A comparison of four epidemic waves of COVID-19 in Malawi; an observational cohort study.

BACKGROUND: Compared to the abundance of clinical and genomic information available on patients hospitalised with COVID-19 disease from high-income countries, there is a paucity of data from low-income countries. Our aim was to explore the relationship between viral lineage and patient outcome. METHODS: We enrolled a prospective observational cohort of adult patients hospitalised with PCR-confirmed COVID-19 disease between July 2020 and March 2022 from Blantyre, Malawi, covering four waves of SARS-CoV-2 infections. Clinical and diagnostic data were collected using an adapted ISARIC clinical characterization protocol for COVID-19. SARS-CoV-2 isolates were sequenced using the MinION™ in Blantyre. RESULTS: We enrolled 314 patients, good quality sequencing data was available for 55 patients. The sequencing data showed that 8 of 11 participants recruited in wave one had B.1 infections, 6/6 in wave two had Beta, 25/26 in wave three had Delta and 11/12 in wave four had Omicron. Patients infected during the Delta and Omicron waves reported fewer underlying chronic conditions and a shorter time to presentation. Significantly fewer patients required oxygen (22.7% [17/75] vs. 58.6% [140/239], p < 0.001) and steroids (38.7% [29/75] vs. 70.3% [167/239], p < 0.001) in the Omicron wave compared with the other waves. Multivariable logistic-regression demonstrated a trend toward increased mortality in the Delta wave (OR 4.99 [95% CI 1.0-25.0 p = 0.05) compared to the first wave of infection. CONCLUSIONS: Our data show that each wave of patients hospitalised with SARS-CoV-2 was infected with a distinct viral variant. The clinical data suggests that patients with severe COVID-19 disease were more likely to die during the Delta wave.

Screening for post-TB lung disease at TB treatment completion: Are symptoms sufficient?

Pulmonary TB survivors face a high burden of post-TB lung disease (PTLD) after TB treatment completion. In this secondary data analysis we investigate the performance of parameters measured at TB treatment completion in predicting morbidity over the subsequent year, to inform programmatic approaches to PTLD screening in low-resource settings. Cohort data from urban Blantyre, Malawi were used to construct regression models for five morbidity outcomes (chronic respiratory symptoms or functional limitation, ongoing health seeking, spirometry decline, self-reported financial impact of TB disease, and death) in the year after PTB treatment, using three modelling approaches: logistic regression; penalised regression with pre-selected predictors; elastic net penalised regression using the full parent dataset. Predictors included demographic, clinical, symptom, spirometry and chest x-ray variables. The predictive performance of models were examined using the area under the receiver-operator curve (ROC AUC) values. Key predictors were identified, and their positive and negative predictive values (NPV) determined. The presence of respiratory symptoms at TB treatment completion was the strongest predictor of morbidity outcomes. TB survivors reporting breathlessness had higher odds of spirometry decline (aOR 20.5, 95%CI:3-199.1), health seeking (aOR 10.2, 2.4-50), and symptoms or functional limitation at 1-year (aOR 16.7, 3.3-133.4). Those reporting activity limitation were more likely to report symptoms or functional limitation at 1-year (aOR 4.2, 1.8-10.3), or severe financial impact of TB disease (aOR2.3, 1.0-5.0). Models were not significantly improved by including spirometry or imaging parameters. ROC AUCs were between 0.65-0.77 for the morbidity outcomes. Activity limitation at treatment completion had a NPV value of 78-98% for adverse outcomes. Our data suggest that whilst challenging to predict the development of post-TB morbidity, the use of symptom screening tools at TB treatment completion to prioritise post-TB care should be explored. We identified little benefit from the additional use of spirometry or CXR imaging.

Primary health care preparedness to integrate diabetes care in Blantyre, Malawi: A mixed methods study.

BACKGROUND: There is limited access to diabetes care services at primary care facilities in Malawi. Assessing the capacity of facilities to provide diabetes care is an initial step to integrating services at primary care. AIM: To assess the preparedness for delivering diabetes services at primary care level within the Blantyre District Health Office (DHO) to support the response to NCD epidemic in Malawi. SETTING: Blantyre DHO primary care facilities. MATERIALS AND METHODS: A mixed methods approach nested in a national needs assessment for NCD response in Malawi was used. Fourteen primary healthcare facilities from Blantyre DHO were assessed. A tool adapted from the WHO rapid assessment questionnaire was used to identify human resource, equipment, supplies, and medication needed for comprehensive diabetes care. Descriptive statistics were done to analyze the quantitative data. Fisher's exact test was used to assess if there was a statistically significant difference between urban and rural facilities. Seventeen health care workers from the selected facilities participated in key informant interviews. Framework analysis method guided the qualitative data analysis. The quantitative and qualitative data were merged and displayed jointly. RESULTS: The quantitative assessment showed that none of the facilities assessed had capacity to provide all the interventions recommended by WHO for diabetes care at primary level. Eight (57%) of the facilities had the capacity to diagnose diabetes, monitor glucose, prevent limb amputations and manage hypoglycemia and hyperglycemia. Four themes emerged from the qualitative data: differences in level of preparedness and implementation of diabetes care; disparities in resources between urban and rural facilities; low utilization of diabetes services; and strategy and policy recommendations for improvement of diabetes care. CONCLUSION: Inadequate health financing resulted in significant disparities in the available resources between the rural and urban facilities to offer diabetes care services. There is need to develop national policies and guidelines for diabetes care to strengthen the capacity of primary care facilities to facilitate achievement of universal health coverage.

Decentralized Heart Failure Management in Neno, Malawi.

Background: Cardiovascular disease (CVD) is a major cause of death in Malawi. In rural districts, heart failure (HF) care is limited and provided by non-physicians. The causes and patient outcomes of HF in rural Africa are largely unknown. In our study, non-physician providers performed focused cardiac ultrasound (FOCUS) for HF diagnosis and longitudinal clinical follow-up in Neno, Malawi. Objectives: We described the clinical characteristics, HF categories, and outcomes of patients presenting with HF in chronic care clinics in Neno, Malawi. Methods: Between November 2018 and March 2021, non-physician providers performed FOCUS for diagnosis and longitudinal follow-up in an outpatient chronic disease clinic in rural Malawi. A retrospective chart review was performed for HF diagnostic categories, change in clinical status between enrollment and follow-up, and clinical outcomes. For study purposes, cardiologists reviewed all available ultrasound images. Results: There were 178 patients with HF, a median age of 67 years (IQR 44 - 75), and 103 (58%) women. During the study period, patients were enrolled for a mean of 11.5 months (IQR 5.1-16.5), after which 139 (78%) were alive and in care. The most common diagnostic categories by cardiac ultrasound were hypertensive heart disease (36%), cardiomyopathy (26%), and rheumatic, valvular or congenital heart disease (12.3%).At follow-up, the proportion of New York Heart Association (NYHA) class I patients increased from 24% to 50% (p < 0.001; 95% CI: 31.5 - 16.4), and symptoms of orthopnea, edema, fatigue, hypervolemia, and bibasilar crackles all decreased (p < 0.05). Conclusion: Hypertensive heart disease and cardiomyopathy are the predominant causes of HF in this elderly cohort in rural Malawi. Trained non-physician providers can successfully manage HF to improve symptoms and clinical outcomes in limited resource areas. Similar care models could improve healthcare access in other rural African settings.

Effect of 13-valent pneumococcal conjugate vaccine on experimental carriage of Streptococcus pneumoniae serotype 6B in Blantyre, Malawi: a randomised controlled trial and controlled human infection study.

BACKGROUND: The effect of childhood pneumococcal conjugate vaccine implementation in Malawi is threatened by absence of herd effect. There is persistent vaccine-type pneumococcal carriage in both vaccinated children and the wider community. We aimed to use a human infection study to measure 13-valent pneumococcal conjugate vaccine (PCV13) efficacy against pneumococcal carriage. METHODS: We did a double-blind, parallel-arm, randomised controlled trial investigating the efficacy of PCV13 or placebo against experimental pneumococcal carriage of Streptococcus pneumoniae serotype 6B (strain BHN418) among healthy adults (aged 18-40 years) from Blantyre, Malawi. We randomly assigned participants (1:1) to receive PCV13 or placebo. PCV13 and placebo doses were prepared by an unmasked pharmacist to maintain research team and participant masking with identification only by a randomisation identification number and barcode. 4 weeks after receiving either PCV13 or placebo, participants were challenged with 20 000 colony forming units (CFUs) per naris, 80 000 CFUs per naris, or 160 000 CFUs per naris by intranasal inoculation. The primary endpoint was experimental pneumococcal carriage, established by culture of nasal wash at 2, 7, and 14 days. Vaccine efficacy was estimated per protocol by means of a log-binomial model adjusting for inoculation dose. The trial is registered with the Pan African Clinical Trials Registry, PACTR202008503507113, and is now closed. FINDINGS: Recruitment commenced on April 27, 2021 and the final visit was completed on Sept 12, 2022. 204 participants completed the study protocol (98 PCV13, 106 placebo). There were lower carriage rates in the vaccine group at all three inoculation doses (0 of 21 vs two [11%] of 19 at 20 000 CFUs per naris; six [18%] of 33 vs 12 [29%] of 41 at 80 000 CFUs per naris, and four [9%] of 44 vs 16 [35%] of 46 at 160 000 CFUs per naris). The overall carriage rate was lower in the vaccine group compared with the placebo group (ten [10%] of 98 vs 30 [28%] of 106; Fisher's p value=0·0013) and the vaccine efficacy against carriage was estimated at 62·4% (95% CI 27·7-80·4). There were no severe adverse events related to vaccination or inoculation of pneumococci. INTERPRETATION: This is, to our knowledge, the first human challenge study to test the efficacy of a pneumococcal vaccine against pneumococcal carriage in Africa, which can now be used to establish vaccine-induced correlates of protection and compare alternative strategies to prevent pneumococcal carriage. This powerful tool could lead to new means to enhance reduction in pneumococcal carriage after vaccination. FUNDING: Wellcome Trust.

A comparison of four epidemic waves of COVID-19 in Malawi; an observational cohort study.

Background: Compared to the abundance of clinical and genomic information available on patients hospitalised with COVID-19 disease from high-income countries, there is a paucity of data from low-income countries. Our aim was to explore the relationship between viral lineage and patient outcome. Methods: We enrolled a prospective observational cohort of adult patients hospitalised with PCR-confirmed COVID-19 disease between July 2020 and March 2022 from Blantyre, Malawi, covering four waves of SARS-CoV-2 infections. Clinical and diagnostic data were collected using an adapted ISARIC clinical characterization protocol for COVID-19. SARS-CoV-2 isolates were sequenced using the MinIONâ"¢ in Blantyre. Results: We enrolled 314 patients, good quality sequencing data was available for 55 patients. The sequencing data showed that 8 of 11 participants recruited in wave one had B.1 infections, 6/6 in wave two had Beta, 25/26 in wave three had Delta and 11/12 in wave four had Omicron. Patients infected during the Delta and Omicron waves reported fewer underlying chronic conditions and a shorter time to presentation. Significantly fewer patients required oxygen (22.7% [17/75] vs. 58.6% [140/239], p<0.001) and steroids (38.7% [29/75] vs. 70.3% [167/239], p<0.001) in the Omicron wave compared with the other waves. Multivariable logistic-regression demonstrated a trend toward increased mortality in the Delta wave (OR 4.99 [95% CI 1.0-25.0 p=0.05) compared to the first wave of infection. Conclusions: Our data show that each wave of patients hospitalised with SARS-CoV-2 was infected with a distinct viral variant. The clinical data suggests that patients with severe COVID-19 disease were more likely to die during the Delta wave. Summary: We used genome sequencing to identify the variants of SARS-CoV-2 causing disease in Malawi, and found that each of the four waves was caused by a distinct variant. Clinical investigation suggested that the Delta wave had the highest mortality.

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.

Use of an electronic medical record to monitor efficacy of diabetes care in out-patients in a central hospital in Malawi: Patterns of glycaemic control and lessons learned.

The Malawian health sector has a strong tradition of systematic data collection for monitoring and evaluation of large-scale services. A highly successful adapted Directly Observed Treatment, Short course "DOTS" framework, based on patient registers and paper-based mastercards was introduced to facilitate the management and monitoring of the scale up of antiretroviral therapy. Subsequently, a simple, touch-screen based electronic medical record system (EMRs) was effectively introduced at high burden ART sites. Based on this model, in 2010, a diabetes specific EMRs was introduced in the diabetes clinic at Queen Elizabeth Central Hospital. In this paper we report on the first 3 years experience with the diabetes EMRs. We highlight the strengths and weaknesses of the diabetes EMRs and present data on glycaemic control recorded in the system.

Age Related Patterns of Disease and Mortality in Hospitalised Adults in Malawi.

BACKGROUND: The epidemic of non-communicable diseases (NCDs) in low and middle income countries (LMICs) is widely recognised as the next major challenge to global health. However, in many LMICs, infectious diseases are still prevalent resulting in a "double burden" of disease. With increased life expectancy and longevity with HIV, older adults may particularly be at risk of this double burden. Here we describe the relative contributions of infections and NCDs to hospital admissions and mortality, according to age, in Malawi's largest hospital. METHODS: Primary diagnosis on discharge/death, mortality rates, and HIV status were recorded prospectively on consecutive adult medical in-patients over 2 years using an electronic medical records system. Diagnoses were classified as infections or NCDs and analysed according to age and gender. FINDINGS: 10,191 records were analysed. Overall, infectious diseases, particularly those associated with HIV, were the leading cause of admission. However, in adults ≥55 years, NCDs were the commonest diagnoses. In adults <55 years 71% of deaths were due to infections whereas in adults ≥55 years 56% of deaths were due to NCDs. INTERPRETATION: Infectious diseases are still the leading cause of adult admission to a central hospital in Malawi but in adults aged ≥55 years NCDs are the most frequent diagnoses. HIV was an underlying factor in the majority of adults with infections and was also present in 53% of those with NCDs. These findings highlight the need for further health sector shifts to address the double burden of infectious and NCDs, particularly in the ageing population.

A survey of the management, control, and complications of diabetes mellitus in patients attending a diabetes clinic in Blantyre, Malawi, an area of high HIV prevalence.

The aim of this study was to describe the current status of diabetes care in an urban diabetes clinic in Malawi and the prevalence of human immunodeficiency virus (HIV) in this population, investigating possible associations between HIV and diabetes. A systematic prospective survey of patients attending the diabetes clinic at a teaching hospital in Blantyre, Malawi was conducted. Six hundred twenty patients were assessed. Seventy-four percent had glycosylated hemoglobin (HbA1C) > 7.5%. Systolic blood pressure was > 140 mm Hg in 52% of patients. Hypertension was more common in patients with raised creatinine (P < 0.003), retinopathy (P = 0.01), and stroke (P < 0.0002). Microvascular complication rates were high, specifically nephropathy (34.7%), retinopathy (34.7%), and neuropathy (46.4%). HIV seroprevalence was 13.7%. HIV-positive subjects had a lower body mass index (BMI) and lower fasting blood sugar, and they were more likely to have albuminuria (48.0% versus 33.3%; P < 0.05). Control of glycemia and hypertension were poor, and microvascular complications were common. Nephropathy in diabetic patients may be affected by HIV status.