BackgroundDemographic and socio-behavioural factors are strong drivers of HIV infection rates in sub-Saharan Africa. These factors are often studied in qualitative research but ignored in quantitative analyses. However, they provide an in-depth insight into the local behaviour, and may help to improve HIV prevention.MethodsTo obtain a comprehensive overview of the socio-behavioural factors influencing HIV prevalence and incidence in Malawi, we systematically reviewed the literature. Due to the choice of broad search terms (“HIV AND Malawi”), our preliminary search revealed many thousands of articles. We, therefore, developed a Python tool to automatically extract, process, and categorise open-access articles published from January 1st, 1987 until October 1st, 2019 in Pubmed, Pubmed Central, JSTOR, Paperity, and arXiV databases. We then used a topic modelling algorithm to classify and identify publications of interest.ResultsOur tool extracted 22’709 unique articles; 16’942 could be further processed. After topic modelling, 519 of these were clustered into relevant topics; 20 of which were kept after hand-screening. We retrieved 7 more publications after examining references so that 27 publications were finally included in the review. Reducing the 16’942 articles to 519 potentially relevant ones by using the software took 5 days. Several factors were identified to contribute to the risk of HIV infection, including religion, gender and relationship dynamics, beliefs, and socio-behavioural attitudes.ConclusionsOur software does not replace traditional systematic reviews, but it returns useful results to broad queries of open-access literature in under a week, without a priori knowledge. This produces a “seed data-set” of relevance which could be further developed. It identified known factors and rare factors that may be specific to Malawi. In the future, we aim to expand the tool by adding more social science databases and applying it to other sub-Saharan African countries.

Background: We aimed to estimate the disease burden of Tuberculosis (TB) and return on investment of TB care in the Western Pacific Region (WPR) until 2030. Methods: We projected the TB epidemic in Viet Nam and Lao People’s Democratic Republic (PDR) for the years 2020-30 with TIME Impact model under various scenarios: no TB care; baseline (TB care continues at current levels); and several interventions. We extracted literature results for China and the Philippines to estimate region-level incidence and deaths. We used a Solow model to estimate the return on investment of TB care and interventions. Findings: In the baseline scenario, TB incidence in the WPR decreased from 95·2/100,000/year (2019) to 91·5/100,000/year (2030), and TB deaths from 79,000/year (2019) to 68,100/year (2030). Active case finding (ACF) strategies (screening people not seeking care for respiratory symptoms) were the most effective single intervention. A combination intervention resulted in TB incidence of 43·9/100,000/year and 18,000 TB deaths in 2030. Estimated return on investment (2020-2030) for TB care in Viet Nam and Lao PDR ranged US$4 to US$49 per dollar spent, Additional interventions brought returns of up to US$2·7 per dollar spent. Interpretation: TB incidence will only modestly decrease in the WPR without additional interventions. Intervention strategies that include ACF can reduce TB burden, but achieving the End TB incidence and mortality targets will be difficult without new transformational tools. TB care can bring a multiple-fold return on investment. Funding Statement: This study was funded by the World Health Organization Western Pacific Regional Office and the Swiss National Science Foundation (grant 163878). Declaration of Interests: We declare no competing interests.

IntroductionHIV incidence varies widely between sub-Saharan African (SSA) countries. This variation coincides with a substantial sociobehavioural heterogeneity, which complicates the design of effective interventions. In this study, we investigated how sociobehavioural heterogeneity in sub-Saharan Africa could account for the variance of HIV incidence between countries.MethodsWe analysed aggregated data, at the national-level, from the most recent Demographic and Health Surveys of 29 SSA countries [2010-2017], which included 594’644 persons (183’310 men and 411’334 women). We preselected 48 demographic, socio-economic, behavioural and HIV-related attributes to describe each country. We used Principal Component Analysis to visualize sociobehavioural similarity between countries, and to identify the variables that accounted for most sociobehavioural variance in SSA. We used hierarchical clustering to identify groups of countries with similar sociobehavioural profiles, and we compared the distribution of HIV incidence (estimates from UNAIDS) and sociobehavioural variables within each cluster.ResultsThe most important characteristics, which explained 69% of sociobehavioural variance across SSA among the variables we assessed were: religion; male circumcision; number of sexual partners; literacy; uptake of HIV testing; women’s empowerment; accepting attitude toward people living with HIV/AIDS; rurality; ART coverage; and, knowledge about AIDS. Our model revealed three groups of countries, each with characteristic sociobehavioural profiles. HIV incidence was mostly similar within each cluster and different between clusters (median(IQR); 0.5/1000(0.6/1000), 1.8/1000(1.3/1000) and 5.0/1000(4.2/1000)).