Background: The Bacille Calmette–Guérin (BCG) vaccine is part of the Extended Programme on Immunization (EPI) and as such is generally administered at birth. The global introduction of BCG not only protected many vaccinated infants against severe complications of tuberculosis but also resulted in markedly reduced overall childhood mortality. Studies in human adults determined that BCG vaccination induces epigenetic reprogramming of innate immune cells (also known as trained immunity) and can also enhance T cell responses to both mycobacterial and non-mycobacterial antigens. Goal and Methods: The current study tested the hypothesis that BCG immunization similarly impacts the functionally distinct infant immune system. Towards this goal, we applied RNA sequencing to assess transcriptome changes in circulating CD4+ T cells of Malawian infants prior to and 2 to 13 weeks after BCG immunization. Results: In the first three months of life, transcriptome changes of infant CD4 T cells implied a functional shift towards T helper 1 and Th17 immunity. Vaccination with BCG resulted in additional modulation of the CD4 T cell transcriptome and differentially expressed genes could be linked to metabolomic function. Conclusions: These findings are consistent with data reported in BCG vaccinated adults and contribute to the understanding of molecular changes in infant CD4 T cells that may explain the improved capacity of the infant immune system to respond to pathogens after BCG vaccination.

Background The association between low-frequency human immunodeficiency virus type 1 (HIV-1) drug resistance mutations (DRMs) and treatment failure (TF) is controversial. We explore this association using next-generation sequencing (NGS) methods that accurately sample low-frequency DRMs.Methods We enrolled women with HIV-1 in Malawi who were either antiretroviral therapy (ART) naive (cohort A), had ART failure (cohort B), or had discontinued ART (cohort C). At entry, cohorts A and C began a nonnucleoside reverse transcriptase inhibitor-based regimen and cohort B started a protease inhibitor-based regimen. We used Primer ID MiSeq to identify regimen-relevant DRMs in entry and TF plasma samples, and a Cox proportional hazards model to calculate hazard ratios (HRs) for entry DRMs. Low-frequency DRMs were defined as <= 20%.Results We sequenced 360 participants. Cohort B and C participants were more likely to have TF than cohort A participants. The presence of K103N at entry significantly increased TF risk among A and C participants at both high and low frequency, with HRs of 3.12 (95% confidence interval [CI], 1.58-6.18) and 2.38 (95% CI, 1.00-5.67), respectively. At TF, 45% of participants showed selection of DRMs while in the remaining participants there was an apparent lack of selective pressure from ART.Conclusions Using accurate NGS for DRM detection may benefit an additional 10% of patients by identifying low-frequency K103N mutations. Carrying the drug resistance mutation K103N at either low or high frequency when starting a nonnucleoside reverse transcriptase inhibitor antiretroviral therapy regimen increases treatment failure risk.

Objectives:To evaluate causes of fever, including resistance patterns, in patients undergoing cancer treatment in Malawi. Methods:In this prospective cohort study, enrolled patients undergoing chemotherapy at Kamuzu Central Hospital in Lilongwe, Malawi were given a thermometer. If a temperature of ≥38°C was recorded, they were instructed to return for hospitalization, standardized fever workup, and antibiotics. All patients were followed through 90 days post-fever event or completion of chemotherapy. Results:One hundred and five patients were screened and 50 were enrolled. Of the enrollees, 26 (52%) were men and 26 (52%) were HIV positive, with a mean ART duration of 7 years and CD4 count of 293 cells/µL. The most common diagnoses were aggressive non-Hodgkin lymphoma (40%) and Hodgkin lymphoma (22%). Twenty-three febrile events were recorded from 15 patients. Of the 23 events, a causative agent was isolated in 13 cases: Escherichia coli (6), Plasmodium falciparum (3), Streptococcus pneumoniae (2), Pseudomonas aeruginosa (1) and Citrobacter freundii (1). Of the six E. coli isolates, all were found to be resistant to fluoroquinolones and 4/6 (66%) were resistant to cephalosporins. All patients but one survived; the death was attributed to Pseudomonas bacteraemia. Conclusions:This study describes laboratory-confirmed causes of neutropenic fever (NF) in cancer patients in Malawi. Gram-negative rods, followed by malaria, were the most common source of infection. Gram-negative rods were associated with high rates of antimicrobial resistance. Malaria and resistant bacterial infections should be considered for NF treatment and prevention in sub-Saharan Africa.

Objectives: To examine the time required to suppress HIV in the genital tract with antiretroviral therapy (ART) in men with urethritis. Design: An observational cohort study. Methods: Men with HIV and urethritis not on ART were enrolled at an STI clinic in Malawi and offered to initiate ART. Blood and semen samples were collected pretreatment and at 1, 2, 4, 8, 12 and 24 weeks posturethritis treatment. Median viral loads (VLs) were calculated by ART initiation groups: ‘within 1 week’, ‘between 1 and 4 weeks’ and ‘no ART before 4 weeks’, based on the men's choice about whether or not to initiate ART. The presence of ART at each visit was confirmed by bioanalytical methods. Findings: Between January 2017 and November 2018, 74 men presented with urethritis and HIV and were confirmed ART naive. The median age was 32 years. Forty-one (55% of men) initiated ART within 1 week; 12 (16%) between 1 and 4 weeks; and 21 (28%) did not initiate ART by week 4. Within the 1 week group, median VL was suppressed within 4 weeks in both semen and blood. Among the 1–4 weeks group, VL was suppressed within 4 weeks in semen and 5 weeks in blood. Among the no ART before 4 weeks group, VL in semen declined within the first 4 weeks but remained unsuppressed through week 24, and there was no significant decline in blood HIV. Conclusion: Treatment of urethritis and prompt initiation of ART with counseling for safer sex for at least one month is a critical measure to reduce transmission of HIV.

The live-attenuated Bacille Calmette-Guérin (BCG) vaccine has been introduced a century ago to prevent tuberculosis and is still administered to >80% of newborns worldwide. Independent of its effect on TB, BCG introduction markedly reduced childhood mortality. Although BCG vaccine is routinely administered to infants, there is a gap in understanding the influence of BCG on the neonatal immune system. In adults, BCG induces trained or heterologous immunity. Here, to better understand the molecular changes in the infant immune system after BCG immunization, we performed RNA sequencing and ATAC sequencing in circulating CD4 T cells and monocytes of 28 infants prior to and 6–12 weeks after administering BCG. Consistent with data from BCG-vaccinated adults, the expression profile of 168 differentially expressed genes (DEG) supports the activation of monocytes after BCG vaccination, and ATAC sequencing data identified epigenetic modification that impact accessibility of genes in Nod1 and Nod 2 signaling pathways. In CD4 T cells, we identified a total of 322 DEG, including 95 upregulated and 226 downregulated genes. The functional enrichment and transcription factor analysis showed the enrichment of ErbB signaling pathways which regulate cell proliferation and differentiation mediated through MAPK signaling pathways. These results combined with peaks identified by ATAC sequencing were indicative of the expansion of Th1 CD4 T cells in BCG vaccinated infants. This study provides an understanding of molecular changes in monocytes and CD4 T cells after BCG vaccination that may explain the improved capacity of the infant immune system to respond to intracellular pathogens.

e18831 Background: Neutropenic fever (NF) is a common, life-threatening complication of chemotherapy. Over 80% of high risk hematological malignancy cases will develop NF, with mortality rates reaching 10%. In high income countries (HIC), NF prevention guidelines including prophylaxis have decreased treatment-related mortality. In sub-Saharan Africa (SSA), little is known about the causes of NF as many deaths occur in facilities without blood culture availability. Pathogens in SSA may vary from those in HIC due to high burden of HIV infection as well as different antibiotic stewardship, endemic infections, and chemotherapy regimens. Unknown bacterial spectrum and resistance patterns prevent extrapolation of NF guidelines to SSA. Methods: Patients undergoing chemotherapy at Kamuzu Central Hospital (KCH) in Lilongwe, Malawi were eligible to participate in the study if they were starting a new chemotherapy regimen, lived within 200 kilometers, and (1) had a hematologic malignancy of any kind or (2) had a solid tumor and were HIV-infected. Enrolled patients were given a thermometer and if a temperature of 38º C or greater was recorded, they were instructed to return for management, including admission and antibiotics. Evaluation consisted of complete blood count with differential, urine and blood cultures, and other testing at the clinician’s discretion. All patients were followed through 90 days post fever event or completion of chemotherapy, whichever came later. Results: 106 patients were screened and 50 were enrolled. The primary reason for screen failure was household distance from KCH. Of the enrollees, 26 (52%) were men and 26 (52%) were HIV positive with an average ART treatment time of 7 years and CD4 count of 293 cells/mL. Diagnoses included: aggressive lymphoma (36%), Hodgkin lymphoma (22%), low-grade lymphoma (10%), multicentric Castleman disease (6%), non-Hodgkin lymphoma, NOS (4%), breast cancer (6%), cervical cancer (4%), and other solid tumors (12%). There were 23 febrile events recorded from 15 patients (10 HIV– and 5 HIV+), with no relationship between HIV status and febrile events (p = 0.08). Of the 23 events, a causative agent was isolated in 13 cases (E. coli (6), Malaria (3) and S. pneumonia (2), Pseudomonas (1) and C. freundii (1). Of the 6 E.coli isolates, 3 were found to be multidrug resistant (ie resistant to fluoroquinolones and cephalosporins) and treatment was escalated with a carbapenem. All patients but one survived; death was attributed to Pseudomonas bacteremia. Conclusions: This study demonstrates the initial laboratory trends of febrile events in cancer patients in Lilongwe, Malawi. GNRs, followed by malaria, were the most common source of infection and GNRs were associated with high rates of resistance. Endemic and resistant bacterial infections should be considered when treating NF. Larger studies are needed across the region to identify the pathogens most commonly associated with NF.

OBJECTIVE:The aim of this study was to understand how vaginal microbiota composition affects antiretroviral concentrations in the setting of hormonal contraception initiation. METHODS:Cervicovaginal fluid (CVF) concentrations of tenofovir, lamivudine, and efavirenz from 73 Malawian women with HIV were compared before and after initiation of depot-medroxyprogesterone acetate (DMPA) or levonorgestrel implant. We evaluated antiretroviral concentrations and vaginal microbiota composition/structure in the context of contraception initiation and predicted genital shedding using multivariable repeated measurements models fit by generalized estimating equations. RESULTS:Mean lamivudine CVF concentrations decreased 37% 1 month after contraception initiation. Subgroup analyses revealed a 41% decrease in women 1 month after initiating levonorgestrel implant, but no significant difference was observed in DMPA group alone. Tenofovir, lamivudine, and efavirenz CVF concentrations were positively correlated with anaerobic bacteria associated with nonoptimal vaginal microbiota. Risk of genital HIV shedding was not significantly associated with tenofovir or lamivudine CVF concentrations [tenofovir relative risk (RR): 0.098, P = 0.75; lamivudine RR: 0.142, P = 0.54]. Lack of association between genital HIV shedding and efavirenz CVF concentrations did not change when adjusting for vaginal microbiota composition and lamivudine/tenofovir CVF concentrations (RR: 1.33, P = 0.531). CONCLUSION:No effect of hormone initiation on genital shedding provides confidence that women with HIV on either DMPA or levonorgestrel implant contraception will not have compromised ART efficacy. The unexpected positive correlation between antiretroviral CVF concentrations and certain bacterial taxa relative abundance requires further work to understand the mechanism and clinical relevance.

The results of the Evidence for Contraceptive Options and HIV Outcomes (ECHO) trial, the first large randomized controlled clinical trial comparing the HIV acquisition risk of women receiving DMPA, the levonorgestrel (LNG) implant, or the copper intrauterine device (IUD), did not reveal an increased risk of HIV acquisition for women on any of these three contraceptives. Our study results confirm that the two different progestin-based hormonal contraceptives DMPA and levonogestrel will not increase the risk for HIV infection.

Background Pre-exposure prophylaxis (PrEP) reduces HIV acquisition risk by >90% and is a critical lever to reduce HIV incidence. Identifying individuals most likely to benefit from PrEP and retaining them on PrEP throughout HIV risk is critical to realize PrEP’s prevention potential. Individuals with sexually transmitted infections (STIs) are an obvious priority PrEP population, but there are no data from sub-Saharan Africa (SSA) confirming the effectiveness of integrating PrEP into STI clinics. Assisted partner notification may further enhance STI clinic–based PrEP programming by recruiting PrEP users from the pool of named sexual partners of individuals presenting with an incident STI. However, the acceptability, feasibility, and effectiveness of these integrated and enhanced strategies are unknown. Objective This study aims to describe the implementation outcomes of acceptability, feasibility, and effectiveness (regarding PrEP uptake and persistence) of integrating an enhanced PrEP implementation strategy into an STI clinic in Malawi. Methods The enhanced PrEP STI study is a prospective cohort study enrolling patients who are eligible for PrEP (aged ≥15 years) who are seeking STI services at a Lilongwe-based STI clinic. Data collection relies on a combination of in-depth interviews, patient and clinic staff surveys, and clinic record review. All enrolled PrEP users will be screened for acute HIV infection and receive quarterly testing for Neisseria gonorrhea, Chlamydia trachomatis, and syphilis. Participants will be asked to name recent sexual partners for assisted notification; returning partners will be screened for PrEP eligibility and, if interested, enrolled into the cohort of PrEP initiators. We will also enroll patients who are eligible for PrEP but choose not to initiate it, from the STI clinic. Patient participants will be followed for 6 months; we will assess self-reported PrEP use, PrEP refills, sexual behaviors, perceived HIV risk, and incident STIs. Clinic staff participants will be interviewed at baseline and at approximately 6 months and will complete surveys examining the perceived acceptability and feasibility of the integrated and enhanced PrEP strategy. Results Enrollment began in March 2022 and is projected to continue until February 2023, with patient participant follow-up through August 2023. The results of this study are expected to be reported in 2024. Conclusions This study will generate important evidence regarding the potential integration of PrEP services into STI clinics in SSA and preliminary data regarding the effectiveness of an enhanced intervention that includes assisted partner notification as a strategy to identify potential PrEP users. Furthermore, this trial will provide some of the first insights into STI incidence among PrEP users recruited from an STI clinic in SSA—critical data to inform the use of etiologic STI testing where syndromic management is the current standard. These findings will help to design future PrEP implementation strategies in SSA. Trial Registration ClinicalTrials.gov NCT05307991; https://clinicaltrials.gov/ct2/show/NCT05307991 International Registered Report Identifier (IRRID) DERR1-10.2196/37395

Background: Persons with acute HIV infection (AHI) are highly infectious and responsible for a disproportionate share of incident infections. Immediate antiretroviral therapy (ART) rapidly reduces blood viral loads (VLs), but genital VLs after ART initiation during AHI are less well described. Setting: Lilongwe, Malawi, 2012-2014. Methods: HIV-seronegative and HIV-serodiscordant persons aged >= 18 years were screened for AHI (RNA positive) and randomized to standard of care, behavioral intervention, or behavioral intervention plus short-term ART (raltegravir/emtricitabine/tenofovir) (1:2:2). Persons who were ART eligible under Malawi guidelines could receive first-line therapy. Blood and genital VLs were assessed at weeks 1, 4, 8, and 12. Fisher's Exact test was used to compare viral suppression by ART status. Results: Overall, 46 persons with AHI were enrolled; of whom, 17 started ART within 12 weeks. Median blood VL at AHI diagnosis was 836,115 copies/mL. At week 12, 7% (1/14) of those who initiated ART had a blood VL of >= 400 copies/mL, compared with 100% (23/23; P < 0.0001) of those who did not initiate ART (median VL: 61,605 copies/mL). Median genital VL at week 1 was 772 copies/mL, with 13 of 22 (59%) having VL of >= 400 copies/mL. At week 12, 0 of 10 (0%) of those who initiated ART had genital VL of >= 400 copies/mL, compared with 7 of 15 (47%) of those who did not initiate ART (P = 0.02). Conclusion: Although highly correlated, VLs in blood and genital fluids occupy discrete biological compartments with distinct virologic dynamics. Our results corroborate the dramatic reduction in both compartments after ART initiation. Increasing AHI screening and rapidly initiating treatment is key to interrupting transmission.

BACKGROUND Plasmodium falciparum malaria dominates throughout sub-Saharan Africa, but the prevalence of P. malariae, P. ovale spp., and P. vivax increasingly contribute to infection in countries which control malaria using P. falciparum-specific diagnostic and treatment strategies. METHODS We performed qPCR on 2,987 dried blood spots from the 2015-2016 Malawi Demographic and Health Survey to identify the presence and distribution of non-falciparum infection. Bivariate models were used to determine species-specific associations with demographic and environmental risk factors. RESULTS Non-falciparum infections had a broad spatial distribution. Weighted prevalence was 0.025 (SE: 0.004) for P. malariae, 0.097 (SE: 0.008) for P. ovale spp., and 0.001 (SE: 0.0005) for P. vivax. Most infections (85.6%) had low-density parasitemias ≤10 parasites/µL, and 66.7% of P. malariae, 34.6% of P. ovale spp., and 40.0% of P. vivax infections were co-infected with P. falciparum. Risk factors for P. malariae were like those known for P. falciparum, however, there were few risk factors recognized for P. ovale spp. and P. vivax, perhaps due to the potential for relapsing episodes. CONCLUSIONS The prevalence of any non-falciparum infection was 11.7%, with infections distributed across Malawi. Continued monitoring of Plasmodium spp. becomes critical as non-falciparum infections become important sources of ongoing transmission.

Self-report of sexual behaviours in clinical studies is often subject to misreporting due to recall or social desirability bias or misinterpretation of the study questionnaires.1 Use of biomarkers of semen exposure, such as the detection of prostate-specific antigen (PSA) in vaginal secretions, offers an additional means of assessing sexual behaviours and condom use that is not subject to reporting biases.2 In a secondary analysis of a clinical trial of hormonal contraception in Malawi,3 we examined associations of discordance between PSA detection and self-report of condomless sex over time with participant characteristics using log-binomial regression analyses with generalised estimating equations for repeated measures. All analyses were conducted using SAS V.9.3 (SAS Institute, Cary, North Carolina, USA). Testing …

Background. Prior to the widespread availability of antiretroviral therapy (ART), men living with human immunodeficiency virus (HIV) with urethritis had increased concentrations of HIV in semen. This study aims to better evaluate HIV shedding in men with urethritis receiving ART, and its implications for the cure of HIV. Methods. Men living with HIV with urethritis taking ART >= 12 weeks were enrolled at a sexually transmitted infections clinic in Lilongwe, Malawi. Study follow-up included visits at 1, 2, 4, 8, 12, 24, 36, and 48 weeks after urethritis diagnosis and treatment. Matched blood and semen samples were collected at all visits, and all additional episodes of urethritis were followed with extra visits 1, 2, and 4 weeks after treatment. Results. There were 111 men enrolled in the study between January 2017-March 2019, and 77 (69%) were suppressed in the blood (<400 copies/mL). Among the 77 men, 87 episodes of urethritis were evaluated during follow-up. Of the 87 episodes, 15 episodes (17%) had instances of seminal viral shedding >= 400 copies/mL despite viral suppression in the blood. During nonurethritis follow-up, <= 6% of men at each visit had a viral load >= 400 copies/mL in the semen while maintaining viral suppression in the blood. Conclusions. An HIV cure requires the elimination of HIV from every body compartment, but available ART does not currently accomplish this. Our study highlights the male genital tract as a local source of HIV that can be reversibly activated. A better understanding of this phenomenon is important to advance the HIV cure field.

Antimicrobial resistance (AMR) is a global threat, including in sub-Saharan Africa. However, little is known about the genetics of resistant bacteria in the region. In Malawi, there is growing concern about increasing rates of antimicrobial resistance to most empirically used antimicrobials. The highly drug resistant Escherichia coli sequence type (ST) 131, which is associated with the extended spectrum β-lactamase blaCTX-M-15 , has been increasing in prevalence globally. Previous data from isolates collected between 2006 and 2013 in southern Malawi have revealed the presence of ST131 and the blaCTX-M-15 gene in the country. We performed whole genome sequencing (WGS) of 58 clinical E. coli isolates at Kamuzu Central Hospital, a tertiary care centre in central Malawi, collected from 2012 to 2018. We used Oxford Nanopore Technologies (ONT) sequencing, which was performed in Malawi. We show that ST131 is observed more often (14.9% increasing to 32.8%) and that the blaCTX-M-15 gene is occurring at a higher frequency (21.3% increasing to 44.8%). Phylogenetics indicates that isolates are highly related between the central and southern geographic regions and confirms that ST131 isolates are contained in a single group. All AMR genes, including blaCTX-M-15 , were widely distributed across sequence types. We also identified an increased number of ST410 isolates, which in this study tend to carry a plasmid-located copy of blaCTX-M-15 gene at a higher frequency than blaCTX-M-15 occurs in ST131. This study confirms the expanding nature of ST131 and the wide distribution of the blaCTX-M-15 gene in Malawi. We also highlight the feasibility of conducting longitudinal genomic epidemiology studies of important bacteria with the sequencing done on site using a nanopore platform that requires minimal infrastructure.

Objectives: Newborn screening in the United States and Europe allows early identification of congenital disorders but does not yet exist in most low-resource settings, especially in sub-Saharan Africa. Newborn screening can identify multiple inherited hematological disorders, but feasibility and effectiveness for Africa are not fully determined. Methods: Surplus dried blood spot collected in Central Malawi through the HIV Early Infant Diagnosis surveillance program were repurposed and tested by isoelectric focusing for sickle cell disease and trait. Additional genetic testing identified G6PD deficiency and alpha thalassemia. Results: Testing of 10,529 cards revealed an overall sickle cell trait prevalence of 7.0% (range 3.9–9.7% by district); 10 of 14 infants identified with sickle cell disease (prevalence 0.1%) were located and received care at a specialized clinic. Subsequent testing of 1,329 randomly selected cards identified alpha thalassemia trait in 45.7% of samples, and G6PD deficiency in 20.4% of males and 3.4% of females, with 29.0% of females as heterozygous carriers. Conclusion: Inherited hematological disorders are common in Central Malawi; early identification through newborn screening can improve clinical outcomes and should be supported throughout Africa.

Overlap in metabolism pathways of endogenous female sex hormones and antiretroviral drugs may lead to altered exposure to these compounds. In a family planning clinic in Lilongwe, Malawi, blood, blood cell, and cervicovaginal fluid (CVF) samples from seventy-three HIV positive Malawian women taken in follicular and luteal menstrual phases were assessed for estradiol and progesterone by chemiluminescent immunoassay, and for antiretroviral concentration by liquid chromatography-mass spectrometry. In both follicular and luteal phases, estradiol concentrations were lower in women receiving efavirenz compared with women on non-efavirenz regimens or no antiretroviral therapy (p < .01). Serum estradiol was moderately and negatively correlated with efavirenz plasma (r = -0.36,p < .001) and CVF (r = -0.50,p < .001) concentrations. Serum estradiol was a significant predictor of efavirenz CVF concentrations even after adjusting for efavirenz plasma concentrations (p = .02). In upper-layer packed cells (ULPCs), tenofovir diphosphate (TFVdp) concentrations were similar between follicular and luteal phases and were not correlated with estradiol or progesterone concentrations. Tenofovir concentrations in CVF were not associated with menstrual cycle or serum hormone concentrations. In CVF and plasma, efavirenz concentrations were negatively correlated with serum estradiol concentrations, suggesting a modulatory effect of estradiol on efavirenz metabolism and/or transport processes, and/or an effect of efavirenz on the metabolism of estradiol. Differences in CVF persisted even after adjusting for plasma concentrations, suggesting a mechanism specific to the female genital compartment separate from absorption or hepatic metabolism. In contrast, TFVdp concentrations in ULPC were not influenced by endogenous estradiol or progesterone concentrations.

Concurrent sexually transmitted infections (STI) can increase the probability of HIV-1 transmission primarily by increasing the viral load present in semen. In this study, we explored the relationship of HIV-1 in blood and seminal plasma in the presence and absence of urethritis and after treatment of the concurrent STI. Primer ID deep sequencing of the V1/V3 region of the HIV-1 env gene was done for paired blood and semen samples from ART-naïve men living in Malawi with (n = 19) and without (n = 5) STI-associated urethritis; for a subset of samples full length env genes were generated for sequence analysis and to test entry phenotype. Cytokine concentrations in the blood and semen were also measured, and a reduction in the levels of pro-inflammatory cytokines was observed following STI treatment. We observed no difference in the prevalence of diverse compartmentalized semen-derived lineages in men with or without STI-associated urethritis, and these viral populations were largely stable during STI treatment. Clonal amplification of one or a few viral sequences accounted for nearly 50% of the viral population indicating a recent bottleneck followed by limited viral replication. We documented a case of superinfection where the new strain was restricted to the genital tract. We conclude that the male genital tract is a site where virus can be brought in from the blood, where localized sustained replication can occur, where a superinfecting strain can persist, and where specific genotypes can be amplified perhaps initially by cellular proliferation but further by limited viral replication. Importance HIV-1 is a sexually transmitted infection that co-exists with other STIs. Here we examine the impact of a concurrent STI resulting in urethritis on the HIV-1 population within the male genital tract. We found that viral populations remain largely stable even with treatment of the STI. These results show that viral populations within the male genital tract are defined by factors beyond transient inflammation associated with a concurrent STI.

Conducting collaborative and comprehensive epidemiological research on neonatal sepsis in low- and middle-income countries (LMICs) is challenging due to a lack of diagnostic tests. This prospective study protocol aims to obtain epidemiological data on bacterial sepsis in newborns and young infants at Kamuzu Central Hospital in Lilongwe, Malawi. The main goal is to determine if the use of whole blood transcriptome host immune response signatures can help in the identification of infants who have sepsis of bacterial causes. The protocol includes a detailed clinical assessment with vital sign measurements, strict aseptic blood culture protocol with state-of-the-art microbial analyses and RNA-sequencing and metagenomics evaluations of host responses and pathogens, respectively. We also discuss the directions of a brief analysis plan for RNA sequencing data. This study will provide robust epidemiological data for sepsis in neonates and young infants in a setting where sepsis confers an inordinate burden of disease.

Malaria remains a significant cause of morbidity and mortality in Malawi, with an estimated 18–19% prevalence of Plasmodium falciparum in children 2–10 years in 2015–2016. While children report the highest rates of clinical disease, adults are thought to be an important reservoir to sustained transmission due to persistent asymptomatic infection. The 2015–2016 Malawi Demographic and Health Survey was a nationally representative household survey which collected dried blood spots from 15,125 asymptomatic individuals ages 15–54 between October 2015 and February 2016. We performed quantitative polymerase chain reaction on 7,393 samples, detecting an overall P. falciparum prevalence of 31.1% (SE = 1.1). Most infections (55.6%) had parasitemias ≤ 10 parasites/µL. While 66.2% of individuals lived in a household that owned a bed net, only 36.6% reported sleeping under a long-lasting insecticide-treated net (LLIN) the previous night. Protective factors included urbanicity, greater wealth, higher education, and lower environmental temperatures. Living in a household with a bed net (prevalence difference 0.02, 95% CI − 0.02 to 0.05) and sleeping under an LLIN (0.01; − 0.02 to 0.04) were not protective against infection. Our findings demonstrate a higher parasite prevalence in adults than published estimates among children. Understanding the prevalence and distribution of asymptomatic infection is essential for targeted interventions.