Distinct clinical and immunological profiles of patients with evidence of SARS-CoV-2 infection in sub-Saharan Africa

Although the COVID-19 pandemic has left no country untouched there has been limited research to understand clinical and immunological responses in African populations. Here we characterise patients hospitalised with suspected (PCR-negative/IgG-positive) or confirmed (PCR-positive) COVID-19, and healthy community controls (PCR-negative/IgG-negative). PCR-positive COVID-19 participants were more likely to receive dexamethasone and a beta-lactam antibiotic, and survive to hospital discharge than PCR-negative/IgG-positive and PCR-negative/IgG-negative participants. PCR-negative/IgG-positive participants exhibited a nasal and systemic cytokine signature analogous to PCR-positive COVID-19 participants, predominated by chemokines and neutrophils and distinct from PCR-negative/IgG-negative participants. PCR-negative/IgG-positive participants had increased propensity for Staphylococcus aureus and Streptococcus pneumoniae colonisation. PCR-negative/IgG-positive individuals with high COVID-19 clinical suspicion had inflammatory profiles analogous to PCR-confirmed disease and potentially represent a target population for COVID-19 treatment strategies

The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance

INTRODUCTION Investment in Africa over the past year with regard to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequencing has led to a massive increase in the number of sequences, which, to date, exceeds 100,000 sequences generated to track the pandemic on the continent. These sequences have profoundly affected how public health officials in Africa have navigated the COVID-19 pandemic. RATIONALE We demonstrate how the first 100,000 SARS-CoV-2 sequences from Africa have helped monitor the epidemic on the continent, how genomic surveillance expanded over the course of the pandemic, and how we adapted our sequencing methods to deal with an evolving virus. Finally, we also examine how viral lineages have spread across the continent in a phylogeographic framework to gain insights into the underlying temporal and spatial transmission dynamics for several variants of concern (VOCs). RESULTS Our results indicate that the number of countries in Africa that can sequence the virus within their own borders is growing and that this is coupled with a shorter turnaround time from the time of sampling to sequence submission. Ongoing evolution necessitated the continual updating of primer sets, and, as a result, eight primer sets were designed in tandem with viral evolution and used to ensure effective sequencing of the virus. The pandemic unfolded through multiple waves of infection that were each driven by distinct genetic lineages, with B.1-like ancestral strains associated with the first pandemic wave of infections in 2020. Successive waves on the continent were fueled by different VOCs, with Alpha and Beta cocirculating in distinct spatial patterns during the second wave and Delta and Omicron affecting the whole continent during the third and fourth waves, respectively. Phylogeographic reconstruction points toward distinct differences in viral importation and exportation patterns associated with the Alpha, Beta, Delta, and Omicron variants and subvariants, when considering both Africa versus the rest of the world and viral dissemination within the continent. Our epidemiological and phylogenetic inferences therefore underscore the heterogeneous nature of the pandemic on the continent and highlight key insights and challenges, for instance, recognizing the limitations of low testing proportions. We also highlight the early warning capacity that genomic surveillance in Africa has had for the rest of the world with the detection of new lineages and variants, the most recent being the characterization of various Omicron subvariants. CONCLUSION Sustained investment for diagnostics and genomic surveillance in Africa is needed as the virus continues to evolve. This is important not only to help combat SARS-CoV-2 on the continent but also because it can be used as a platform to help address the many emerging and reemerging infectious disease threats in Africa. In particular, capacity building for local sequencing within countries or within the continent should be prioritized because this is generally associated with shorter turnaround times, providing the most benefit to local public health authorities tasked with pandemic response and mitigation and allowing for the fastest reaction to localized outbreaks. These investments are crucial for pandemic preparedness and response and will serve the health of the continent well into the 21st century

Convalescent plasma in patients admitted to hospital with COVID-19 (RECOVERY): a randomised controlled, open-label, platform trial

SummaryBackground Azithromycin has been proposed as a treatment for COVID-19 on the basis of its immunomodulatoryactions. We aimed to evaluate the safety and efficacy of azithromycin in patients admitted to hospital with COVID-19.Methods In this randomised, controlled, open-label, adaptive platform trial (Randomised Evaluation of COVID-19Therapy [RECOVERY]), several possible treatments were compared with usual care in patients admitted to hospitalwith COVID-19 in the UK. The trial is underway at 176 hospitals in the UK. Eligible and consenting patients wererandomly allocated to either usual standard of care alone or usual standard of care plus azithromycin 500 mg once perday by mouth or intravenously for 10 days or until discharge (or allocation to one of the other RECOVERY treatmentgroups). Patients were assigned via web-based simple (unstratified) randomisation with allocation concealment andwere twice as likely to be randomly assigned to usual care than to any of the active treatment groups. Participants andlocal study staff were not masked to the allocated treatment, but all others involved in the trial were masked to theoutcome data during the trial. The primary outcome was 28-day all-cause mortality, assessed in the intention-to-treatpopulation. The trial is registered with ISRCTN, 50189673, and ClinicalTrials.gov, NCT04381936.Findings Between April 7 and Nov 27, 2020, of 16 442 patients enrolled in the RECOVERY trial, 9433 (57%) wereeligible and 7763 were included in the assessment of azithromycin. The mean age of these study participants was65·3 years (SD 15·7) and approximately a third were women (2944 [38%] of 7763). 2582 patients were randomlyallocated to receive azithromycin and 5181 patients were randomly allocated to usual care alone. Overall,561 (22%) patients allocated to azithromycin and 1162 (22%) patients allocated to usual care died within 28 days(rate ratio 0·97, 95% CI 0·87–1·07; p=0·50). No significant difference was seen in duration of hospital stay (median10 days [IQR 5 to >28] vs 11 days [5 to >28]) or the proportion of patients discharged from hospital alive within 28 days(rate ratio 1·04, 95% CI 0·98–1·10; p=0·19). Among those not on invasive mechanical ventilation at baseline, nosignificant difference was seen in the proportion meeting the composite endpoint of invasive mechanical ventilationor death (risk ratio 0·95, 95% CI 0·87–1·03; p=0·24).Interpretation In patients admitted to hospital with COVID-19, azithromycin did not improve survival or otherprespecified clinical outcomes. Azithromycin use in patients admitted to hospital with COVID-19 should be restrictedto patients in whom there is a clear antimicrobial indication

A Multi-Dimensional Characterization of Aging and Wellbeing Among HIV-Positive Adults in Malawi

There is relatively little research on aging with HIV and wellbeing in sub-Saharan Africa. A cross-sectional survey was implemented in Malawi; eligible respondents were ≥ 30 years old and on ART for ≥ 2 years. Univariate and multiple regression analyses were stratified by age (younger adults: aged 30-49; older adults: aged ≥ 50) and gender. The median age was 51 years (total sample n = 134). Viral suppression was less common among older respondents (83.7% versus 93.0% among younger respondents) although not significant in adjusted models. Despite exhibiting worse physical and cognitive functioning (any physical functioning challenge: aOR 5.35, p = 0.02; cognitive functioning score difference: - 0.89 points, p = 0.04), older adults reported less interpersonal violence and fewer depressive symptoms (mild depression: aOR 0.23 p = 0.002; major depression: aOR 0.16, p = 0.004); in gender-stratified models, these relationships were significant only for females. More research is needed to disentangle the interplay between aging, gender and HIV in high-burden contexts and develop interventions to support comprehensive wellbeing in this population

"A loving man has a very huge responsibility": A mixed methods study of Malawian men's knowledge and beliefs about cervical cancer.

BackgroundIn Malawi, numerous barriers may prevent women from accessing cervical cancer screening services - including social factors such as male partner involvement. We conducted surveys that included open- and closed-ended questions with married Malawian men to evaluate their knowledge and beliefs about cervical cancer.MethodsHIV-positive adult (≥18 years) men (married or in a stable relationship) were recruited from an antiretroviral therapy clinic in Lilongwe, Malawi. Men were asked a series of survey questions to assess their knowledge about cervical cancer, experience with cervical cancer, their female partner's screening history, and their beliefs about gender norms and household decision-making. Following the survey, participants responded to a set of open-ended interview questions about cervical cancer screening, and men's role in prevention.ResultsOne hundred-twenty men were enrolled with average age 44 years and 55% having completed secondary school or higher education. Despite only moderate knowledge about cervical cancer and screening (average assessment score of 62% correct), all men expressed support of cervical cancer screening, and most (86%) believed they should be involved in their female partner's decision to be screened. Over half (61%) of men said their female partner had previously been screened for cervical cancer, and this was positively correlated with the male respondent having more progressive gender norms around sexual practices. Some men expressed concerns about the screening process, namely the propriety of vaginal exams when performed by male clinicians, and whether the procedure was painful.ConclusionsMale partners in Malawi want to be involved in decisions about cervical cancer screening, but have limited knowledge about screening, and hold rigid beliefs about gender norms that may affect their support for screening. Messaging campaigns addressing men's concerns may be instrumental in improving women's adoption of cervical cancer screening services in Malawi and similar settings

Association of HIV status and treatment characteristics with VIA screening outcomes in Malawi: A retrospective analysis.

BackgroundAlthough evidence from high-resource settings indicates that women with HIV are at higher risk of acquiring high-risk HPV and developing cervical cancer, data from cervical cancer "screen and treat" programs using visual inspection with acetic acid (VIA) in lower-income countries have found mixed evidence about the association between HIV status and screening outcomes. Moreover, there is limited evidence regarding the effect of HIV-related characteristics (e.g., viral suppression, treatment factors) on screening outcomes in these high HIV burden settings.MethodsThis study aimed to evaluate the relationship between HIV status, HIV treatment, and viral suppression with cervical cancer screening outcomes. Data from a "screen and treat" program based at a large, free antiretroviral therapy (ART) clinic in Lilongwe, Malawi was retrospectively analyzed to determine rates of abnormal VIA results and suspected cancer, and coverage of same-day treatment. Multivariate logistic regression assessed associations between screening outcomes and HIV status, and among women living with HIV, viremia, ART treatment duration and BMI.ResultsOf 1405 women receiving first-time VIA screening between 2017-2019, 13 (0.9%) had suspected cancer and 68 (4.8%) had pre-cancerous lesions, of whom 50 (73.5%) received same-day lesion treatment. There was no significant association found between HIV status and screening outcomes. Among HIV+ women, abnormal VIA was positively associated with viral load ≥ 1000 copies/mL (aOR 3.02, 95% CI: 1.22, 7.49) and negatively associated with ART treatment duration (aOR 0.88 per additional year, 95% CI: 0.80, 0.98).ConclusionIn this population of women living with HIV with high rates of ART coverage and viral suppression, HIV status was not significantly associated with abnormal cervical cancer screening results. We hypothesize that ART treatment and viral suppression may mitigate the elevated risk of cervical cancer for women living with HIV, and we encourage further study on this relationship in high HIV burden settings

Training Course in Focused Assessment with Sonography for HIV/TB in HIV Prevalent Medical Centers in Malawi

Purpose: This article describes the process of training medical providers of different backgrounds about the “focused assessment with sonography for HIV-associated TB” (FASH) exam to expand the availability of ultrasound for TB diagnosis in resource poor settings in the central region of Malawi. Methods and Materials: A survey was completed by the 19 eligible participants before and after a 4-day training course regarding the utility of the FASH exam. A six-question quiz was used to assess knowledge of the use of ultrasound in the FASH exam before and after the course. Results: Participants’ knowledge of the FASH technique significantly improved after the four-day course with a 32% increase in total quiz questions answered correctly (p<0.001). Ninety-five percent (n= 18) of participants answered that they would “likely” incorporate FASH in their clinical practice. Furthermore, 100% (n=19) of participants agreed that the FASH exam would improve their ability to diagnose TB and 95% (n=18) agreed that FASH would improve patient care in their clinic. Conclusions: After completing a 4-day training course, medical providers were more knowledgeable about the FASH exam and its findings, and felt more comfortable using ultrasound for the diagnosis of TB. Participants were also unanimous in opinion that the FASH ultrasound exam would improve their ability to diagnose TB

High Rates of Uncontrolled Blood Pressure in Malawian Adults Living with HIV and Hypertension.

BackgroundHypertension is among the most commonly diagnosed non-communicable diseases in Africa, and studies have demonstrated a high prevalence of hypertension among individuals with HIV. Despite high prevalence, there has been limited attention on the clinical outcomes of hypertension treatment in this population.ObjectiveWe sought to characterize rates of and factors associated with blood pressure control over one year among individuals on antiretroviral therapy (ART) and antihypertensive medications.MethodsWe performed a prospective observational cohort study at an HIV clinic in Malawi. We defined uncontrolled hypertension as a systolic blood pressure ≥140 mm Hg and/or diastolic blood pressure ≥90 mm Hg at two or more follow-up visits during the year, while controlled hypertension was defined as &lt;140 mm Hg systolic and &lt;90 mm Hg diastolic at all visits, or at all but one visit. We calculated an antihypertensive non-adherence score based on self-report of missed doses at each visit (higher score = worse adherence) and used rank sum and chi-square tests to compare sociodemographic and clinical factors (including adherence) associated with blood pressure control over the year.ResultsAt study entry, 158 participants (23.5%) were on antihypertensive medication; participants had a median age of 51.0 years, were 66.5% female, and had a median of 6.9 years on ART. 19.0% (n = 30) achieved blood pressure control over the year of follow-up. Self-reported non-adherence to hypertension medications was the only factor significantly associated with uncontrolled blood pressure. The average non-adherence score for those with controlled blood pressure was 0.22, and for those with uncontrolled blood pressure was 0.61 (p = 0.009).ConclusionsAdults living with HIV and hypertension in our cohort had low rates of blood pressure control over one year associated with self-reported non-adherence to antihypertensive medications. Given the high prevalence and incidence of hypertension, interventions to improve blood pressure control are needed to prevent associated long-term cardio- and cerebrovascular morbidity and mortality

High rate of left ventricular hypertrophy on screening echocardiography among adults living with HIV in Malawi.

BackgroundThere are limited data on structural heart disease among people living with HIV in southern Africa, where the success of antiretroviral therapy (ART) has drastically improved life expectancy and where risk factors for cardiovascular disease are prevalent.MethodsWe performed a cross-sectional study of screening echocardiography among adults (≥18 years) with HIV in Malawi presenting for routine ART care. We used univariable and multivariable logistic regression to evaluate correlates of abnormal echocardiogram.ResultsA total of 202 individuals were enrolled with a median age of 45 years (IQR 39-52); 52% were female, and 27.7% were on antihypertensive medication. The most common clinically significant abnormality was left ventricular hypertrophy (LVH) (12.9%, n=26), and other serious structural heart lesions were rare (&lt;2% with ejection fraction less than 40%, moderate-severe valve lesions or moderate-severe pericardial effusion). Characteristics associated with abnormal echocardiogram included older age (OR 1.04, 95% CI 1.01 to 1.08), higher body mass index (OR 1.09, 95% CI 1.02 to 1.17), higher mean systolic blood pressure (OR 1.03, 95% CI 1.02 to 1.05) and higher mean diastolic blood pressure (OR 1.03, 95% CI 1.01 to 1.05). In a multivariable model including age, duration on ART, body mass index, and systolic and diastolic blood pressure, only mean body mass index (adjusted OR 1.10, 95% CI 1.02 to 1.19), systolic blood pressure (aOR 1.05, 95% CI 1.03 to 1.08) and diastolic blood pressure (aOR 0.96, 95% CI 0.92 to 1.00) remained associated with abnormal echocardiogram.ConclusionsLVH was common in this population of adults on ART presenting for routine care and was associated with elevated blood pressure. Further research is needed to characterise the relationship between chronic hypertension, LVH and downstream consequences, such as diastolic dysfunction and heart failure in people living with HIV