Diagnosing paediatric tuberculosis (TB) remains challenging. Currently available diagnostic tests have limited accuracy, and most sampling methods are invasive. In 2021, the World Health Organisation (WHO) endorsed the use of molecular WHO-recommended rapid diagnostic tests (mWRDs) with stool as an initial diagnostic tool for paediatric TB. In this study, we evaluated the diagnostic test accuracy (DTA) of stool samples processed with the Stool Processing Kit (SPK), one of three centrifugation-free methods available at the time. We conducted a multi-centre prospective diagnostic validation study in South Africa, Tanzania, Malawi, Mozambique, and India. Children (< 15 years) under investigation for TB provided at least two (induced) sputum samples at enrolment, one stool sample, and one nasopharyngeal aspirate (NPA) if aged < 5 years and a chest x-ray. TB testing included Xpert® MTB/RIF Ultra (Ultra) and culture. Diagnostic classification followed NIH consensus statements. Stool samples were processed using the SPK and tested with Ultra. We calculated DTA in the overall cohort and predefined subgroups of interest. Out of 5313 children screened, 975 were enrolled, and data from 817 children recruited between January 2019 and June 2021 were analysed. The overall microbiological confirmation rate was 203/817 (24.9

Background In 2020, the WHO-approved Molbio Truenat platform and MTB assays to detect Mycobacterium tuberculosis complex ( MTB ) and resistance to rifampicin directly on sputum specimens. This primary health care center-based trial in Mozambique and Tanzania investigates the effect of Truenat platform/MTB assays (intervention arm) combined with rapid communication of results compared to standard of care on TB diagnosis and treatment initiation for microbiologically confirmed TB at 7 days from enrolment. Methods The Tuberculosis Close the Gap, Increase Access, and Provide Adequate Therapy (TB-CAPT) CORE trial employs a pragmatic cluster randomized controlled design to evaluate the impact of a streamlined strategy for delivery of Truenat platform/MTB assays testing at primary health centers. Twenty-nine centers equipped with TB microscopy units were selected to participate in the trial. Among them, fifteen health centers were randomized to the intervention arm (which involves onsite molecular testing using Truenat platform/MTB assays, process process optimization to enable same-day TB diagnosis and treatment initiation, and feedback on Molbio platform performance) or the control arm (which follows routine care, including on-site sputum smear microscopy and the referral of sputum samples to off-site Xpert testing sites). The primary outcome of the study is the absolute number and proportion of participants with TB microbiological confirmation starting TB treatment within 7 days of their first visit. Secondary outcomes include time to bacteriological confirmation, health outcomes up to 60 days from first visit, as well as user preferences, direct cost, and productivity analyses. Ethics and dissemination TB-CAPT CORE trial has been approved by regulatory and ethical committees in Mozambique and Tanzania, as well as by each partner organization. Consent is informed and voluntary, and confidentiality of participants is maintained throughout. Study findings will be presented at scientific conferences and published in peer-reviewed international journals. Trial Registration US National Institutes of Health’s ClinicalTrials.gov, NCT04568954. Registered 23 September 2020.

Early diagnosis of SARS-CoV-2 is fundamental to reduce the risk of community transmission and mortality, as well as public sector expenditures. Three years after the onset of the SARS-CoV-2 pandemic, there are still gaps on what is known regarding costs and cost drivers for the major diagnostic testing strategies in low- middle-income countries (LMICs). This study aimed to estimate the cost of SARS-CoV-2 diagnosis of symptomatic suspected patients by reverse transcription polymerase chain reaction (RT-PCR) and antigen rapid diagnostic tests (Ag-RDT) in Mozambique. We conducted a retrospective cost analysis from the provider’s perspective using a bottom-up, micro-costing approach, and compared the direct costs of two nasopharyngeal Ag-RDTs (Panbio and Standard Q) against the costs of three nasal Ag-RDTs (Panbio, COVIOS and LumiraDx), and RT-PCR. The study was undertaken from November 2020 to December 2021 in the country’s capital city Maputo, in four healthcare facilities at primary, secondary and tertiary levels of care, and at one reference laboratory. All the resources necessary for RT-PCR and Ag-RDT tests were identified, quantified, valued, and the unit costs per test and per facility were estimated. Our findings show that the mean unit cost of SARS-CoV-2 diagnosis by nasopharyngeal Ag-RDTs was MZN 728.00 (USD 11.90, at 2020 exchange rates) for Panbio and MZN 728.00 (USD 11.90) for Standard Q. For diagnosis by nasal Ag-RDTs, Panbio was MZN 547.00 (USD 8.90), COVIOS was MZN 768.00 (USD 12.50), and LumiraDx was MZN 798.00 (USD 13.00). Medical supplies expenditures represented the main driver of the final cost (>50%), followed by personnel and overhead costs (mean 15% for each). The mean unit cost regardless of the type of Ag-RDT was MZN 714.00 (USD 11.60). Diagnosis by RT-PCR cost MZN 2,414 (USD 39.00) per test. Our sensitivity analysis suggests that focussing on reducing medical supplies costs would be the most cost-saving strategy for governments in LMICs, particularly as international prices decrease. The cost of SARS-CoV-2 diagnosis using Ag-RDTs was three times lower than RT-PCR testing. Governments in LMICs can include cost-efficient Ag-RDTs in their screening strategies, or RT-PCR if international costs of such supplies decrease further in the future. Additional analyses are recommended as the costs of testing can be influenced by the sample referral system.

Mozambique reported the first case of coronavirus disease 2019 (COVID-19) in March 2020 and it has since spread to all provinces in the country. To investigate the introductions and spread of SARS-CoV-2 in Mozambique, 1 142 whole genome sequences sampled within Mozambique were phylogenetically analyzed against a globally representative set, reflecting the first 25 months of the epidemic. The epidemic in the country was marked by four waves of infection, the first associated with B.1 ancestral lineages, while the Beta, Delta, and Omicron Variants of Concern (VOCs) were responsible for most infections and deaths during the second, third, and fourth waves. Large-scale viral exchanges occurred during the latter three waves and were largely attributed to southern African origins. Not only did the country remain vulnerable to the introductions of new variants but these variants continued to evolve within the borders of the country. Due to the Mozambican health system already under constraint, and paucity of data in Mozambique, there is a need to continue to strengthen and support genomic surveillance in the country as VOCs and Variants of interests (VOIs) are often reported from the southern African region.

BACKGROUND:Childhood tuberculosis remains a major cause of morbidity and mortality in part due to missed diagnosis. Diagnostic methods with enhanced sensitivity using easy-to-obtain specimens are needed. We aimed to assess the diagnostic accuracy of the Cepheid Mycobacterium tuberculosis Host Response prototype cartridge (MTB-HR), a candidate test measuring a three-gene transcriptomic signature from fingerstick blood, in children with presumptive tuberculosis disease. METHODS:RaPaed-TB was a prospective diagnostic accuracy study conducted at four sites in African countries (Malawi, Mozambique, South Africa, and Tanzania) and one site in India. Children younger than 15 years with presumptive pulmonary or extrapulmonary tuberculosis were enrolled between Jan 21, 2019, and June 30, 2021. MTB-HR was performed at baseline and at 1 month in all children and was repeated at 3 months and 6 months in children on tuberculosis treatment. Accuracy was compared with tuberculosis status based on standardised microbiological, radiological, and clinical data. FINDINGS:5313 potentially eligible children were screened, of whom 975 were eligible. 784 children had MTB-HR test results, of whom 639 had a diagnostic classification and were included in the analysis. MTB-HR differentiated children with culture-confirmed tuberculosis from those with unlikely tuberculosis with a sensitivity of 59·8% (95% CI 50·8-68·4). Using any microbiological confirmation (culture, Xpert MTB/RIF Ultra, or both), sensitivity was 41·6% (34·7-48·7), and using a composite clinical reference standard, sensitivity was 29·6% (25·4-34·2). Specificity for all three reference standards was 90·3% (95% CI 85·5-94·0). Performance was similar in different age groups and by malnutrition status. Among children living with HIV, accuracy against the strict reference standard tended to be lower (sensitivity 50·0%, 15·7-84·3) compared with those without HIV (61·0%, 51·6-69·9), although the difference did not reach statistical significance. Combining baseline MTB-HR result with one Ultra result identified 71·2% of children with microbiologically confirmed tuberculosis. INTERPRETATION:MTB-HR showed promising diagnostic accuracy for culture-confirmed tuberculosis in this large, geographically diverse, paediatric cohort and hard-to-diagnose subgroups. FUNDING:European and Developing Countries Clinical Trials Partnership, UK Medical Research Council, Swedish International Development Cooperation Agency, Bundesministerium für Bildung und Forschung; German Center for Infection Research (DZIF).

Background In 2021, an estimated 4800 people developed rifampicin-resistant tuberculosis in Mozambique, 75% of which went undiagnosed. Detailed molecular data on rifampicin-resistant and multidrug-resistant (MDR) tuberculosis are not available. Here, we aimed at gaining precise data on the determinants of rifampicin-resistant and MDR tuberculosis in Mozambique. Methods In this retrospective observational study, we performed whole-genome sequencing of 704 rifampicin-resistant Mycobacterium tuberculosis complex (Mtbc) strains submitted to the National Tuberculosis Reference Laboratory (NTRL) in Maputo, Mozambique, between 2015 and 2021. Phylogenetic strain classification, genomic resistance prediction, and cluster analysis were performed. Findings Between Jan 1, 2015, and July 31, 2021, 2606 Mtbc isolates with an isoniazid or rifampicin resistance were identified in the NTRL biobank, of which, 1483 (56·9%) were from men, 1114 (42·7%) from women, and nine (0·4%) were unknown. Genome-based drug-resistant prediction classified 704 Mtbc strains as rifampicin resistant. 628 (89%) of the 704 Mtbc strains were classified MDR; of those, 146 (23%) were pre-extensively drug resistant (pre-XDR; additional fluoroquinolone resistance), and 24 (4%) extensively drug resistant (XDR; combined fluoroquinolone and bedaquiline resistance). Overall, 61 (9%) of 704 strains revealed resistance to bedaquiline: five (7%) of 76 rifampicin resistant plus bedaquiline resistant, 32 (7%) of 458 MDR plus bedaquiline resistant, and 24 (100%) of 24 XDR. Prevalence of bedaquiline resistance increased from 3% in 2016 to 14% in 2021. The cluster rate (12 single-nucleotide polymorphism threshold) was 42% for rifampicin-resistant strains, 78% for MDR strains, 94% for pre-XDR strains, and 96% for XDR Mtbc strains. 31 (4%) of 704 Mtbc strains, belonging to a diagnostic escape outbreak strain previously described in Eswatini (group_56), had an rpoB Ile491Phe mutation which is not detected by Xpert MTB/RIF (no other rpoB mutation). Of these, 23 (74%) showed additional resistance to bedaquiline, 13 (42%) had bedaquiline and fluoroquinolone resistance, and two (6%) were bedaquiline, fluoroquinolone, and delamanid resistant. Interpretation Pre-XDR resistance is highly prevalent among MDR Mtbc strains in Mozambique and so is bedaquiline resistance; and the frequency of bedaquiline resistance quadrupled over time and was found even in Mtbc strains without fluoroquinolone resistance. Importantly, strains with Ile491Phe mutation were frequent, accounting for 31% (n=10) of MDR plus bedaquiline-resistant strains and 54% (n=13) of XDR Mtbc strains. Given the current diagnostic algorithms and treatment regimens, both the emergence of rifampicin resistance due to Ile491Phe and bedaquiline resistance might jeopardise MDR tuberculosis prevention and care unless sequencing-based technology is rolled out. The potential cross border spread of diagnostic escape strains needs further investigation. Funding The German Ministry of Health through the Seq_MDRTB-Net project, the Deutsche Forschungsgemeinschaft under Germany's Excellence Strategy Precision Medicine in Inflammation and the Research Training Group 2501 TransEvo, the Leibniz Science Campus Evolutionary Medicine of the Lung, and the German Ministry of Education and Research via the German Center for Infection Research.

ABSTRACT Dried blood spot (DBS) may overestimate the viral RNA, mainly in patients with low viral load (VL), due to proviral DNA and intracellular RNA. The Burnett and HemaSpot provide integrated solutions for the collection, separation, and drying of plasma from whole blood. This study aims to evaluate the performance of both devices compared to plasma to identify antiretroviral therapy (ART) failure. The devices were separately evaluated in a cross-sectional design. Patients on ART were included for the studies (Burnett: 611, October 2019 to January 2020) and (HemaSpot: 620, November 2020 to April 2021). VL was tested using CAP/CTM96. The sensitivity and specificity of DBS, Burnett, and HemaSpot were determined, and plasma results were considered as a reference at a threshold of 1,000 copies/ml. For the Burnett study, 2,444 specimens, including plasma, DBS, venous Burnett (vBurnett), and capillary Burnett (cBurnett), were collected. Sensitivity of DBS, vBurnett, and cBurnett was 97.4%, 98.3%, and 97.5%, respectively, whereas specificity was 86.8% for DBS, 96.9% for vBurnett, and 93.9% for cBurnett. For the HemaSpot study, 1,860 specimens were collected, including plasma, DBS, and vHemaSpot. Sensitivity of DBS and vHemaSpot was 95.0% and 91.3%, respectively, whereas specificity was 86.9% for DBS and 94.5% for vHemaSpot. The misclassification rate was more prominent in DBS (4.8%) and HemaSpot (8.4%) but lower in vBurnett (2.0%) and cBurnett (3.2%). The Burnett showed better performance than DBS, whereas HemaSpot showed poorer performance than DBS. Nevertheless, both Burnett and HemaSpot have high rate of non-reportable results. In the current format, neither of the two devices is feasible for VL scale-up in resource-limited settings. IMPORTANCE Burnett and HemaSpot are two novel technologies that allow whole blood collection and plasma separation and stabilization at room temperature without the need of additional equipment. Hence, these devices are potential alternatives to fresh plasma as a suitable specimen for viral load scale-up to monitor antiretroviral therapy in resource-limited settings

WWDISA is an optional module of the DISA Laboratory Information system (LIS) that offers a web portal that allows access to test results over the internet for patient clinical management. This study aims to assess the applicability of using the WWDISA web application, and the lessons learned from its implementation in six health facilities in Mabote district, Inhambane province. Data from 2463 and 665 samples for HIV-viral load (HIVVL) tests, extracted from paper-based and WWDISA systems, respectively, were included, from January to December 2020. Data were simultaneously collected on a quarterly basis from both systems to allow comparison. The WWDISA turnaround time (TAT) from sample collection to results becoming available was found to be 10 (IQR: 8–12) days and significantly lower than the health unit manual logbook (p value < 0.001). Regarding the system efficiency, it was found that among 1978 search results, only 642 (32.5%) were found, and the main challenges according to the users were lack of connectivity (77%) and the website going down (62%). The WWDISA module has been shown to be effective in reducing the TAT, although a stable internet connection and accurate data entry are essential to make the system functional.

OBJECTIVES:Our study aimed to evaluate the stability of human immunodeficiency virus 1 (HIV-1) RNA on cobas plasma separation card (PSC) specimens for viral load (VL) testing after being exposed to varied temperatures and storage times. METHODS:For this purpose, venous PSC specimens were collected and stored at 25ºC to 42ºC for a period of up to 28 days. Plasma VL at baseline was used as reference, against which PSC VL was compared at different time points. RESULTS:From the 30 patients included in the study, 600 PSC and 30 fresh plasma specimens were obtained. Plasma VL at baseline was fewer than 1,000 copies/mL in 16 patients, and 99.4% of PSCs from these patients yielded nonquantifiable VL at all temperature ranges and time points. During the study period, minor variation of VL was observed in PSCs obtained from 13 patients with plasma VL fewer than 1,000 copies/mL at baseline. For the patient with plasma VL at 1,000 copies/mL, the PSC VL varied from undetectable to 1,670 copies/mL. CONCLUSIONS:Our results show minor variation of VL in PSC specimens in the study conditions. HIV RNA is stable in PSCs exposed to high temperatures for up to 28 days.

Mycobacterium tuberculosis complex (MTBC) Lineage 3 (L3) strains are abundant in world regions with the highest tuberculosis burden. To investigate the population structure and the global diversity of this major lineage, we analyzed a dataset comprising 2682 L3 strains from 38 countries over 5 continents, by employing 24-loci mycobacterial interspersed repetitive unit-variable number of tandem repeats genotyping (MIRU-VNTR) and drug susceptibility testing. We further combined whole-genome sequencing (WGS) and phylogeographic analysis for 373 strains representing the global L3 genetic diversity. Ancestral state reconstruction confirmed that the origin of L3 strains is located in Southern Asia and further revealed multiple independent introduction events into North-East and East Africa. This study provides a systematic understanding of the global diversity of L3 strains and reports phylogenetic variations that could inform clinical trials which evaluate the effectivity of new drugs/regimens or vaccine candidates.

There are many challenges that impact the current referral network for Tuberculosis (TB) sputum specimens in Mozambique. In some cases, health facilities are remote and the road infrastructure is poor and at times impassable, leading to delays in laboratory specimen transportation and long turn-around times for results. Drone transportation is a promising solution to reduce transportation time and improve access to laboratory diagnostics if the sample quality is not compromised during transport. This study evaluated the impact of drone transportation on the quality of TB sputum specimens with suspected Mycobacterium tuberculosis. 156 specimens were collected at five (5) health centers and sent to the Instituto Nacional de Saúde (INS) National TB Reference Laboratory. Specimens were then equally divided into two aliquots; one to be transported on land and the other by air using a drone. Control and study group specimens were processed using the NALC-NaOH method. Agreement between sample and control specimens was acceptable, indicating that drone transportation did not affect the quality of TB specimens. The authors recommend additional studies to validate drone transportation of TB specimens over a longer period of time to give further confidence in the adoption of drone delivery in Mozambique.

(1) Background: Laboratory-based molecular assays are the gold standard to detect SARS-CoV-2. In resource-limited settings, the implementation of these assays has been hampered by operational challenges and long turnaround times. Rapid antigen detection tests are an attractive alternative. Our aim is to evaluate the clinical performance of two SARS-CoV-2 rapid antigen tests during a high transmission period. (2) Methods: A total of 1277 patients seeking SARS-CoV-2 diagnosis were enrolled at four health facilities. Nasopharyngeal swabs for rapid antigen and real time PCR testing were collected for each patient. Sensitivity, specificity, positive and negative predictive values, misclassification rate, and agreement were determined. (3) Results: The overall sensitivity of Panbio COVID-19 was 41.3% (95% CI: 34.6–48.4%) and the specificity was 98.2% (95% CI: 96.2–99.3%). The Standard Q had an overall sensitivity and specificity of 45.0% (95% CI: 39.9–50.2%) and 97.6% (95% CI: 95.3–99.0%), respectively. The positive predictive value of a positive test was 93.3% and 95.4% for the Panbio and Standard Q Ag-RDTs, respectively. A higher sensitivity of 43.2% and 49.4% was observed in symptomatic cases for the Panbio and Standard Q Ag-RDTs, respectively. (4) Conclusions: Despite the overall low sensitivity, the two evaluated rapid tests are useful to improve the diagnosis of symptomatic SARS-CoV-2 infections during high transmission periods.

BackgroundTuberculosis (TB) is a difficult-to-treat disease requiring the combination of four antibiotics for a minimum of 6 months. Rapid and quantitative biomarkers to monitor treatment response are urgently needed for individual patient management and clinical trials. C-reactive protein (CRP) is often used clinically as a rapid marker of inflammation caused by infection. We assessed the relationship of TB bacillary load and CRP as biomarkers of treatment response.MethodsXpert MTB/RIF-confirmed pulmonary TB cases were enrolled for treatment response assessment in Mozambique. Treatment response was measured using the Tuberculosis Molecular Bacterial Load Assay (TB-MBLA) in comparison with standard-of-care Mycobacterium Growth Indicator Tube (MGIT) culture at baseline and at weeks 1, 2, 4, 8, 12, 17, and 26 of treatment. Blood CRP concentration was measured at baseline, week 8, and week 26. Treatment response was defined as increase in MGIT culture time to positivity (TTP), and reduction in TB-MBLA-measured bacillary load and blood CRP concentration.ResultsOut of the 81 screened presumptive TB cases, 69 were enrolled for 6-month treatment follow-up resulting in 94% treatment completion rate. Four participants did not complete TB treatment and 22 participants had missing CRP or TB-MBLA results and were excluded from TB-MBLA-CRP analysis. The remaining 43 participants—median age, 31 years old [interquartile range (IQR): 18–56]; 70% (30/43) male; and 70% (30/43) infected with HIV—were considered for analysis. Culture TTP and bacillary load were inversely correlated, Spearman’s r = −0.67, p < 0.0001. Resolution of sputum bacillary load concurred with reduction of blood CRP, r = 0.70, p < 0.0001. At baseline, bacillary load had a median (IQR) of 6.4 (5.5–7.2), which reduced to 2.4 (0.0–2.9) and 0.0 (0.0–0.0) log10 CFU/ml at months 2 and 6 of treatment, respectively. Correspondingly, blood CRP reduced from 1.9 (1.6–2.1) at baseline to 1.3 (0.9–1.7) and 0.4 (0.1–0.8) log10 mg/dl at months 2 and 6 of treatment, respectively. CRP reduction trialed bacteriological resolution at a rate of −0.06 log10 mg/dl compared to a bacillary load of 0.23 log10 CFU/ml per week. Consequently, 14 (33%) and 37 (88%) patients had reduced CRP to normal concentration and bacillary load to zero by the end of treatment, respectively. Pre-treatment CRP concentration and bacillary load, and resolution during treatment were slightly lower in HIV co-infected patients but not significantly different from HIV-uninfected TB patients.ConclusionTB-MBLA-measured bacillary load and blood CRP complement each other in response to anti-TB therapy. Slow CRP reduction probably reflects residual TB bacilli in the lung not expectorated in sputum. Combining both measures can improve the accuracy of these biomarkers for monitoring TB treatment response and shorten turnaround time since the results of both assays could be available in 24 h.

Background: Since the SARS-CoV-2 outbreak, sequencing efforts from virtually all countries have led to an unprecedented amount of genome data from the virus. Even so, unequal sampling between Global North and South hinders the implementation of global genomic surveillance systems.Methods: UShER is able to reconstruct a phylogeny with millions of sequences by efficient sample placement in a tree. We used this tool to understand the dynamics of Beta and Delta waves in Mozambique, maximising the use of available genomic data. We reconstructed two phylogenies with ~7.6 million sequences to which we added Beta and Delta samples. Thanks to pandemic-scale phylogenies, we identified the timing of introduction events of the variants in the country and their potential geographic origin.Findings: We identified 187 Beta introductions, divided in 42 transmission groups and 145 unique introductions, mostly from South Africa, between August 2020 and July 2021. For Delta, we identified 220 introductions, with 49 transmission groups and 171 unique introductions, mostly from the United Kingdom, India and South Africa, between April 2021 and November 2021.Interpretation: The high number of introductions and their origins suggests that movement restrictions effectively avoided imports from non-African countries, but not from surrounding countries. Our results raise questions about the imbalance between economic cost, imposed by these restrictions, and health benefits. This new understanding of pandemic dynamics in Mozambique can be used to inform public health interventions to control the spread of new variants in the country.Funding Information: This publication was produced by MozCovid which is part of the EDCTP2 programme supported by the European Union (grant number RIA2020EF-3005-MozCOVID). This work was also supported by the CHAMPS project which is funded by the Bill & Melinda Gates Foundation under the Grant OPP1126780 to Robert Breiman, subcontract SC00003286), the European Research Council under the European Union’s Horizon 2020 Research and Innovation Program Grant 101001038 (TB-RECONNECT), the European Commission – NextGenerationEU (Regulation EU 2020/2094), through CSIC's Global Health Platform (PTI Salud Global), and the Departament d’Universitats i Recerca de la Generalitat de Catalunya (AGAUR; 2017 SGR 664). In addition, this work was funded by the Ministerio de Ciencia e Innovación (Spanish Government) Project PID2019-104477RB-I00. CISM is supported by the Government of Mozambique and the Spanish Agency for International Development (AECID). ISGlobal is a member of the CERCA Programme, Generalitat de Catalunya (http://cerca.cat/en/suma/). We also acknowledge support from the Spanish Ministry of Science and Innovation through the “Centro de Excelencia Severo Ochoa 2019-2023” Program (CEX2018-000806-S).Declaration of Interests: We declare no competing interests.Ethics Approval Statement: Informed written consent was obtained from all participants. The study was approved by Centro de Investigação em Saúde de Manhiça (CISM) institutional ethics committee and the Mozambican Ministry of Health National Bioethics Committee (Approval No. 80/CNBS/2020).

"Ancestral" Mycobacterium tuberculosis complex (MTBC) strains of Lineage 1 (L1, East African Indian) are a prominent tuberculosis (TB) cause in countries around the Indian Ocean. However, the pathobiology of L1 strains is insufficiently characterized. Here, we used whole genome sequencing (WGS) of 312 L1 strains from 43 countries to perform a characterization of the global L1 population structure and correlate this to the analysis of the synthesis of phenolic glycolipids (PGL) - known MTBC polyketide-derived virulence factors. Our results reveal the presence of eight major L1 sub-lineages, whose members have specific mutation signatures in PGL biosynthesis genes, e.g., pks15/1 or glycosyltransferases Rv2962c and/or Rv2958c. Sub-lineage specific PGL production was studied by NMR-based lipid profiling and strains with a completely abolished phenolphthiocerol dimycoserosate biosynthesis showed in average a more prominent growth in human macrophages. In conclusion, our results show a diverse population structure of L1 strains that is associated with the presence of specific PGL types. This includes the occurrence of mycoside B in one sub-lineage, representing the first description of a PGL in an M. tuberculosis lineage other than L2. Such differences may be important for the evolution of L1 strains, e.g., allowing adaption to different human populations.

Background: In resource-poor countries, antigen-based rapid tests (Ag-RDTs) performed at primary healthcare and community settings improved access to SARS-CoV-2 diagnostics. However, the technical skills and biosafety requirements inherent to nasopharyngeal and oropharyngeal (OP) specimens limit the scale-up of SARS-CoV-2 testing. The collection of nasal-swabs is programmatically viable, but its performance has not been evaluated in resource-poor settings. Methods: We first evaluated the performance of SteriPack self-collected nasal swabs for the detection of SARS-CoV-2 by real-time PCR in 1498 consecutively enrolled patients with suspected infection. Next, we evaluated the clinical performance of three nasal swab-based Ag-RDTs against real-time PCR on OP specimens. Results: The sensitivity of nasal swabs was 80.6% [95% CI: 75.3–85.2%] compared to OP specimens. There was a good correlation (r = 0.58; p < 0.0001) between Ct values of 213 positive cases obtained using nasal and OP swabs. Our findings show sensitivities of 79.7% [95% CI: 73.3–85.1%] for Panbio COVID-19 Ag-RDT, 59.6% [95% CI: 55.2–63.8%] for COVIOS Ag-RDT, and 78.0% [95% CI: 73.5–82.0%] for the LumiraDx SARS-CoV-2 Ag-RDT. Conclusions: In our setting, the COVIOS Ag-RDT did not meet WHO requirements. Nasal swab-based Ag-RDTs for SARS-CoV-2 detection constitute a viable and accurate diagnostic option in resource-poor settings.

The US President's Emergency Plan for AIDS Relief (PEPFAR) supports molecular HIV and tuberculosis diagnostic networks and information management systems in low- and middle-income countries. We describe how national programs leveraged these PEPFAR-supported laboratory resources for SARS-CoV-2 testing during the COVID-19 pandemic. We sent a spreadsheet template consisting of 46 indicators for assessing the use of PEPFAR-supported diagnostic networks for COVID-19 pandemic response activities during April 1, 2020, to March 31, 2021, to 27 PEPFAR-supported countries or regions. A total of 109 PEPFAR-supported centralized HIV viral load and early infant diagnosis laboratories and 138 decentralized HIV and TB sites reported performing SARS-CoV-2 testing in 16 countries. Together, these sites contributed to >3.4 million SARS-CoV-2 tests during the 1-year period. Our findings illustrate that PEPFAR-supported diagnostic networks provided a wide range of resources to respond to emergency COVID-19 diagnostic testing in 16 low- and middle-income countries.

Background Mozambique is among the highest tuberculosis, tuberculosis–HIV and multidrug-resistant-tuberculosis burden countries. Although molecular technologies are available in-country, mycobacterial isolation through culture remains an important tool for tuberculosis diagnostics and drug susceptibility testing. Objective We evaluated the use of the Ogawa-Kudoh (OK) mycobacterial culture, a simple technique, to isolate Mycobacterium tuberculosis in two health units, in Maputo City, Mozambique. Methods From May to December 2014, 122 patient samples were collected in Chamanculo General Hospital and Polana Caniço General Hospital. The specimens were first tested in the health units using the OK method and afterwards shipped to the National Tuberculosis Reference Laboratory for mycobacterial culture using the NALC-NaOH-Citrate (NALC) decontamination method followed by inoculation in Lowenstein Jensen (LJ) solid media as the reference standard. Results Among 107 samples with valid results, 98 (91.6%) had concordant results in both methods; 9 (8.4%) had discordant results. The contamination rate was 4.1% (5/122) for the OK and 9.0% (11/122) for the NALC/LJ methods. The sensitivity of OK was 80% (95% confident interval [CI]: 51.4–94.7) and the specificity was 94% (95% CI: 85.8–97.3). The degree of agreement between both methods was moderate (Kappa: 0.68; 95% CI: 0.48–0.89). Conclusion The OK method showed satisfactory sensitivity and specificity. The method also had a lower contamination rate when compared to the NALC/LJ. Similar to other studies in resource-limited settings, our findings showed that the OK method can effectively be implemented in settings with limited laboratory capacity to isolate tuberculosis bacteria by culture for further testing.