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.

A Longitudinal, Observational Study of Etiology and Long-Term Outcomes of Sepsis in Malawi Revealing the Key Role of Disseminated Tuberculosis.

BACKGROUND: Sepsis protocols in sub-Saharan Africa are typically extrapolated from high-income settings, yet sepsis in sub-Saharan Africa is likely caused by distinct pathogens and may require novel treatment strategies. Data to guide such strategies are lacking. We aimed to define causes and modifiable factors associated with sepsis outcomes in Blantyre, Malawi, in order to inform the design of treatment strategies tailored to sub-Saharan Africa. METHODS: We recruited 225 adults who met a sepsis case definition defined by fever and organ dysfunction in an observational cohort study at a single tertiary center. Etiology was defined using culture, antigen detection, serology, and polymerase chain reaction. The effect of treatment on 28-day outcomes was assessed using Bayesian logistic regression. RESULTS: There were 143 of 213 (67%) participants living with human immunodeficiency virus (HIV). We identified a diagnosis in 145 of 225 (64%) participants, most commonly tuberculosis (TB; 34%) followed by invasive bacterial infections (17%), arboviral infections (13%), and malaria (9%). TB was associated with HIV infection, whereas malaria and arboviruses with the absence of HIV infection. Antituberculous chemotherapy was associated with survival (adjusted odds ratio for 28-day death, 0.17; 95% credible interval, 0.05-0.49 for receipt of antituberculous therapy). Of those with confirmed etiology, 83% received the broad-spectrum antibacterial ceftriaxone, but it would be expected to be active in only 24%. CONCLUSIONS: Sepsis in Blantyre, Malawi, is caused by a range of pathogens; the majority are not susceptible to the broad-spectrum antibacterials that most patients receive. HIV status is a key determinant of etiology. Novel antimicrobial strategies for sepsis tailored to sub-Saharan Africa, including consideration of empiric antituberculous therapy in individuals living with HIV, should be developed and trialed.

Population Incidence and Mortality of Sepsis in an Urban African Setting, 2013-2016.

BACKGROUND: Sepsis is an important cause of mortality globally, although population incidence estimates from low-income settings, including sub-Saharan Africa, are absent. We aimed to estimate sepsis incidence burden using routinely available data from a large urban hospital in Malawi. METHODS: We linked routine-care databases at Queen Elizabeth Central Hospital, Blantyre, Malawi, to provide admission and discharge data for 217 149 adults from 2013-2016. Using a definition of sepsis based on systemic inflammatory response syndrome criteria and Blantyre census population data, we calculated population incidence estimates of sepsis and severe sepsis and used negative binomial regression to assess for trends over time. Missing data were multiply imputed with chained equations. RESULTS: We estimate that the incidence rate of emergency department-attending sepsis and severe sepsis in adults was 1772 per 100 000 person-years (95% confidence interval [CI], 1754-1789) and 303 per 100 000 person-years (95% CI, 295-310), respectively, between 2013 and 2016, with a year-on-year decrease in incidence. In-hospital mortality for patients admitted to the hospital with sepsis and severe sepsis was 23.7% (95% CI, 22.7-24.7%) and 28.1% (95% CI, 26.1 - 30.0%), respectively, with no clear change over time. CONCLUSIONS: Sepsis incidence is higher in Blantyre, Malawi, than in high-income settings, from where the majority of sepsis incidence data are derived. Worldwide sepsis burden is likely to be underestimated, and data from low-income countries are needed to inform the public health response.

Critical Care Units in Malawi: A Cross-Sectional Study.

Background: The global burden of critical illness falls disproportionately outside high-income countries. Despite younger patient populations with similar or lower disease severity, critical illness outcomes are poor outside high-income countries. A lack of data limits attempts to understand and address the drivers of critical care outcomes outside high-income countries. Objectives: We aim to characterize the organization, available resources, and service capacity of public sector critical care units in Malawi and identify barriers to improving care. Methods: We conducted a secondary analysis of the Malawi Emergency and Critical Care Survey, a cross-sectional study performed from January to February 2020 at all four central hospitals and a simple random sample of nine out of 24 public sector district hospitals in Malawi, a predominantly rural, low-income country of 19.6 million in southern Africa. Data from critical care units were used to characterize resources, processes, and barriers to care. Findings: There were four HDUs and four ICUs across the 13 hospitals in the Malawi Emergency and Critical Care Survey sample. The median critical care beds per 1,000,000 catchment was 1.4 (IQR: 0.9 to 6.7). Absent equipment was the most common barrier in HDUs (46% [95% CI: 32% to 60%]). Stockouts was the most common barriers in ICUs (48% [CI: 38% to 58%]). ICUs had a median 3.0 (range: 2 to 8) functional ventilators per unit and reported an ability to perform several quality mechanical ventilation interventions. Conclusions: Although significant gaps exist, Malawian critical care units report the ability to perform several complex clinical processes. Our results highlight regional inequalities in access to care and support the use of process-oriented questions to assess critical care capacity. Future efforts should focus on basic critical care capacity outside of urban areas and quantify the impact of context-specific variables on critical care mortality.

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.

The Malawi emergency and critical care survey: A cross-sectional national facility assessment.

BACKGROUND: Data on emergency and critical care (ECC) capacity in low-income countries (LICs) are needed to improve outcomes and make progress towards realizing the goal of Universal Health Coverage. METHODS: We developed a novel research instrument to assess public sector ECC capacity and service readiness in LICs. From January 20th to February 18th, 2020 we administered the instrument at all four central hospitals and a simple random sample of nine of 24 district hospitals in Malawi, a landlocked and predominantly rural LIC of 19·1 million people in Southern Africa. The instrument contained questions on the availability of key resources across three domains and was administered to hospital administrators and clinicians from outpatient departments, emergency departments, and inpatient units. Results were used to generate an ECC Readiness Score, with a possible range of 0 to 1, for each facility. FINDINGS: A total of 114 staff members across 13 hospitals completed interviews for this study. Three (33%) district hospitals and all four central hospitals had ECC Readiness Scores above 0·5 (p-value 0·070). Absent equipment was identified as the most common barrier to ECC Readiness. Central hospitals had higher median ECC Readiness Scores with less variability 0·82 (interquartile range: 0·80-0·89) than district hospitals (0·33, 0·23 to 0·50, p-value 0·021). INTERPRETATION: This is the first study to employ a systematic approach to assessing ECC capacity and service readiness at both district and central hospitals in Malawi and provides a framework for measuring ECC capacity in other LICs. Prior ECC assessments potentially overestimated equipment availability and our methodology may provide a more accurate approach. There is an urgent need for investments in ECC services, particularly at district hospitals which are more accessible to Malawi's predominantly rural population. These findings highlight the need for long-term investments in health systems strengthening and underscore the importance of understanding capacity in LIC settings to inform these efforts. FUNDING: Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital and Department of Emergency Medicine, Brigham and Women's Hospital.

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 Prevalence and Outcomes of Sepsis in Adult Patients in Two Hospitals in Malawi.

There are an estimated 19.4 million sepsis cases every year, many of them in low-income countries. The newly adopted definition of sepsis uses Sequential Organ Failure Assessment Score (SOFA), a score which is not feasible in many low-resource settings. A simpler quick-SOFA (qSOFA) based solely on vital signs score has been devised for identification of suspected sepsis. This study aimed to determine in-hospital prevalence and outcomes of sepsis, as defined as suspected infection and a qSOFA score of 2 or more, in two hospitals in Malawi. The secondary aim was to evaluate qSOFA as a predictor of mortality. A cross-sectional study of adult in-patients in two hospitals in Malawi was conducted using prospectively collected single-day point-prevalence data and in-hospital follow-up. Of 1,135 participants, 81 (7.1%) had sepsis. Septic patients had a higher hospital mortality rate (17.5%) than non-septic infected patients (9.0%, p = 0.027, odds ratio 2.1 [1.1-4.3]), although the difference was not statistically significant after adjustment for baseline characteristics. For in-hospital mortality among patients with suspected infection, qSOFA ≥ 2 had a sensitivity of 31.8%, specificity of 82.1%, a positive predictive value of 17.5%, and a negative predictive value of 91.0%. In conclusion, sepsis is common and is associated with a high risk of death in admitted patients in hospitals in Malawi. In low-resource settings, qSOFA score that uses commonly available vital signs data may be a tool that could be used for identifying patients at risk-both for those with and without a suspected infection.