Omicron B.1.1.529 variant infections associated with severe disease are uncommon in a COVID-19 under-vaccinated, high SARS-CoV-2 seroprevalence population in Malawi

Background

The B.1.1.529 (Omicron) variant of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has resulted in the fourth COVID-19 pandemic wave across the southern African region, including Malawi. The seroprevalence of SARS-CoV-2 antibodies and their association with epidemiological trends of hospitalisations and deaths are needed to aid locally relevant public health policy decisions.

Methods

We conducted a population-based serosurvey from December 27, 2021 to January 17, 2022, in 7 districts across Malawi to determine the seroprevalence of SARS-CoV-2 antibodies. Serum samples were tested for antibodies against SARS-CoV-2 receptor binding domain using WANTAI SARS-CoV-2 Receptor Binding Domain total antibody commercial enzyme-linked immunosorbent assay (ELISA). We also evaluated COVID-19 epidemiologic trends in Malawi, including cases, hospitalisations and deaths from April 1, 2021 through April 30, 2022, collected using the routine national COVID-19 reporting system. A multivariable logistic regression model was developed to investigate the factors associated with SARS-CoV-2 seropositivity.

Findings

Serum samples were analysed from 4619 participants (57% female; 60% aged 18-50 years), of whom 878/3794 (23%) of vaccine eligible adults had received a single dose of any COVID-19 vaccine. The overall assay-adjusted seroprevalence was 83.7% (95% confidence interval (CI), 79.3%-93.4%). Seroprevalence was lowest among children <13 years of age (66%) and highest among adults 18-50 years of age (82%). Seroprevalence was higher among vaccinated compared to unvaccinated participants (1 dose, 94% vs. 77%, adjusted odds ratio 4.89 [95% CI, 3.43-7.22]; 2 doses, 97% vs. 77%, aOR 6.62 [95% CI, 4.14-11.3]). Urban residents were more likely to be seropositive than those from rural settings (91% vs. 78%, aOR 2.76 [95% CI, 2.16-3.55]). There was at least a two-fold reduction in the proportion of hospitalisations and deaths among the reported cases in the fourth wave compared to the third wave (hospitalisations, 10.7% (95% CI, 10.2-11.3) vs. 4.86% (95% CI, 4.52-5.23), p < 0.0001; deaths, 3.48% (95% CI, 3.18-3.81) vs. 1.15% (95% CI, 1.00-1.34), p < 0.0001).

Interpretation

We report reduction in proportion of hospitalisations and deaths from SARS-CoV-2 infections during the Omicron variant dominated wave in Malawi, in the context of high SARS-CoV-2 seroprevalence and low COVID-19 vaccination coverage. These findings suggest that COVID-19 vaccination policy in high seroprevalence settings may need to be amended from mass campaigns to targeted vaccination of reported at-risk populations.

Funding

Supported by the Bill and Melinda Gates Foundation (INV-039481).

Assessing the potential of HTA to inform resource allocation decisions in low-income settings: The case of Malawi

Health technology assessment (HTA) offers a set of analytical tools to support health systems' decisions about resource allocation. Although there is increasing interest in these tools across the world, including in some middle-income countries, they remain rarely used in low-income countries (LICs). In general, the focus of HTA is narrow, mostly limited to assessments of efficacy and cost-effectiveness. However, the principles of HTA can be used to support a broader series of decisions regarding new health technologies. We examine the potential for this broad use of HTA in LICs, with a focus on Malawi. We develop a framework to classify the main decisions on health technologies within health systems. The framework covers decisions on identifying and prioritizing technologies for detailed assessment, deciding whether to adopt an intervention, assessing alternative investments for implementation and scale-up, and undertaking further research activities. We consider the relevance of the framework to policymakers in Malawi and we use two health technologies as examples to investigate the main barriers and enablers to the use of HTA methods. Although the scarcity of local data, expertise, and other resources could risk limiting the operationalisation of HTA in LICs, we argue that even in highly resource constrained health systems, such as in Malawi, the use of HTA to support a broad range of decisions is feasible and desirable.

Pain Is Widespread and Predicts Poor Mental Health Among Older Adults in Rural Malawi

Background and Objectives

Pain is common among older persons and has been documented as an important predictor of disability, health, and economic outcomes. Evidence about its prevalence and relationship to well-being is scarce in rural sub-Saharan Africa (SSA), where work is frequently physically demanding, and pain prevention or treatment options are limited. We investigate the prevalence of pain and its association with mental health and subjective well-being in a population-based study of older adults in rural Malawi.

Research Design and Methods

We estimate the prevalence, severity, and duration of pain along with its sociodemographic distribution in a sample of 1,577 individuals aged 45 and older. We assess the association of pain with clinically validated measures of mental health, including depression and anxiety, and subjective well-being.

Results

Pain is widespread in this mature population with an average age of 60 years: 62% of respondents report the experience of at least minor pain during the last year, and half of these cases report severe or disabling pain. Women are more likely to report pain than men. Pain is a strong predictor of mental health and subjective well-being for both genders. More severe or longer pain episodes are associated with worse mental states. Individuals reporting pain are more likely to suffer from depression or express suicidal thoughts.

Discussion and Implications

Our study identifies key subpopulations such as older women in a SSA low-income context who are particularly affected by the experience of pain in daily life and calls for interventions targeting pain and its consequences for mental health and subjective well-being.

Urine selenium concentration is a useful biomarker for assessing population level selenium status

Plasma selenium (Se) concentration is an established population level biomarker of Se status, especially in Se-deficient populations. Previously observed correlations between dietary Se intake and urinary Se excretion suggest that urine Se concentration is also a potentially viable biomarker of Se status. However, there are only limited data on urine Se concentration among Se-deficient populations. Here, we test if urine is a viable biomarker for assessing Se status among a large sample of women and children in Malawi, most of whom are likely to be Se-deficient based on plasma Se status. Casual (spot) urine samples (n = 1406) were collected from a nationally representative sample of women of reproductive age (WRA, n =741) and school aged children (SAC, n=665) across Malawi as part of the 2015/16 Demographic and Health Survey. Selenium concentration in urine was determined using inductively coupled plasma mass spectrometry (ICP-MS). Urinary dilution corrections for specific gravity, osmolality, and creatinine were applied to adjust for hydration status. Plasma Se status had been measured for the same survey participants. There was between-cluster variation in urine Se concentration that corresponded with variation in plasma Se concentration, but not between households within a cluster, or between individuals within a household. Corrected urine Se concentrations explained more of the between-cluster variation in plasma Se concentration than uncorrected data. These results provide new evidence that urine may be used in the surveillance of Se status at the population level in some groups. This could be a cost-effective option if urine samples are already being collected for other assessments, such as for iodine status analysis as in the Malawi and other national Demographic and Health Surveys.

The risk of selenium deficiency in Malawi is large and varies over multiple spatial scales

Selenium (Se) is an essential human micronutrient. Deficiency of Se decreases the activity of selenoproteins and can compromise immune and thyroid function and cognitive development, and increase risks from non-communicable diseases. The prevalence of Se deficiency is unknown in many countries, especially in sub-Saharan Africa (SSA). Here we report that the risk of Se deficiency in Malawi is large among a nationally representative population of 2,761 people. For example, 62.5% and 29.6% of women of reproductive age (WRA, n = 802) had plasma Se concentrations below the thresholds for the optimal activity of the selenoproteins glutathione peroxidase 3 (GPx3; <86.9 ng mL⁻¹) and iodothyronine deiodinase (IDI; <64.8 ng mL⁻¹), respectively. This is the first nationally representative evidence of widespread Se deficiency in SSA. Geostatistical modelling shows that Se deficiency risks are influenced by soil type, and also by proximity to Lake Malawi where more fish is likely to be consumed. Selenium deficiency should be quantified more widely in existing national micronutrient surveillance programmes in SSA given the marginal additional cost this would incur.

Aflatoxin-lysine adducts in blood serum of the Malawian rural population and aflatoxin contamination in foods (groundnuts, maize) in the corresponding areas

Aflatoxin-lysine (AFB₁-lys) adduct levels in blood samples collected from 230 individuals living in three districts of Malawi (Kasungu, Mchinji, and Nkhotakota) and aflatoxin B₁ (AFB₁) levels in groundnut and maize samples collected from their respective homesteads were determined using indirect competitive enzyme-linked immunosorbent assay (IC-ELISA) methods. AFB₁-lys adducts were detected in 67% of blood samples, with a mean concentration of 20.5 ± 23.4 pg/mg of albumin. AFB₁ was detected in 91% of groundnut samples and in 70% of maize samples, with mean AFB₁ levels of 52.4 and 16.3 μg/kg, respectively. All participants of this study reported consuming maize on a daily basis and consuming groundnuts regularly (mean consumption frequency per week: 3.2 ± 1.7). According to regression analysis, a frequency of groundnut consumption of more than four times per week, being female, and being a farmer were significant (p < 0.05) contributors to elevated AFB₁-lys adduct levels in the blood. This is the first report on AFB₁-lys adducts in blood samples of residents in Malawi. The results reinforce the urgent need for interventions, aiming at a reduction of aflatoxin exposure of the population.

Assessment of water, sanitation and hygiene interventions in response to an outbreak of typhoid fever in Neno District, Malawi

On May 2, 2009 an outbreak of typhoid fever began in rural villages along the Malawi-Mozambique border resulting in 748 illnesses and 44 deaths by September 2010. Despite numerous interventions, including distribution of WaterGuard (WG) for in-home water treatment and education on its use, cases of typhoid fever continued. To inform response activities during the ongoing Typhoid outbreak information on knowledge, attitudes, and practices surrounding typhoid fever, safe water, and hygiene were necessary to plan future outbreak interventions. In September 2010, a survey was administered to female heads in randomly selected households in 17 villages in Neno District, Malawi. Stored household drinking water was tested for free chlorine residual (FCR) levels using the N,N diethyl-p-phenylene diamine colorimetric method (HACH Company, Loveland, CO, USA). Attendance at community-wide educational meetings was reported by 56% of household respondents. Respondents reported that typhoid fever is caused by poor hygiene (77%), drinking unsafe water (49%), and consuming unsafe food (25%), and that treating drinking water can prevent it (68%). WaterGuard, a chlorination solution for drinking water treatment, was observed in 112 (56%) households, among which 34% reported treating drinking water. FCR levels were adequate (FCR ≥ 0.2 mg/L) in 29 (76%) of the 38 households who reported treatment of stored water and had stored water available for testing and an observed bottle of WaterGuard in the home. Soap was observed in 154 (77%) households, among which 51% reported using soap for hand washing. Educational interventions did not reach almost one-half of target households and knowledge remains low. Despite distribution and promotion of WaterGuard and soap during the outbreak response, usage was low. Future interventions should focus on improving water, sanitation and hygiene knowledge, practices, and infrastructure. Typhoid vaccination should be considered.

Factors associated with HIV status awareness and Linkage to Care following home based testing in rural Malawi

OBJECTIVE

HIV diagnosis and linkage to care are the main barriers in Africa to achieving the UNAIDS 90-90-90 targets. We assessed HIV-positive status awareness and linkage to care among survey participants in Chiradzulu District, Malawi.

METHOD

Nested cohort study within a population-based survey of persons aged 15-59 years between February and May 2013. Participants were interviewed and tested for HIV (and CD4 if found HIV-positive) in their homes. Multivariable regression was used to determine factors associated with HIV-positive status awareness prior to the survey and subsequent linkage to care.

RESULTS

Of 8277 individuals eligible for the survey, 7270 (87.8%) participated and were tested for HIV. The overall HIV prevalence was 17.0%. Among HIV-positive participants, 77.0% knew their status and 72.8% were in care. Women (adjusted odds ratio [aOR] 6.5, 95% CI 3.2-13.1) and older participants (40-59 vs. 15-29 years, aOR 10.1, 95% CI 4.0-25.9) were more likely to be aware of their positive status. Of those newly diagnosed, 47.5% were linked to care within 3 months. Linkage to care was higher among older participants (40-59 vs. 15-29, adjusted hazard ratio [aHR] 3.39, 95% CI 1.83-6.26), women (aHR 1.73, 95% CI 1.12-2.67) and those eligible for ART (aHR 1.61, 95% CI 1.03-2.52).

CONCLUSIONS

In settings with high levels of HIV awareness, home-based testing remains an efficient strategy to diagnose and link to care. Men were less likely to be diagnosed, and when diagnosed to link to care, underscoring the need for a gender focus in order to achieve the 90-90-90 targets.

Iodine source apportionment in the Malawian diet

The aim of this study was to characterise nutritional-I status in Malawi. Dietary-I intakes were assessed using new datasets of crop, fish, salt and water-I concentrations, while I status was assessed for 60 women living on each of calcareous and non-calcareous soils as defined by urinary iodine concentration (UIC). Iodine concentration in staple foods was low, with median concentrations of 0.01 mg kg⁻¹ in maize grain, 0.008 mg kg⁻¹ in roots and tubers, but 0.155 mg kg⁻¹ in leafy vegetables. Freshwater fish is a good source of dietary-I with a median concentration of 0.51 mg kg⁻¹. Mean Malawian dietary-Iodine intake from food, excluding salt, was just 7.8 μg d⁻¹ compared to an adult requirement of 150 μg d⁻¹. Despite low dietary-I intake from food, median UICs were 203 μg L⁻¹ with only 12% defined as I deficient whilst 21% exhibited excessive I intake. Iodised salt is likely to be the main source of dietary I intake in Malawi; thus, I nutrition mainly depends on the usage and concentration of I in iodised salt. Drinking water could be a significant source of I in some areas, providing up to 108 μg d⁻¹ based on consumption of 2 L d⁻¹.

Formative investigation of acceptability of typhoid vaccine during a typhoid fever outbreak in Neno District, Malawi

Typhoid fever affects an estimated 22 million people annually and causes 216,000 deaths worldwide. We conducted an investigation in August and September 2010 to examine the acceptability of typhoid vaccine in Neno District, Malawi where a typhoid outbreak was ongoing. We used qualitative methods, including freelisting exercises, key informant and in-depth interviews, and group discussions. Respondents associated illness with exposure to "bad wind," and transmission was believed to be airborne. Typhoid was considered extremely dangerous because of its rapid spread, the debilitating conditions it produced, the number of related fatalities, and the perception that it was highly contagious. Respondents were skeptical about the effectiveness of water, sanitation, and hygiene (WaSH) interventions. The perceived severity of typhoid and fear of exposure, uncertainty about the effectiveness of WaSH measures, and widespread belief in the efficacy of vaccines in preventing disease resulted in an overwhelming interest in receiving typhoid vaccine during an outbreak.

A high prevalence of zinc- but not iron-deficiency among women in rural Malawi: a cross-sectional study

BACKGROUND

Zinc deficiency is often associated with nutritional iron deficiency (ID), and may be exacerbated by low selenium status.

AIM

To investigate risk of iron and zinc deficiency in women with contrasting selenium status.

METHODS

In a cross-sectional study, 1-day diet composites and blood samples were collected from self-selected Malawian women aged 18-50 years from low- (Zombwe) (n=60) and high-plant-available soil selenium (Mikalango) (n=60) districts. Diets were analyzed for trace elements and blood for biomarkers.

RESULTS

Zinc deficiency (>90 %) was greater than ID anemia (6 %), or ID (5 %), attributed to diets low in zinc (median 5.7 mg/day) with high phytate:zinc molar ratios (20.0), but high in iron (21.0 mg/day) from soil contaminant iron. Zombwe compared to Mikalango women had lower (p<0.05) intakes of selenium (6.5 vs. 55.3 µg/day), zinc (4.8 vs. 6.4 mg/day), iron (16.6 vs. 29.6 mg/day), lower plasma selenium (0.72 vs. 1.60 µmol/L), and higher body iron (5.3 vs. 3.8 mg/kg), although plasma zinc was similar (8.60 vs. 8.87 µmol/L). Body iron and plasma zinc were positive determinants of hemoglobin.

CONCLUSION

Risk of zinc deficiency was higher than ID and was shown not to be associated with selenium status. Plasma zinc was almost as important as body iron as a hemoglobin determinant.

Dietary mineral supplies in Africa

Dietary micronutrient deficiencies (MNDs) are widespread, yet their prevalence can be difficult to assess. Here, we estimate MND risks due to inadequate intakes for seven minerals in Africa using food supply and composition data, and consider the potential of food-based and agricultural interventions. Food Balance Sheets (FBSs) for 46 countries were integrated with food composition data to estimate per capita supply of calcium (Ca), copper (Cu), iron (Fe), iodine (I), magnesium (Mg), selenium (Se) and zinc (Zn), and also phytate. Deficiency risks were quantified using an estimated average requirement (EAR) 'cut-point' approach. Deficiency risks are highest for Ca (54% of the population), followed by Zn (40%), Se (28%) and I (19%, after accounting for iodized salt consumption). The risk of Cu (1%) and Mg (<1%) deficiency are low. Deficiency risks are generally lower in the north and west of Africa. Multiple MND risks are high in many countries. The population-weighted mean phytate supply is 2770 mg capita(-1) day(-1). Deficiency risks for Fe are lower than expected (5%). However, 'cut-point' approaches for Fe are sensitive to assumptions regarding requirements; e.g. estimates of Fe deficiency risks are 43% under very low bioavailability scenarios consistent with high-phytate, low-animal protein diets. Fertilization and breeding strategies could greatly reduce certain MNDs. For example, meeting HarvestPlus breeding targets for Zn would reduce dietary Zn deficiency risk by 90% based on supply data. Dietary diversification or direct fortification is likely to be needed to address Ca deficiency risks.

Multidrug-resistant typhoid fever with neurologic findings on the Malawi-Mozambique border

BACKGROUND

Salmonella enterica serovar Typhi causes an estimated 22 million cases of typhoid fever and 216 000 deaths annually worldwide. We investigated an outbreak of unexplained febrile illnesses with neurologic findings, determined to be typhoid fever, along the Malawi-Mozambique border.

METHODS

The investigation included active surveillance, interviews, examinations of ill and convalescent persons, medical chart reviews, and laboratory testing. Classification as a suspected case required fever and ≥1 other finding (eg, headache or abdominal pain); a probable case required fever and a positive rapid immunoglobulin M antibody test for typhoid (TUBEX TF); a confirmed case required isolation of Salmonella Typhi from blood or stool. Isolates underwent antimicrobial susceptibility testing and subtyping by pulsed-field gel electrophoresis (PFGE).

RESULTS

We identified 303 cases from 18 villages with onset during March-November 2009; 214 were suspected, 43 were probable, and 46 were confirmed cases. Forty patients presented with focal neurologic abnormalities, including a constellation of upper motor neuron signs (n = 19), ataxia (n = 22), and parkinsonism (n = 8). Eleven patients died. All 42 isolates tested were resistant to ampicillin, chloramphenicol, and trimethoprim-sulfamethoxazole; 4 were also resistant to nalidixic acid. Thirty-five of 42 isolates were indistinguishable by PFGE.

CONCLUSIONS

The unusual neurologic manifestations posed a diagnostic challenge that was resolved through rapid typhoid antibody testing in the field and subsequent blood culture confirmation in the Malawi national reference laboratory. Extending laboratory diagnostic capacity, including blood culture, to populations at risk for typhoid fever in Africa will improve outbreak detection, response, and clinical treatment.

Optimization of a low cost and broadly sensitive genotyping assay for HIV-1 drug resistance surveillance and monitoring in resource-limited settings

Commercially available HIV-1 drug resistance (HIVDR) genotyping assays are expensive and have limitations in detecting non-B subtypes and circulating recombinant forms that are co-circulating in resource-limited settings (RLS). This study aimed to optimize a low cost and broadly sensitive in-house assay in detecting HIVDR mutations in the protease (PR) and reverse transcriptase (RT) regions of pol gene. The overall plasma genotyping sensitivity was 95.8% (N = 96). Compared to the original in-house assay and two commercially available genotyping systems, TRUGENE® and ViroSeq®, the optimized in-house assay showed a nucleotide sequence concordance of 99.3%, 99.6% and 99.1%, respectively. The optimized in-house assay was more sensitive in detecting mixture bases than the original in-house (N = 87, P<0.001) and TRUGENE® and ViroSeq® assays. When the optimized in-house assay was applied to genotype samples collected for HIVDR surveys (N = 230), all 72 (100%) plasma and 69 (95.8%) of the matched dried blood spots (DBS) in the Vietnam transmitted HIVDR survey were genotyped and nucleotide sequence concordance was 98.8%; Testing of treatment-experienced patient plasmas with viral load (VL) ≥ and <3 log10 copies/ml from the Nigeria and Malawi surveys yielded 100% (N = 46) and 78.6% (N = 14) genotyping rates, respectively. Furthermore, all 18 matched DBS stored at room temperature from the Nigeria survey were genotyped. Phylogenetic analysis of the 236 sequences revealed that 43.6% were CRF01_AE, 25.9% subtype C, 13.1% CRF02_AG, 5.1% subtype G, 4.2% subtype B, 2.5% subtype A, 2.1% each subtype F and unclassifiable, 0.4% each CRF06_CPX, CRF07_BC and CRF09_CPX.

Impairment of a pregnant woman's acquired ability to limit Plasmodium falciparum by infection with human immunodeficiency virus type-1

In Africa, the human immunodeficiency virus (HIV) is the most serious emerging infection and Plasmodium falciparum malaria is one of the most prevalent infectious diseases. Both infections have serious consequences in pregnant women, their fetuses, and infants. We examined the association between HIV and P. falciparum in pregnant women enrolled in a malaria chemoprophylaxis study in rural Malawi. Pregnant women (n = 2,946) were enrolled at their first antenatal clinic visit (mean 5.6 months of pregnancy), placed on one of three chloroquine regimens, and followed through delivery. Plasmodium falciparum parasitemia was measured at enrollment, monthly thereafter, at delivery, and 2-6 months postpartum; placental and newborn (umbilical cord blood) infection was measured for hospital-delivered infants. Serum collected during pregnancy was tested for antibodies to HIV by enzyme-linked immunoassay with Western blot confirmation. Parasitemia was detected in 46% of 2,946 women at enrollment and 19.1% at delivery; HIV seroprevalence was 5.5%. The prevalence and geometric mean density (GMPD) of parasitemia at enrollment and at delivery were higher in HIV-seropositive(+) than in HIV-seronegative(-) women (at enrollment: 57% prevalence and a GMPD of 1,558 parasites/mm3 versus 44% and 670/mm3, respectively; P < 0.0001; and at delivery: 35% and 1,589/mm3 versus 18% and 373/mm3; P < 0.0005). Placental infection rates were higher in HIV(+) compared with HIV(-) women, (38% versus 23%; P < 0.0005). This association was strongest in multigravidas. Compared with infants born to HIV(-) women, newborns born to HIV(+) women had higher rates of umbilical cord blood parasitemia. Both HIV(+) and HIV(-) women had similar rates of parasitemia 2-6 months postpartum. The HIV infection diminishes a pregnant woman's capacity to control P. falciparum parasitemia and placental and newborn infection, the major determinants of the impact of P. falciparum on fetal growth and infant survival.

Maternal HIV infection and infant mortality in Malawi: evidence for increased mortality due to placental malaria infection

OBJECTIVES

To examine the relationship between maternal HIV infection, placental malaria infection, and infant mortality as a first step in investigating the possibility of increased vertical transmission of HIV due to placental malaria infection.

DESIGN

Retrospective analysis of data from a cohort study of mothers and infants in rural Malawi conducted from 1987 to 1990.

METHODS

Pregnant women in Malawi were enrolled in a study examining chemoprophylaxis during pregnancy. At delivery, placental malaria infection status was determined. Infants born into this study were visited every 2 months for the first 2-3 years of life. Deaths were investigated using a standardized 'verbal autopsy' interview. Maternal serum collected during pregnancy was tested for antibodies to HIV-1 by enzyme-linked immunosorbent assay with Western blot confirmation.

RESULTS

Overall, 138 (5.3%) of 2608 women in the study were HIV-1-seropositive. Infant mortality rates were 144 and 235 per 1000 live births for children born to HIV-seronegative and HIV-seropositive women, respectively (P < 0.001). In a multivariate model, the odds of dying during the post-neonatal period for an infant born to a mother with both placental malaria and HIV infection was 4.5 times greater than an infant born to a mother with only placental malaria, and between 2.7 and 7.7 times greater (depending on birthweight) than an infant born to a mother with only HIV infection.

CONCLUSIONS

This study strongly suggests that exposure to both placental malaria infection and maternal HIV infection increases post-neonatal mortality beyond the independent risk associated with exposure to either maternal HIV or placental malaria infection. If confirmed, malaria chemoprophylaxis during pregnancy could decrease the impact of transmission of HIV from mother to infant.