Covid-19 deaths in Africa: prospective systematic postmortem surveillance study

Pandemic preparedness improves national-level SARS-CoV-2 infection and mortality data completeness: a cross-country ecologic analysis

BACKGROUND

Heterogeneity in national SARS-CoV-2 infection surveillance capabilities may compromise global enumeration and tracking of COVID-19 cases and deaths and bias analyses of the pandemic's tolls. Taking account of heterogeneity in data completeness may thus help clarify analyses of the relationship between COVID-19 outcomes and standard preparedness measures.

METHODS

We examined country-level associations of pandemic preparedness capacities inventories, from the Global Health Security (GHS) Index and Joint External Evaluation (JEE), on SARS-CoV-2 infection and COVID-19 death data completion rates adjusted for income. Analyses were stratified by 100, 100-300, 300-500, and 500-700 days after the first reported case in each country. We subsequently reevaluated the relationship of pandemic preparedness on SARS-CoV-2 infection and age-standardized COVID-19 death rates adjusted for cross-country differentials in data completeness during the pre-vaccine era.

RESULTS

Every 10% increase in the GHS Index was associated with a 14.9% (95% confidence interval 8.34-21.8%) increase in SARS-CoV-2 infection completion rate and a 10.6% (5.91-15.4%) increase in the death completion rate during the entire observation period. Disease prevention (infections: β = 1.08 [1.05-1.10], deaths: β = 1.05 [1.04-1.07]), detection (infections: β = 1.04 [1.01-1.06], deaths: β = 1.03 [1.01-1.05]), response (infections: β = 1.06 [1.00-1.13], deaths: β = 1.05 [1.00-1.10]), health system (infections: β = 1.06 [1.03-1.10], deaths: β = 1.05 [1.03-1.07]), and risk environment (infections: β = 1.27 [1.15-1.41], deaths: β = 1.15 [1.08-1.23]) were associated with both data completeness outcomes. Effect sizes of GHS Index on infection completion (Low income: β = 1.18 [1.04-1.34], Lower Middle income: β = 1.41 [1.16-1.71]) and death completion rates (Low income: β = 1.19 [1.09-1.31], Lower Middle income: β = 1.25 [1.10-1.43]) were largest in LMICs. After adjustment for cross-country differences in data completeness, each 10% increase in the GHS Index was associated with a 13.5% (4.80-21.4%) decrease in SARS-CoV-2 infection rate at 100 days and a 9.10 (1.07-16.5%) decrease at 300 days. For age-standardized COVID-19 death rates, each 10% increase in the GHS Index was with a 15.7% (5.19-25.0%) decrease at 100 days and a 10.3% (- 0.00-19.5%) decrease at 300 days.

CONCLUSIONS

Results support the pre-pandemic hypothesis that countries with greater pandemic preparedness capacities have larger SARS-CoV-2 infection and mortality data completeness rates and lower COVID-19 disease burdens. More high-quality data of COVID-19 impact based on direct measurement are needed.

Enhancing SARS-CoV-2 surveillance in Malawi using telephone syndromic surveillance from July 2020 to April 2022

INTRODUCTION

Monitoring the SARS-CoV-2 pandemic in low-resource countries such as Malawi requires cost-effective surveillance strategies. This study explored the potential utility of phone-based syndromic surveillance in terms of its reach, monitoring trends in reported SARS-CoV-2-like/influenza-like symptoms (CLS/ILS), SARS-CoV-2 testing and mortality.

METHODS

Mobile phone-based interviews were conducted between 1 July 2020 and 30 April 2022, using a structured questionnaire. Randomly digital dialled numbers were used to reach individuals aged ≥18 years who spoke Chichewa or English. Verbal consent was obtained, and trained research assistants with clinical and nursing backgrounds collected information on age, sex, region of residence, reported CLS/ILS in the preceding 2 weeks, SARS-CoV-2 testing and history of household illness and death. Data were captured on tablets using the Open Data Kit database. We performed a descriptive analysis and presented the frequencies and proportions with graphical representations over time.

FINDINGS

Among 356 525 active phone numbers, 138 751 (38.9%) answered calls, of which 104 360 (75.2%) were eligible, 101 617 (97.4%) consented to participate, and 100 160 (98.6%) completed the interview. Most survey respondents were aged 25-54 years (72.7%) and male (65.1%). The regional distribution of the respondents mirrored the regional population distribution, with 45% (44%) in the southern region, 41% (43%) in the central region and 14% (13%) in the northern region. The reported SARS-CoV2 positivity rate was 11.5% (107/934). Of the 7298 patients who reported CLS/ILS, 934 (12.8%) reported having undergone COVID-19 testing. Of the reported household deaths, 47.2% (982 individuals) experienced CLS/ILS 2 weeks before their death.

CONCLUSION

Telephonic surveillance indicated that the number of SARS-CoV-2 cases was at least twice as high as the number of confirmed cases in Malawi. Our findings also suggest a substantial under-reporting of SARS-CoV-2-related deaths. Telephonic surveillance has proven feasible in Malawi, achieving the ability to characterise SARS-CoV-2 morbidity and mortality trends in low-resource settings.

Diagnostics for Public Health - Infectious Disease Surveillance and Control

AbstractAccurate diagnostics are critical in public health to ensure successful disease tracking, prevention, and control. Many of the same characteristics are desirable for diagnostic procedures in both medicine and public health: for example, low cost, high speed, low invasiveness, ease of use and interpretation, day-to-day consistency, and high accuracy. This review lays out five principles that are salient when the goal of diagnosis is to improve the overall health of a population rather than that of a particular patient, and it applies them in two important use cases: pandemic infectious disease and antimicrobial resistance.

COVID-19 mortality sentinel surveillance at a tertiary referral hospital in Lusaka, Zambia, 2020-2021

Deaths from COVID-19 likely exceeded official statistics in Zambia because of limited testing and incomplete death registration. We describe a sentinel COVID-19 mortality surveillance system in Lusaka, Zambia. We analyzed surveillance data on deceased persons of all ages undergoing verbal autopsy (VA) and COVID-19 testing at the University Teaching Hospital (UTH) mortuary in Lusaka, Zambia, from April 2020 through August 2021. VA was done by surveillance officers for community deaths and in-patient deaths that occurred <48 hours after admission. A standardized questionnaire about the circumstances proximal to death was used, with a probable cause of death assigned by a validated computer algorithm. Nasopharyngeal specimens from deceased persons were tested for COVID-19 using polymerase chain reaction and rapid diagnostic tests. We analyzed the cause of death by COVID-19 test results. Of 12,919 deceased persons at UTH mortuary during the study period, 5,555 (43.0%) had a VA and COVID-19 test postmortem, of which 79.7% were community deaths. Overall, 278 (5.0%) deceased persons tested COVID-19 positive; 7.1% during waves versus 1.4% during nonwave periods. Most (72.3%) deceased persons testing COVID-19 positive reportedly had fever, cough, and/or dyspnea and most (73.5%) reportedly had an antemortem COVID-19 test. Common causes of death for those testing COVID-19 positive included acute cardiac disease (18.3%), respiratory tract infections (16.5%), other types of cardiac diseases (12.9%), and stroke (7.2%). A notable portion of deceased persons at a sentinel site in Lusaka tested COVID-19 positive during waves, supporting the notion that deaths from COVID-19 might have been undercounted in Zambia. Many had displayed classic COVID-19 symptoms and been tested before death yet nevertheless died in the community, potentially indicating strained medical services during waves. The high proportion of cardiovascular diseases deaths might reflect the hypercoagulable state during severe COVID-19. Early supportive treatment and availability of antivirals might lessen future mortality.

Global, regional, and national age-specific progress towards the 2020 milestones of the WHO End TB Strategy: a systematic analysis for the Global Burden of Disease Study 2021

BACKGROUND

Global evaluations of the progress towards the WHO End TB Strategy 2020 interim milestones on mortality (35% reduction) and incidence (20% reduction) have not been age specific. We aimed to assess global, regional, and national-level burdens of and trends in tuberculosis and its risk factors across five separate age groups, from 1990 to 2021, and to report on age-specific progress between 2015 and 2020.

METHODS

We used the Global Burden of Diseases, Injuries, and Risk Factors Study 2021 (GBD 2021) analytical framework to compute age-specific tuberculosis mortality and incidence estimates for 204 countries and territories (1990-2021 inclusive). We quantified tuberculosis mortality among individuals without HIV co-infection using 22 603 site-years of vital registration data, 1718 site-years of verbal autopsy data, 825 site-years of sample-based vital registration data, 680 site-years of mortality surveillance data, and 9 site-years of minimally invasive tissue sample (MITS) diagnoses data as inputs into the Cause of Death Ensemble modelling platform. Age-specific HIV and tuberculosis deaths were established with a population attributable fraction approach. We analysed all available population-based data sources, including prevalence surveys, annual case notifications, tuberculin surveys, and tuberculosis mortality, in DisMod-MR 2.1 to produce internally consistent age-specific estimates of tuberculosis incidence, prevalence, and mortality. We also estimated age-specific tuberculosis mortality without HIV co-infection that is attributable to the independent and combined effects of three risk factors (smoking, alcohol use, and diabetes). As a secondary analysis, we examined the potential impact of the COVID-19 pandemic on tuberculosis mortality without HIV co-infection by comparing expected tuberculosis deaths, modelled with trends in tuberculosis deaths from 2015 to 2019 in vital registration data, with observed tuberculosis deaths in 2020 and 2021 for countries with available cause-specific mortality data.

FINDINGS

We estimated 9·40 million (95% uncertainty interval [UI] 8·36 to 10·5) tuberculosis incident cases and 1·35 million (1·23 to 1·52) deaths due to tuberculosis in 2021. At the global level, the all-age tuberculosis incidence rate declined by 6·26% (5·27 to 7·25) between 2015 and 2020 (the WHO End TB strategy evaluation period). 15 of 204 countries achieved a 20% decrease in all-age tuberculosis incidence between 2015 and 2020, eight of which were in western sub-Saharan Africa. When stratified by age, global tuberculosis incidence rates decreased by 16·5% (14·8 to 18·4) in children younger than 5 years, 16·2% (14·2 to 17·9) in those aged 5-14 years, 6·29% (5·05 to 7·70) in those aged 15-49 years, 5·72% (4·02 to 7·39) in those aged 50-69 years, and 8·48% (6·74 to 10·4) in those aged 70 years and older, from 2015 to 2020. Global tuberculosis deaths decreased by 11·9% (5·77 to 17·0) from 2015 to 2020. 17 countries attained a 35% reduction in deaths due to tuberculosis between 2015 and 2020, most of which were in eastern Europe (six countries) and central Europe (four countries). There was variable progress by age: a 35·3% (26·7 to 41·7) decrease in tuberculosis deaths in children younger than 5 years, a 29·5% (25·5 to 34·1) decrease in those aged 5-14 years, a 15·2% (10·0 to 20·2) decrease in those aged 15-49 years, a 7·97% (0·472 to 14·1) decrease in those aged 50-69 years, and a 3·29% (-5·56 to 9·07) decrease in those aged 70 years and older. Removing the combined effects of the three attributable risk factors would have reduced the number of all-age tuberculosis deaths from 1·39 million (1·28 to 1·54) to 1·00 million (0·703 to 1·23) in 2020, representing a 36·5% (21·5 to 54·8) reduction in tuberculosis deaths compared to those observed in 2015. 41 countries were included in our analysis of the impact of the COVID-19 pandemic on tuberculosis deaths without HIV co-infection in 2020, and 20 countries were included in the analysis for 2021. In 2020, 50 900 (95% CI 49 700 to 52 400) deaths were expected across all ages, compared to an observed 45 500 deaths, corresponding to 5340 (4070 to 6920) fewer deaths; in 2021, 39 600 (38 300 to 41 100) deaths were expected across all ages compared to an observed 39 000 deaths, corresponding to 657 (-713 to 2180) fewer deaths.

INTERPRETATION

Despite accelerated progress in reducing the global burden of tuberculosis in the past decade, the world did not attain the first interim milestones of the WHO End TB Strategy in 2020. The pace of decline has been unequal with respect to age, with older adults (ie, those aged >50 years) having the slowest progress. As countries refine their national tuberculosis programmes and recalibrate for achieving the 2035 targets, they could consider learning from the strategies of countries that achieved the 2020 milestones, as well as consider targeted interventions to improve outcomes in older age groups.

FUNDING

Bill & Melinda Gates Foundation.

Preparing healthcare facilities in sub-Saharan Africa for future outbreaks: insights from a multi-country digital self-assessment of COVID-19 preparedness

BACKGROUND

Despite previous experience with epidemics, African healthcare systems were inadequately prepared and substantially impacted by the coronavirus disease 2019 (COVID-19) pandemic. Limited information about the level of COVID-19 preparedness of healthcare facilities in Africa hampers policy decision-making to fight future outbreaks in the region, while maintaining essential healthcare services running.

METHODS

Between May-November 2020, we performed a survey study with SafeCare4Covid - a free digital self-assessment application - to evaluate the COVID-19 preparedness of healthcare facilities in Africa following World Health Organization guidelines. The tool assessed (i) COVID-19-related capabilities with 31 questions; and (ii) availability of essential medical supplies with a 23-supplies checklist. Tailored quality improvement plans were provided after assessments. Information about facilities' location, type, and ownership was also collected.

RESULTS

Four hundred seventy-one facilities in 11 African countries completed the capability assessment; 412 also completed the supplies checklist. The average capability score on a scale of 0-100 (n=471) was 58.0 (interquartile range 40.0-76.0), and the average supplies score (n=412) was 61.6 (39.0-83.0). Both scores were significantly lower in rural (capability score, mean 53.6 [95%CI:50.3-57.0]/supplies score, 59.1 [55.5-62.8]) versus urban facilities (capability score, 65.2 [61.7-68.7]/supplies score, 70.7 [67.2-74.1]) (P<0.0001 for both comparisons). Likewise, lower scores were found for public versus private clinics, and for primary healthcare centres versus hospitals. Guidelines for triage and isolation, clinical management of COVID-19, staff mental support, and contact tracing forms were largely missing. Handwashing stations were partially equipped in 33% of facilities. The most missing medical supply was COVID-19 specimen collection material (71%), while 43% of facilities did not have N95/FFP2 respirators and 19% lacked medical masks.

CONCLUSIONS

A large proportion of public and private African facilities providing basic healthcare in rural areas, lacked fundamental COVID-19-related capabilities and life-saving personal protective equipment. Decentralization of epidemic preparedness efforts in these settings is warranted to protect healthcare workers and patients alike in future epidemics. Digital tools are of great value to timely measure and improve epidemic preparedness of healthcare facilities, inform decision-making, create a more stakeholder-broad approach and increase health-system resilience for future disease outbreaks.

[Retrospective estimation of initial COVID-19 infections in the Santiago Metropolitan Region in Chile]

OBJECTIVE

Estimate daily infections of COVID-19 during the first year of the pandemic in the Santiago Metropolitan Region (SRM) in Chile and Chile that are more realistic than those officially registered.

METHOD

Retrospective estimate of daily infections from daily data on COVID-19 deaths, a seroprevalence study, and the REMEDID (Retrospective Methodology to Estimate Daily Infections from Deaths) algorithm.

RESULTS

In SRM, it is observed that: 1) the maximum peak of infections was more than double that registered in the official statistics; 2) such peak was reached on May 22 (95% CI: 20-24 May), 2022, that is, 24 days before the official date of the peak of infections; and 3) the first estimated contagion took place on January 28, 2020 (95% CI: January 21 to February 16), that is, 36 days before the official date. In Chile, the situation is similar. During the first wave SRM accounted for 70%-76% of those infected in Chile, while from August 2020 onwards it accounted for 36%-39%.

CONCLUSIONS

The official records of COVID-19 infections in SRM and Chile underestimated the real number of positives and showed a delay of about a month in the dynamics of infections. This is not an isolated situation, as it is known to have been the case in other countries as well. However, it is important to have reliable estimates for a correct modeling of the spread of the virus.

Host Genetic Impact on Infectious Diseases among Different Ethnic Groups

Infectious diseases such as malaria, tuberculosis (TB), human immunodeficiency virus (HIV), and the coronavirus disease of 2019 (COVID-19) are problematic globally, with high prevalence particularly in Africa, attributing to most of the death rates. There have been immense efforts toward developing effective preventative and therapeutic strategies for these pathogens globally, however, some remain uncured. Disease susceptibility and progression for malaria, TB, HIV, and COVID-19 vary among individuals and are attributed to precautionary measures, environment, host, and pathogen genetics. While studying individuals with similar attributes, it is suggested that host genetics contributes to most of an individual's susceptibility to disease. Several host genes are identified to associate with these pathogens. Interestingly, many of these genes and polymorphisms are common across diseases. This paper analyzes genes and genetic variations within host genes associated with HIV, TB, malaria, and COVID-19 among different ethnic groups. The differences in host-pathogen interaction among these groups, particularly of Caucasian and African descent, and which gene polymorphisms are prevalent in an African population that possesses protection or risk to disease are reviewed. The information in this review could potentially help develop personalized treatment that could effectively combat the high disease burden in Africa.

Intersecting epidemics: COVID-19 and HIV in sub-Saharan Africa. A systematic review (2020-2022)

There has been significant progress with regards to winning the fight against HIV globally, particularly due to the introduction of antiretroviral therapy (ART). COVID-19 threatened to derail gains in the fight against HIV. As we have started to see with studies on COVID-19 and HIV, there is a need to 'provide an in-depth view' in understanding the dynamics between the two epidemics, especially in sub-Saharan Africa. We, therefore, undertook a systemic review of existing literature to synthesize the effects of COVID-19 on the utilization of HIV services in sub-Saharan Africa, the literature on the risks associated with HIV during the COVID-19 pandemic, and lastly, the innovations and strategies adopted to continue receiving treatment in sub-Saharan Africa. We conducted a systematic review of studies published between 2020 and April 2022. We searched for relevant sub-Saharan studies in the following databases: PubMed, Google Scholar, J-STOR, and Science Direct. The review followed the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines. The search identified 647 papers, and after screening, 41 were in line with the inclusion criteria and were included in the review. There was evidence of the negative effects of COVID-19 on reducing HIV testing, ART treatment, and HIV prevention services. There is evidence pointing to the need for people living with HIV to be prioritized for COVID-19 vaccinations. Innovations and strategies implemented to mitigate the effects of COVID-19 on HIV services include community-based ART distribution, multi-month ART dispensing, the use of digital technologies, and the use of the already existing HIV infrastructure to fight COVID-19. It is still imperative that future studies explore the predictors of utilization of HIV services in the advent of COVID-19.

Immune interaction between SARS-CoV-2 and Mycobacterium tuberculosis

SARS-CoV-2 and Mycobacterium tuberculosis (Mtb) are major infectious causes of death, with meta-analyses and population-based studies finding increased mortality in co-infected patients simultaneously diagnosed with COVID-19 and tuberculosis (TB). There is a need to understand the immune interaction between SARS-CoV-2 and Mtb which impacts poor outcomes for those co-infected. We performed a PubMed and preprint search using keywords [SARS-CoV-2] AND [tuberculosis] AND [Immune response], including publications after January 2020, excluding reviews or opinions. Abstracts were evaluated by authors for inclusion of data specifically investigating the innate and/or acquired immune responses to SARS-CoV-2 and Mtb in humans and animal models, immunopathological responses in co-infection and both trials and investigations of potential protection against SARS-CoV-2 by Bacille Calmette Guérin (BCG). Of the 248 articles identified, 39 were included. Incidence of co-infection is discussed, considering in areas with a high burden of TB, where reported co-infection is likely underestimated. We evaluated evidence of the clinical association between COVID-19 and TB, discuss differences and similarities in immune responses in humans and in murine studies, and the implications of co-infection. SARS-CoV-2 and Mtb have both been shown to modulate immune responses, particularly of monocytes, macrophages, neutrophils, and T cells. Co-infection may result in impaired immunity to SARS-CoV-2, with an exacerbated inflammatory response, while T cell responses to Mtb may be modulated by SARS-CoV-2. Furthermore, there has been no proven potential COVID-19 clinical benefit of BCG despite numerous large-scale clinical trials.

Changing face of socio-economic vulnerability and COVID-19: An analysis of country wealth during the first two years of the pandemic

There are numerous academic studies on the relationship between population wealth and the incidence of COVID-19. However, research developed shows contradictory results on their relationship. In accordance with this question, this work pursues two objectives: on the one hand, to check whether wealth and disease incidence have a unidirectional and stable relationship. And on the other hand, to find out if the country's statistical production capacity is masking the real incidence of the COVID-19 pandemic. In order to achieve this objective, an ecological study has been designed at international level with the countries established as study units. The analytical strategy utilized involves the consecutive application of cross-sectional analysis, specifically employing multivariate linear regression daily throughout the first two years of the pandemic (from 03/14/2020 to 03/28/2022). The application of multiple cross-sectional analysis has shown that country wealth has a dynamic relationship with the incidence of COVID-19. Initially, it appears as a risk factor and, in the long term, as a protective element. In turn, statistical capacity appears as an explanatory variable for the number of published COVID-19 cases and deaths. Therefore, the inadequate statistical production capacity of low income countries may be masking the real incidence of the disease.

Seroprevalence of anti-SARS-CoV-2 IgG antibodies in HIV-positive and HIV-negative patients in clinical settings in Douala, Cameroon

Background

The asymptomatic nature of COVID-19 coupled with differential testing are confounders in the assessment of SARS-CoV-2 incidence among people living with HIV (PLWH). As various comorbidities increase the risk of SARS-CoV-2 infection, it is crucial to assess the potential contribution of HIV to the risk of acquiring COVID-19. Our study aimed to compare the anti-SARS-CoV-2 IgG seroprevalence among people living with and without HIV.

Methods

PLWH were enrolled in the HIV units of two health facilities in Douala, Cameroon. Participants were consecutively enrolled, among which 47 were people living with HIV and 31 were HIV-negative patients. SARS-CoV-2 antibody tests were performed on all participants. Overall, medical consultation was conducted. For HIV-positive participants only, viral load, antiretroviral regimen, duration of HIV infection, and duration of antiretroviral treatment were retrieved from medical records.

Results

We found an overall SARS-CoV-2 IgG seroprevalence of 42.31% within the study population, with a SARS-CoV-2 IgG seroprevalence of 44.6% for PLWH and 38.7% among those without HIV infection; no significant statistical difference was observed. Adjusting for sex, HIV status, and BCG vaccination, the odds of previous SARS-CoV-2 infection were higher among married persons in the study population. Sex, BCG vaccination, and HIV status were not found to be associated with SARS-CoV-2 IgG seropositivity.

Conclusions

Our findings support the lack of association between HIV status and susceptibility to SARS-CoV-2 infection. The ARV regimen, suppressed viral load, and Tenofovir boasted ARV regimen might not affect the body's immune response after exposure to SARS-CoV-2 among PLWH. Thus, if HIV is well treated, the susceptibility to COVID-19 in PLWH would be like that of the general population.

High SARS-CoV-2 seroprevalence in Lagos, Nigeria with robust antibody and cellular immune responses

Background

Early evidence suggested that the impact of the COVID-19 pandemic was less severe in Africa compared to other parts of the world. However, more recent studies indicate higher SARS-CoV-2 infection and COVID-19 mortality rates on the continent than previously documented. Research is needed to better understand SARS-CoV-2 infection and immunity in Africa.

Methods

In early 2021, we studied the immune responses in healthcare workers (HCWs) at Lagos University Teaching Hospital (n = 134) and Oxford-AstraZeneca COVID-19 vaccine recipients from the general population (n = 116) across five local government areas (LGAs) in Lagos State, Nigeria. Western blots were used to simultaneously detect SARS-CoV-2 spike and nucleocapsid (N) antibodies (n = 250), and stimulation of peripheral blood mononuclear cells with N followed by an IFN-γ ELISA was used to examine T cell responses (n = 114).

Results

Antibody data demonstrated high SARS-CoV-2 seroprevalence of 72·4% (97/134) in HCWs and 60·3% (70/116) in the general population. Antibodies directed to only SARS-CoV-2 N, suggesting pre-existing coronavirus immunity, were seen in 9·7% (13/134) of HCWs and 15·5% (18/116) of the general population. T cell responses against SARS-CoV-2 N (n = 114) were robust in detecting exposure to the virus, demonstrating 87·5% sensitivity and 92·9% specificity in a subset of control samples tested. T cell responses against SARS-CoV-2 N were also observed in 83.3% of individuals with N-only antibodies, further suggesting that prior non-SARS-CoV-2 coronavirus infection may provide cellular immunity to SARS-CoV-2.

Conclusions

These results have important implications for understanding the paradoxically high SARS-CoV-2 infection with low mortality rate in Africa and supports the need to better understand the implications of SARS-CoV-2 cellular immunity.

Investigating the Possible Reasons for the Low Reported Morbidity and Mortality of COVID-19 in African Countries: An Integrative Review

BACKGROUND

COVID-19 has impacted the world differentially with the highest mortality and morbidity rate burden in Europe and the USA and the lowest mortality and morbidity burden in Africa. This study aims to investigate the possible reasons why Africa recorded the lowest COVID-19 mortality and morbidity.

METHODS

The following search terms were used PubMed database: ["mortalit*" (tw) OR "morbidit*" (tw) AND "COVID-19" (tw) AND "Africa" (tw)]. Studies that discuss a factor for the low COVID-19 burden in Africa have a defined methodology, discuss its research question and mention its limitations are selected for review. Data from the final articles were extracted using a data collection tool.

RESULTS

Twenty-one studies were used in this integrative review. Results were grouped into 10 themes, which are younger African population, lower health capacity, weather, vaccines and drugs, effective pandemic response, lower population density and mobility, African socioeconomic status, lower prevalence of comorbidities, genetic difference and previous infection exposure. The low COVID-19 mortality and morbidity in Africa is largely a result of a combined effect of the younger African population and underreporting of COVID-19 cases.

CONCLUSIONS

There is a need to strengthen the health capacities of African countries. Moreover, African countries that have other health problem priorities may use a tailored approach to vaccinating the elderly. More definitive studies are needed to know the role of BCG vaccination, weather, genetic makeup and prior infection exposure in the differential impact of the COVID-19 pandemic.

Excess mortality associated with the COVID-19 pandemic during the 2020 and 2021 waves in Antananarivo, Madagascar

INTRODUCTION

COVID-19-associated mortality remains difficult to estimate in sub-Saharan Africa because of the lack of comprehensive systems of death registration. Based on death registers referring to the capital city of Madagascar, we sought to estimate the excess mortality during the COVID-19 pandemic and calculate the loss of life expectancy.

METHODS

Death records between 2016 and 2021 were used to estimate weekly excess mortality during the pandemic period. To infer its synchrony with circulation of SARS-CoV-2, a cross-wavelet analysis was performed. Life expectancy loss due to the COVID-19 pandemic was calculated by projecting mortality rates using the Lee and Carter model and extrapolating the prepandemic trends (1990-2019). Differences in life expectancy at birth were disaggregated by cause of death.

RESULTS

Peaks of excess mortality in 2020-21 were associated with waves of COVID-19. Estimates of all-cause excess mortality were 38.5 and 64.9 per 100 000 inhabitants in 2020 and 2021, respectively, with excess mortality reaching ≥50% over 6 weeks. In 2021, we quantified a drop of 0.8 and 1.0 years in the life expectancy for men and women, respectively attributable to increased risks of death beyond the age of 60 years.

CONCLUSION

We observed high excess mortality during the pandemic period, in particular around the peaks of SARS-CoV-2 circulation in Antananarivo. Our study highlights the need to implement death registration systems in low-income countries to document true toll of a pandemic.

Attributed causes of excess mortality during the COVID-19 pandemic in a south Indian city

Globally, excess deaths during 2020-21 outnumbered documented COVID-19 deaths by 9.5 million, primarily driven by deaths in low- and middle-income countries (LMICs) with limited vital surveillance. Here we unravel the contributions of probable COVID-19 deaths from other changes in mortality related to pandemic control measures using medically-certified death registrations from Madurai, India-an urban center with well-functioning vital surveillance. Between March, 2020 and July, 2021, all-cause deaths in Madurai exceeded expected levels by 30% (95% confidence interval: 27-33%). Although driven by deaths attributed to cardiovascular or cerebrovascular conditions, diabetes, senility, and other uncategorized causes, increases in these attributions were restricted to medically-unsupervised deaths, and aligned with surges in confirmed or attributed COVID-19 mortality, likely reflecting mortality among unconfirmed COVID-19 cases. Implementation of lockdown measures was associated with a 7% (0-13%) reduction in all-cause mortality, driven by reductions in deaths attributed to injuries, infectious diseases and maternal conditions, and cirrhosis and other liver conditions, respectively, but offset by a doubling in cancer deaths. Our findings help to account for gaps between documented COVID-19 mortality and excess all-cause mortality during the pandemic in an LMIC setting.

Alternative epidemic indicators for COVID-19 in three settings with incomplete death registration systems

Not all COVID-19 deaths are officially reported, and particularly in low-income and humanitarian settings, the magnitude of reporting gaps remains sparsely characterized. Alternative data sources, including burial site worker reports, satellite imagery of cemeteries, and social media-conducted surveys of infection may offer solutions. By merging these data with independently conducted, representative serological studies within a mathematical modeling framework, we aim to better understand the range of underreporting using examples from three major cities: Addis Ababa (Ethiopia), Aden (Yemen), and Khartoum (Sudan) during 2020. We estimate that 69 to 100%, 0.8 to 8.0%, and 3.0 to 6.0% of COVID-19 deaths were reported in each setting, respectively. In future epidemics, and in settings where vital registration systems are limited, using multiple alternative data sources could provide critically needed, improved estimates of epidemic impact. However, ultimately, these systems are needed to ensure that, in contrast to COVID-19, the impact of future pandemics or other drivers of mortality is reported and understood worldwide.

Evaluation of the Global Health Security Index as a predictor of COVID-19 excess mortality standardised for under-reporting and age structure

BACKGROUND

Previous studies have observed that countries with the strongest levels of pandemic preparedness capacities experience the greatest levels of COVID-19 burden. However, these analyses have been limited by cross-country differentials in surveillance system quality and demographics. Here, we address limitations of previous comparisons by exploring country-level relationships between pandemic preparedness measures and comparative mortality ratios (CMRs), a form of indirect age standardisation, of excess COVID-19 mortality.

METHODS

We indirectly age standardised excess COVID-19 mortality, from the Institute for Health Metrics and Evaluation modelling database, by comparing observed total excess mortality to an expected age-specific COVID-19 mortality rate from a reference country to derive CMRs. We then linked CMRs with data on country-level measures of pandemic preparedness from the Global Health Security (GHS) Index. These data were used as input into multivariable linear regression analyses that included income as a covariate and adjusted for multiple comparisons. We conducted a sensitivity analysis using excess mortality estimates from WHO and The Economist.

RESULTS

The GHS Index was negatively associated with excess COVID-19 CMRs (table 2; β= -0.21, 95% CI= -0.35 to -0.08). Greater capacities related to prevention (β= -0.11, 95% CI= -0.22 to -0.00), detection (β= -0.09, 95% CI= -0.19 to -0.00), response (β = -0.19, 95% CI= -0.36 to -0.01), international commitments (β= -0.17, 95% CI= -0.33 to -0.01) and risk environments (β= -0.30, 95% CI= -0.46 to -0.15) were each associated with lower CMRs. Results were not replicated using excess mortality models that rely more heavily on reported COVID-19 deaths (eg, WHO and The Economist).

CONCLUSION

The first direct comparison of COVID-19 excess mortality rates across countries accounting for under-reporting and age structure confirms that greater levels of preparedness were associated with lower excess COVID-19 mortality. Additional research is needed to confirm these relationships as more robust national-level data on COVID-19 impact become available.

Thirty-Day Outcomes of Young and Middle-Aged Adults Admitted with Severe COVID-19 in Uganda: A Retrospective Cohort Study

Background

There is scarcity of data regarding young and middle-aged adults hospitalized with severe Corona Virus Disease 2019 (COVID-19) in Africa. In this study, we describe the clinical characteristics and 30-day survival among adults aged 18 to 49 years admitted with severe COVID-19 in Uganda.

Methods

We reviewed treatment records of patients admitted with severe COVID-19 across five COVID-19 treatment units (CTU) in Uganda. We included individuals aged 18 to 49 years, who had a positive test or met the clinical criteria for COVID-19. We defined severe COVID-19 as having an oxygen saturation <94%, lung infiltrates >50% on imaging and presence of a co-morbidity that required admission in the CTU. Our main outcome was the 30-day survival from the time of admission. We used a Cox proportional hazards model to determine the factors associated with 30-day survival at a 5% level of significance.

Results

Of the 246 patient files reviewed, 50.8% (n = 125) were male, the mean ± (standard deviation) age was 39 ± 8 years, majority presented with cough, 85.8% (n = 211) and median C-reactive protein (interquartile range) was 48 (47.5, 178.8) mg/L. The 30-day mortality was 23.9% (59/246). At admission, anemia (hazard ratio (HR): 3.00, 95% confidence interval (CI), 1.32-6.82; p = 0.009) and altered mental state (GCS <15) (HR: 6.89, 95% CI: 1.48-32.08, p = 0.014) were significant predictors of 30-day mortality.

Conclusion

There was a high 30-day mortality among young and middle-aged adults with severe COVID-19 in Uganda. Early recognition and targeted management of anemia and altered consciousness are needed to improve clinical outcomes.

COVID-19 surveillance in Democratic Republic of Congo, Nigeria, Senegal and Uganda: strengths, weaknesses and key Lessons

INTRODUCTION

As part of efforts to rapidly identify and care for individuals with COVID-19, trace and quarantine contacts, and monitor disease trends over time, most African countries implemented interventions to strengthen their existing disease surveillance systems. This research describes the strengths, weaknesses and lessons learnt from the COVID-19 surveillance strategies implemented in four African countries to inform the enhancement of surveillance systems for future epidemics on the continent.

METHODS

The four countries namely the Democratic Republic of Congo (DRC), Nigeria, Senegal, and Uganda, were selected based on their variability in COVID-19 response and representation of Francophone and Anglophone countries. A mixed-methods observational study was conducted including desk review and key informant interviews, to document best practices, gaps, and innovations in surveillance at the national, sub-national, health facilities, and community levels, and these learnings were synthesized across the countries.

RESULTS

Surveillance approaches across countries included - case investigation, contact tracing, community-based, laboratory-based sentinel, serological, telephone hotlines, and genomic sequencing surveillance. As the COVID-19 pandemic progressed, the health systems moved from aggressive testing and contact tracing to detect virus and triage individual contacts into quarantine and confirmed cases, isolation and clinical care. Surveillance, including case definitions, changed from contact tracing of all contacts of confirmed cases to only symptomatic contacts and travelers. All countries reported inadequate staffing, staff capacity gaps and lack of full integration of data sources. All four countries under study improved data management and surveillance capacity by training health workers and increasing resources for laboratories, but the disease burden was under-detected. Decentralizing surveillance to enable swifter implementation of targeted public health measures at the subnational level was a challenge. There were also gaps in genomic and postmortem surveillance including community level sero-prevalence studies, as well as digital technologies to provide more timely and accurate surveillance data.

CONCLUSION

All the four countries demonstrated a prompt public health surveillance response and adopted similar approaches to surveillance with some adaptations as the pandemic progresses. There is need for investments to enhance surveillance approaches and systems including decentralizing surveillance to the subnational and community levels, strengthening capabilities for genomic surveillance and use of digital technologies, among others. Investing in health worker capacity, ensuring data quality and availability and improving ability to transmit surveillance data between and across multiple levels of the health care system is also critical. Countries need to take immediate action in strengthening their surveillance systems to better prepare for the next major disease outbreak and pandemic.

Priority age targets for COVID-19 vaccination in Ethiopia under limited vaccine supply

The worldwide inequitable access to vaccination claims for a re-assessment of policies that could minimize the COVID-19 burden in low-income countries. Nine months after the launch of the national vaccination program in March 2021, only 3.4% of the Ethiopian population received two doses of COVID-19 vaccine. We used a SARS-CoV-2 transmission model to estimate the level of immunity accrued before the launch of vaccination in the Southwest Shewa Zone (SWSZ) and to evaluate the impact of alternative age priority vaccination targets in a context of limited vaccine supply. The model was informed with available epidemiological evidence and detailed contact data collected across different geographical settings (urban, rural, or remote). We found that, during the first year of the pandemic, the mean proportion of critical cases occurred in SWSZ attributable to infectors under 30 years of age would range between 24.9 and 48.0%, depending on the geographical setting. During the Delta wave, the contribution of this age group in causing critical cases was estimated to increase on average to 66.7-70.6%. Our findings suggest that, when considering the vaccine product available at the time (ChAdOx1 nCoV-19; 65% efficacy against infection after 2 doses), prioritizing the elderly for vaccination remained the best strategy to minimize the disease burden caused by Delta, irrespectively of the number of available doses. Vaccination of all individuals aged ≥ 50 years would have averted 40 (95%PI: 18-60), 90 (95%PI: 61-111), and 62 (95%PI: 21-108) critical cases per 100,000 residents in urban, rural, and remote areas, respectively. Vaccination of all individuals aged ≥ 30 years would have averted an average of 86-152 critical cases per 100,000 individuals, depending on the setting considered. Despite infections among children and young adults likely caused 70% of critical cases during the Delta wave in SWSZ, most vulnerable ages should remain a key priority target for vaccination against COVID-19.

SARS-CoV-2 persistence and infectivity in COVID-19 corpses: a systematic review

The persistence and infectivity of SARS-CoV-2 in different postmortem COVID-19 specimens remain unclear despite numerous published studies. This information is essential to improve corpses management related to clinical biosafety and viral transmission in medical staff and the public community. We aim to understand SARS-CoV-2 persistence and infectivity in COVID-19 corpses. We conducted a systematic review according to Preferred Reporting Items for Systematic Reviews and Meta-Analysis (PRISMA) protocols. A systematic literature search was performed in PubMed, Science Direct Scopus, and Google Scholar databases using specific keywords. We critically reviewed the collected studies and selected the articles that met the criteria. We included 33 scientific papers that involved 491 COVID-19 corpses. The persistence rate and maximum postmortem interval (PMI) range of the SARS-CoV-2 findings were reported in the lungs (138/155, 89.0%; 4 months), followed by the vitreous humor (7/37, 18.9%; 3 months), nasopharynx/oropharynx (156/248, 62.9%; 41 days), abdominal organs (67/110, 60.9%; 17 days), skin (14/24, 58.3%; 17 days), brain (14/31, 45.2%; 17 days), bone marrow (2/2, 100%; 12 days), heart (31/69, 44.9%; 6 days), muscle tissues (9/83, 10.8%; 6 days), trachea (9/20, 45.0%; 5 days), and perioral tissues (21/24, 87.5%; 3.5 days). SARS-CoV-2 infectivity rates in viral culture studies were detected in the lungs (9/15, 60%), trachea (2/4, 50%), oropharynx (1/4, 25%), and perioral (1/4, 25%) at a maximum PMI range of 17 days. The SARS-CoV-2 persists in the human body months after death and should be infectious for weeks. This data should be helpful for postmortem COVID-19 management and viral transmission preventive strategy.

Characteristics and outcomes of patients hospitalized with COVID-19 at a tertiary hospital in Nigeria

Background

Data regarding the features and outcomes of hospitalized COVID-19 patients in Africa are increasingly available.

Objectives

To describe socio-demographic, clinical and laboratory characteristics and outcomes of COVID-19 patients.

Methods

A cross-sectional study of 86 adult patients hospitalized with COVID-19 between March and November 2020. Characteristics were described in survivors and non-survivors.

Results

Mean age was 60.9±16.1 years, 53(61.6%) were male. Co-morbidities were found in 77(89.5%) patients. On severity, 6(7%) were mild, 23(26.7%) moderate, 51(59.3%) severe and 6(7%) critical. Oxygen saturation and respiratory rate were 71±22% and 38±11/minute in non-survivors and 90±7% and 31±7/minute in survivors respectively (p<0.001, p<0.001)). Overall mortality was 47.7% with no death among patients with mild disease and deaths in all patients with critical disease. Duration of hospitalization was 2.0(1.0-4.5) days in those who died and 12(7.0-15.0) days in those who survived (p<0.001). Of the 42 patients that received dexamethasone, 11(26.2%) died, while 31(73.8%) survived (p=<0.001).

Conclusion

Most of the patients had co-morbidities and there was high mortality in patients with severe and critical COVID-19. Mean oxygen saturation was low and respiratory rate high overall. Factors associated with mortality included: Significantly greater hypoxia and tachypnea, less dexamethasone use and shorter hospitalization.

Vaccine inequity-induced COVID-19 dilemma: Time to sober up

UNSTRUCTURED

The ongoing coronavirus disease 2019 pandemic has not only posed a serious threat to public health but has also imposed a heavy burden on medical systems and global economies. To combat this challenge, unprecedented efforts have been made by governments and the scientific community in the development and production of vaccines. As a result, less than a year elapsed between identification of a novel pathogen sequence and large-scale vaccine rollout. However, much of the focus and debate has increasingly shifted to the looming risk of global vaccine inequity and whether we could do more to modify this risk. In this paper, we first outline the scope of inequitable vaccine distribution and identify its truly catastrophic consequences. Then, from the perspectives of political will, free markets and profit-driven enterprises based on patent and intellectual property protection, we analyze in-depth the root causes why this phenomenon is so difficult to combat. Apart from these, some specific and crucial solutions that should be undertaken in the long term were also put forward, in order to provide a useful reference for the authorities, stakeholders and researchers involved in addressing this global crisis and the next one.

Value of Verbal Autopsy in a Fragile Setting: Reported versus Estimated Community Deaths Associated with COVID-19, Banadir, Somalia

BACKGROUND

Accurate mortality data associated with infectious diseases such as coronavirus disease 2019 (COVID-19) are often unavailable in countries with fragile health systems such as Somalia. We compared officially reported COVID-19 deaths in Somalia with COVID-19 deaths estimated using verbal autopsy.

METHODS

We interviewed relatives of deceased persons to collect information on symptoms, cause, and place of death. We compared these data with officially reported data and estimated the positive and negative predictive values of verbal autopsy.

RESULTS

We identified 530 deaths during March-October 2020. We classified 176 (33.2%) as probable COVID-19 deaths. Most deaths (78.5%; 416/530) occurred at home and 144 (34.6%) of these were attributed to COVID-19. The positive predictive value of verbal autopsy was lower for home deaths (22.3%; 95% CI: 15.7-30.1%) than for hospital deaths (32.3%; 95% CI: 16.7-51.4%). The negative predictive value was higher: 97.8% (95% CI: 95.0-99.3%) for home deaths and 98.4% (95% CI: 91.5-100%) for hospital deaths. Conclusions Verbal autopsy has acceptable predictive value to estimate COVID-19 deaths where disease prevalence is high and can provide data on the COVID-19 burden in countries with low testing and weak mortality surveillance where home deaths may be missed.

[Impact of COVID-19 on public health in sub-Saharan Africa]

Objective

This work aimed to assess the impact of COVID-19 on healthcare supply in sub-Saharan Africa except South Africa.

Method

A search through PubMed® between April 2020 and August 2022 selected 135 articles. The impact of COVID-19 was assessed on comparisons with the months prior to the onset of COVID-19 or an identical season in previous years.

Results

The decline of health services, associated with a reduction in their quality, and the closure of specialized health units have been reported. Many control programs and public health interventions have been interrupted, with the risk of an increase of the corresponding diseases. Social disorganization has generated mental health issues among the population, including health personnel. The impact was heterogeneous in space and time. The main causes were attributed to containment measures (transport restrictions, trade closures) and the lack of human and material resources. The increase in costs, in addition to the impoverishment of the population, and the fear of being contaminated or stigmatized have discouraged patients from going to health centres. The studies mention the gradual return to normal after the first epidemic wave and the resilience of the healthcare system.

Conclusion

Several articles make recommendations aimed at reducing the impact of future epidemics: support for community workers, training of health workers and reorganization of services to improve the reception and care of patients, technological innovations (use of telephones, drones, etc.) and better information monitoring.

Effects of tuberculosis and/or HIV-1 infection on COVID-19 presentation and immune response in Africa

Few studies from Africa have described the clinical impact of co-infections on SARS-CoV-2 infection. Here, we investigate the presentation and outcome of SARS-CoV-2 infection in an African setting of high HIV-1 and tuberculosis prevalence by an observational case cohort of SARS-CoV-2 patients. A comparator group of non SARS-CoV-2 participants is included. The study includes 104 adults with SARS-CoV-2 infection of whom 29.8% are HIV-1 co-infected. Two or more co-morbidities are present in 57.7% of participants, including HIV-1 (30%) and active tuberculosis (14%). Amongst patients dually infected by tuberculosis and SARS-CoV-2, clinical features can be typical of either SARS-CoV-2 or tuberculosis: lymphopenia is exacerbated, and some markers of inflammation (D-dimer and ferritin) are further elevated (p < 0.05). Amongst HIV-1 co-infected participants those with low CD4 percentage strata exhibit reduced total, but not neutralising, anti-SARS-CoV-2 antibodies. SARS-CoV-2 specific CD8 T cell responses are present in 35.8% participants overall but undetectable in combined HIV-1 and tuberculosis. Death occurred in 30/104 (29%) of all COVID-19 patients and in 6/15 (40%) of patients with coincident SARS-CoV-2 and tuberculosis. This shows that in a high incidence setting, tuberculosis is a common co-morbidity in patients admitted to hospital with COVID-19. The immune response to SARS-CoV-2 is adversely affected by co-existent HIV-1 and tuberculosis.

COVID-19-related excess mortality - an overview of the current evidence

Analysis of excess deaths, defined as the difference in the total number of deaths in an emergency compared to the number of deaths expected under normal conditions, allows a more reliable assessment of the impact on health systems caused by the global threat of SARS-CoV-2 (Severe Acute Respiratory Syndrome Coronavirus-2). So far, data for the two years of the pandemic (2020-2021) indicates the occurrence of 14.9 million excess deaths according to WHO (World Health Organization) estimates. The purpose of the analysis conducted was to define the concept and identify the causes of excess mortality during the COVID-19 pandemic. Inconsistent and unreliable death registration systems; overburdened health systems in low- and middle-income countries; reduced access to medical services for patients with health problems other than COVID-19; the introduction of social distancing and lockdown rules, which translated into increased deaths from psychiatric illnesses and addictions; political considerations and media messages that interfered with vaccination acceptance and adherence; and the additional impact of other natural disasters (hurricanes, floods, drought) were identified as the most important reasons for excess deaths occurrence. The correct identification of country-specific factors and the correct response and countermeasures taken appear crucial in terms of limiting the negative impact of the current pandemic, but also of future threats of a similar nature, in order to reduce excess deaths.

SARS-CoV-2 diagnostic testing rates determine the sensitivity of genomic surveillance programs

The first step in SARS-CoV-2 genomic surveillance is testing to identify people who are infected. However, global testing rates are falling as we emerge from the acute health emergency and remain low in many low- and middle-income countries (mean = 27 tests per 100,000 people per day). We simulated COVID-19 epidemics in a prototypical low- and middle-income country to investigate how testing rates, sampling strategies and sequencing proportions jointly impact surveillance outcomes, and showed that low testing rates and spatiotemporal biases delay time to detection of new variants by weeks to months and can lead to unreliable estimates of variant prevalence, even when the proportion of samples sequenced is increased. Accordingly, investments in wider access to diagnostics to support testing rates of approximately 100 tests per 100,000 people per day could enable more timely detection of new variants and reliable estimates of variant prevalence. The performance of global SARS-CoV-2 genomic surveillance programs is fundamentally limited by access to diagnostic testing.

What is the prevalence of COVID-19 detection by PCR among deceased individuals in Lusaka, Zambia? A postmortem surveillance study

OBJECTIVES

To determine the prevalence of COVID-19 postmortem setting in Lusaka, Zambia.

DESIGN

A systematic, postmortem prevalence study.

SETTING

A busy, inner-city morgue in Lusaka.

PARTICIPANTS

We sampled a random subset of all decedents who transited the University Teaching Hospital morgue. We sampled the posterior nasopharynx of decedents using quantitative PCR. Prevalence was weighted to account for age-specific enrolment strategies.

INTERVENTIONS

Not applicable-this was an observational study.

PRIMARY OUTCOMES

Prevalence of COVID-19 detections by PCR. Results were stratified by setting (facility vs community deaths), age, demographics and geography and time.

SECONDARY OUTCOMES

Shifts in viral variants; causal inferences based on cycle threshold values and other features; antemortem testing rates.

RESULTS

From 1118 decedents enrolled between January and June 2021, COVID-19 was detected among 32.0% (358/1116). Roughly four COVID-19+ community deaths occurred for every facility death. Antemortem testing occurred for 52.6% (302/574) of facility deaths but only 1.8% (10/544) of community deaths and overall, only ~10% of COVID-19+ deaths were identified in life. During peak transmission periods, COVID-19 was detected in ~90% of all deaths. We observed three waves of transmission that peaked in July 2020, January 2021 and ~June 2021: the AE.1 lineage and the Beta and Delta variants, respectively. PCR signals were strongest among those whose deaths were deemed 'probably due to COVID-19', and weakest among children, with an age-dependent increase in PCR signal intensity.

CONCLUSIONS

COVID-19 was common among deceased individuals in Lusaka. Antemortem testing was rarely done, and almost never for community deaths. Suspicion that COVID-19 was the cause of deaths was highest for those with a respiratory syndrome and lowest for individuals <19 years.

Clinical Characteristics and Outcomes of Patients Hospitalized With COVID-19 During the First 4 Waves in Zambia

IMPORTANCE

Few epidemiologic studies related to COVID-19 have emerged from countries in Africa, where demographic characteristics, epidemiology, and health system capacity differ from other parts of the world.

OBJECTIVES

To describe the characteristics and outcomes of patients admitted to COVID-19 treatment centers, assess risk factors for in-hospital death, and explore how treatment center admissions were affected by COVID-19 waves in Zambia.

DESIGN, SETTING, AND PARTICIPANTS

This retrospective cohort study assessed patients admitted to COVID-19 treatment centers in 5 Zambian cities between March 1, 2020, and February 28, 2022.

EXPOSURES

Risk factors for in-hospital mortality, including patient age and severity of COVID-19, at treatment center admission.

MAIN OUTCOMES AND MEASURES

Patient information was collected, including inpatient disposition (discharged or died). Differences across and within COVID-19 waves were assessed. Mixed-effects logistic regression models were used to assess associations between risk factors and in-hospital mortality as well as between characteristics of admitted patients and timing of admission.

RESULTS

A total of 3876 patients were admitted during 4 COVID-19 waves (mean [SD] age, 50.6 [19.5] years; 2103 male [54.3%]). Compared with the first 3 waves (pooled), the proportion of patients who were 60 years or older admitted during wave 4, when the Omicron variant was circulating, was significantly lower (250 of 1009 [24.8%] vs 1116 of 2837 [39.3%]; P < .001). Factors associated with in-hospital mortality included older age (≥60 vs <30 years; adjusted odds ratio [aOR], 3.55; 95% CI, 2.34-5.52) and HIV infection (aOR, 1.39; 95% CI, 1.07-1.79). Within waves, patients who were admitted during weeks 5 to 9 had significantly higher odds of being 60 years or older (aOR, 2.09; 95% CI, 1.79-2.45) or having severe COVID-19 at admission (aOR, 2.49; 95% CI, 2.14-2.90) than those admitted during the first 4 weeks.

CONCLUSIONS AND RELEVANCE

The characteristics of admitted patients during the Omicron wave and risk factors for in-hospital mortality in Zambia reflect data reported elsewhere. Within-wave analyses revealed a pattern in which it appeared that admission of higher-risk patients was prioritized during periods when there were surges in demand for health services during COVID-19 waves. These findings support the need to expand health system capacity and improve health system resiliency in Zambia and other countries with resource-limited health systems.

Comparison of COVID-19 Pandemic Waves in 10 Countries in Southern Africa, 2020-2021

We used publicly available data to describe epidemiology, genomic surveillance, and public health and social measures from the first 3 COVID-19 pandemic waves in southern Africa during April 6, 2020-September 19, 2021. South Africa detected regional waves on average 7.2 weeks before other countries. Average testing volume 244 tests/million/day) increased across waves and was highest in upper-middle-income countries. Across the 3 waves, average reported regional incidence increased (17.4, 51.9, 123.3 cases/1 million population/day), as did positivity of diagnostic tests (8.8%, 12.2%, 14.5%); mortality (0.3, 1.5, 2.7 deaths/1 million populaiton/day); and case-fatality ratios (1.9%, 2.1%, 2.5%). Beta variant (B.1.351) drove the second wave and Delta (B.1.617.2) the third. Stringent implementation of safety measures declined across waves. As of September 19, 2021, completed vaccination coverage remained low (8.1% of total population). Our findings highlight opportunities for strengthening surveillance, health systems, and access to realistically available therapeutics, and scaling up risk-based vaccination.

Knowledge and practices toward COVID-19 among healthcare students: A cross-sectional study at the University of Zambia

Background

The COVID-19 pandemic led to the disruption of physical classes for university students globally, as large gatherings fuelled the transmission of the virus. In the efforts to mitigate its transmission and return to normality, prevention measures, including vaccination, have been encouraged. Therefore, it is critical to understand the knowledge and practices of students regarding COVID-19. This study assessed the knowledge and practices toward COVID-19 among healthcare students at the University of Zambia.

Materials and methods

This questionnaire-based cross-sectional study was carried out from August 2021 to October 2021 among 478 healthcare students (pharmacy, physiotherapy, nursing, biomedical, medicine, and radiography). We used a previously validated questionnaire to measure knowledge and practice. The predictors of knowledge and practices were assessed using logistic regression with robust estimation of standard errors. Statistical analysis was conducted using Stata/BE version 17.0.

Results

Of the 478 respondents, 243 (50.8%) were females. A larger proportion, 175 (36.6%) were in Pharmacy training, and 156 (32.6%) were in their fifth year of study. The overall mean knowledge score of the participants was 87.9 (SD = 16.1), being higher at 89.6 (SD = 14.3) among medical students and the lowest at 86.7 (SD = 17.1) among Pharmacy students, although this was statistically non-significant (p = 0.488). The overall mean practice score was 60.0 (SD = 24.7), being significantly higher at 63.5 (23.4) among nursing, physiotherapy and environmental students compared to other students (p = 0.048). In multivariable analysis, the participant training program was non-significantly associated with knowledge and practice toward COVID-19. However, increased age (AOR = 1.09, 95% CI: 1.01-1.117) and residing in urban areas (AOR = 1.79, 95% CI: 1.07-3.01) than in rural areas were associated with higher odds of good practice toward COVID-19.

Conclusion

The healthcare students generally showed good knowledge levels and poor practices toward COVID-19. Further, there was no evidence of a difference in knowledge of COVID-19 among healthcare students. These findings suggest the need for implementation strategies to be centered on improving the practices of students toward COVID-19.

Country-Level Governance Indicators as Predictors of COVID-19 Morbidity, Mortality, and Vaccination Coverage: An Exploratory Global Analysis

As the COVID-19 pandemic continues to affect all countries across the globe, this study seeks to investigate the relationship between nations' governance, COVID-19 national data, and nation-level COVID-19 vaccination coverage. National-level governance indicators (corruption index, voice and accountability, political stability, and absence of violence/terrorism), officially reported COVID-19 national data (cases, death, and tests per one million population), and COVID-19 vaccination coverage was considered for this study to predict COVID-19 morbidity and mortality. Results indicate a strong relationship between nations' governance and officially reported COVID-19 data. Countries were grouped into three clusters using only the governance data: politically stable countries, average countries or "less corrupt countries," and corrupt countries or "more corrupt countries." The clusters were then tested for significant differences in reporting various aspects of the COVID-19 data. According to multinomial regression, countries in the cluster of politically stable nations reported significantly more deaths, tests per one million, total cases per one million, and higher vaccination coverage compared with nations both in the clusters of corrupt countries and average countries. The countries in the cluster of average nations reported more tests per one million and higher vaccination coverage than countries in the cluster of corrupt nations. Countries included in the corrupt cluster reported a lower death rate and morbidity, particularly compared with the politically stable nations cluster, a trend that can be attributed to poor governance and inaccurate COVID-19 data reporting. The epidemic evaluation indices of the COVID-19 cases demonstrate that the pandemic is still evolving on a global level.

Elective surgery system strengthening: development, measurement, and validation of the surgical preparedness index across 1632 hospitals in 119 countries

BACKGROUND

The 2015 Lancet Commission on global surgery identified surgery and anaesthesia as indispensable parts of holistic health-care systems. However, COVID-19 exposed the fragility of planned surgical services around the world, which have also been neglected in pandemic recovery planning. This study aimed to develop and validate a novel index to support local elective surgical system strengthening and address growing backlogs.

METHODS

First, we performed an international consultation through a four-stage consensus process to develop a multidomain index for hospital-level assessment (surgical preparedness index; SPI). Second, we measured surgical preparedness across a global network of hospitals in high-income countries (HICs), middle-income countries (MICs), and low-income countries (LICs) to explore the distribution of the SPI at national, subnational, and hospital levels. Finally, using COVID-19 as an example of an external system shock, we compared hospitals' SPI to their planned surgical volume ratio (SVR; ie, operations for which the decision for surgery was made before hospital admission), calculated as the ratio of the observed surgical volume over a 1-month assessment period between June 6 and Aug 5, 2021, against the expected surgical volume based on hospital administrative data from the same period in 2019 (ie, a pre-pandemic baseline). A linear mixed-effects regression model was used to determine the effect of increasing SPI score.

FINDINGS

In the first phase, from a longlist of 103 candidate indicators, 23 were prioritised as core indicators of elective surgical system preparedness by 69 clinicians (23 [33%] women; 46 [67%] men; 41 from HICs, 22 from MICs, and six from LICs) from 32 countries. The multidomain SPI included 11 indicators on facilities and consumables, two on staffing, two on prioritisation, and eight on systems. Hospitals were scored from 23 (least prepared) to 115 points (most prepared). In the second phase, surgical preparedness was measured in 1632 hospitals by 4714 clinicians from 119 countries. 745 (45·6%) of 1632 hospitals were in MICs or LICs. The mean SPI score was 84·5 (95% CI 84·1-84·9), which varied between HIC (88·5 [89·0-88·0]), MIC (81·8 [82·5-81·1]), and LIC (66·8 [64·9-68·7]) settings. In the third phase, 1217 (74·6%) hospitals did not maintain their expected SVR during the COVID-19 pandemic, of which 625 (51·4%) were from HIC, 538 (44·2%) from MIC, and 54 (4·4%) from LIC settings. In the mixed-effects model, a 10-point increase in SPI corresponded to a 3·6% (95% CI 3·0-4·1; p<0·0001) increase in SVR. This was consistent in HIC (4·8% [4·1-5·5]; p<0·0001), MIC (2·8 [2·0-3·7]; p<0·0001), and LIC (3·8 [1·3-6·7%]; p<0·0001) settings.

INTERPRETATION

The SPI contains 23 indicators that are globally applicable, relevant across different system stressors, vary at a subnational level, and are collectable by front-line teams. In the case study of COVID-19, a higher SPI was associated with an increased planned surgical volume ratio independent of country income status, COVID-19 burden, and hospital type. Hospitals should perform annual self-assessment of their surgical preparedness to identify areas that can be improved, create resilience in local surgical systems, and upscale capacity to address elective surgery backlogs.

FUNDING

National Institute for Health Research (NIHR) Global Health Research Unit on Global Surgery, NIHR Academy, Association of Coloproctology of Great Britain and Ireland, Bowel Research UK, British Association of Surgical Oncology, British Gynaecological Cancer Society, and Medtronic.

COVID-19 Pneumonia: Clinical Manifestations

Coronavirus disease-2019 (COVID-19) pneumonia has diverse clinical manifestations, which have shifted throughout the pandemic. Formal classifications include presymptomatic infection and mild, moderate, severe, and critical illness. Social risk factors are numerous, with Black, Hispanic, and Native American populations in the United States having suffered disproportionately. Biological risk factors such as age, sex, underlying comorbid burden, and certain laboratory metrics can assist the clinician in triage and management. Guidelines for classifying radiographic findings have been proposed and may assist in prognosis. In this article, we review the risk factors, clinical course, complications, and imaging findings of COVID-19 pneumonia.

Leveraging Serosurveillance and Postmortem Surveillance to Quantify the Impact of Coronavirus Disease 2019 in Africa

BACKGROUND

The coronavirus disease 2019 (COVID-19) pandemic has had a devastating impact on global health, the magnitude of which appears to differ intercontinentally: For example, reports suggest that 271 900 per million people have been infected in Europe versus 8800 per million people in Africa. While Africa is the second-largest continent by population, its reported COVID-19 cases comprise <3% of global cases. Although social and environmental explanations have been proposed to clarify this discrepancy, systematic underascertainment of infections may be equally responsible.

METHODS

We sought to quantify magnitudes of underascertainment in COVID-19's cumulative incidence in Africa. Using serosurveillance and postmortem surveillance, we constructed multiplicative factors estimating ratios of true infections to reported cases in Africa since March 2020.

RESULTS

Multiplicative factors derived from serology data (subset of 12 nations) suggested a range of COVID-19 reporting rates, from 1 in 2 infections reported in Cape Verde (July 2020) to 1 in 3795 infections reported in Malawi (June 2020). A similar set of multiplicative factors for all nations derived from postmortem data points toward the same conclusion: Reported COVID-19 cases are unrepresentative of true infections, suggesting that a key reason for low case burden in many African nations is significant underdetection and underreporting.

CONCLUSIONS

While estimating the exact burden of COVID-19 is challenging, the multiplicative factors we present furnish incidence estimates reflecting likely-to-worst-case ranges of infection. Our results stress the need for expansive surveillance to allocate resources in areas experiencing discrepancies between reported cases, projected infections, and deaths.

SARS-CoV-2 diagnostic testing rates determine the sensitivity of genomic surveillance programs

The first step in SARS-CoV-2 genomic surveillance is testing to identify infected people. However, global testing rates are falling as we emerge from the acute health emergency and remain low in many low- and middle-income countries (LMICs) (mean = 27 tests/100,000 people/day). We simulated COVID-19 epidemics in a prototypical LMIC to investigate how testing rates, sampling strategies, and sequencing proportions jointly impact surveillance outcomes and showed that low testing rates and spatiotemporal biases delay time-to-detection of new variants by weeks-to-months and can lead to unreliable estimates of variant prevalence even when the proportion of samples sequenced is increased. Accordingly, investments in wider access to diagnostics to support testing rates of ~100 tests/100,000 people/day could enable more timely detection of new variants and reliable estimates of variant prevalence. The performance of global SARS-CoV-2 genomic surveillance programs is fundamentally limited by access to diagnostic testing.

The first year of the COVID-19 pandemic in the ECOWAS region

Objective

to analyse the pandemic after one year in terms of the evolution of morbidity and mortality and factors that may contribute to this evolution.

Design

This is a secondary analysis of data gathered to respond to the COVID-19 pandemic. The number of cases, incidence rate, cumulative incidence rate, number of deaths, case fatality rate and their trends were analysed during the first year of the pandemic. Testing and other public health measures were also described according to the information available.

Settings

The 15 States members of the Economic Community of West African States (ECOWAS) were considered.

Results

As of 31st March 2021, the ECOWAS region reported 429,760 COVID-19 cases and 5,620 deaths. In the first year, 1,110.75 persons were infected per million, while 1.31% of the confirmed patients died. The ECOWAS region represents 30% of the African population. One year after the start of COVID-19 in ECOWAS, this region reported 10% of the cases and 10% of the deaths in the continent. Cumulatively, the region has had two major epidemic waves; however, countries show different patterns. The case fatality rate presented a fast growth in the first months and then decreased to a plateau.

Conclusion

We learn that the context of COVID-19 is specific to each country. This analysis shows the importance of better understanding each country's response. During this first year of the pandemic, the problem of variants of concern and the vaccination were not posed.

Funding

The study was funded by the International Development Research Centre (IDRC) under CATALYSE project.

Genomic Surveillance of SARS-CoV-2 in the Southern Province of Zambia: Detection and Characterization of Alpha, Beta, Delta, and Omicron Variants of Concern

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern (VOCs) have significantly impacted the global epidemiology of the pandemic. From December 2020 to April 2022, we conducted genomic surveillance of SARS-CoV-2 in the Southern Province of Zambia, a region that shares international borders with Botswana, Namibia, and Zimbabwe and is a major tourist destination. Genetic analysis of 40 SARS-CoV-2 whole genomes revealed the circulation of Alpha (B.1.1.7), Beta (B.1.351), Delta (AY.116), and multiple Omicron subvariants with the BA.1 subvariant being predominant. Whereas Beta, Delta, and Omicron variants were associated with the second, third, and fourth pandemic waves, respectively, the Alpha variant was not associated with any wave in the country. Phylogenetic analysis showed evidence of local transmission and possible multiple introductions of SARS-CoV-2 VOCs in Zambia from different European and African countries. Across the 40 genomes analysed, a total of 292 mutations were observed, including 182 missense mutations, 66 synonymous mutations, 23 deletions, 9 insertions, 1 stop codon, and 11 mutations in the non-coding region. This study stresses the need for the continued monitoring of SARS-CoV-2 circulation in Zambia, particularly in strategically positioned regions such as the Southern Province which could be at increased risk of introduction of novel VOCs.

Collecting mortality data via mobile phone surveys: A non-inferiority randomized trial in Malawi

Despite the urgent need for timely mortality data in low-income and lower-middle-income countries, mobile phone surveys rarely include questions about recent deaths. Such questions might a) be too sensitive, b) take too long to ask and/or c) generate unreliable data. We assessed the feasibility of mortality data collection using mobile phone surveys in Malawi. We conducted a non-inferiority trial among a random sample of mobile phone users. Participants were allocated to an interview about their recent economic activity or recent deaths in their family. In the group that was asked mortality-related questions, half of the respondents completed an abridged questionnaire, focused on information necessary to calculate recent mortality rates, whereas the other half completed an extended questionnaire that also included questions about symptoms and healthcare. The primary trial outcome was the cooperation rate, i.e., the number of completed interviews divided by the number of mobile subscribers invited to participate. Secondary outcomes included self-reports of negative feelings and stated intentions to participate in future interviews. We called more than 7,000 unique numbers and reached 3,054 mobile subscribers. In total, 1,683 mobile users were invited to participate. The difference in cooperation rates between those asked to complete a mortality-related interview and those asked to answer questions about economic activity was 0.9 percentage points (95% CI = -2.3, 4.1), which satisfied the non-inferiority criterion. The mortality questionnaire was non-inferior to the economic questionnaire on all secondary outcomes. Collecting mortality data required 2 to 4 additional minutes per reported death, depending on the inclusion of questions about symptoms and healthcare. More than half of recent deaths elicited during mobile phone interviews had not been registered with the National Registration Bureau. Including mortality-related questions in mobile phone surveys is feasible. It might help strengthen the surveillance of mortality in countries with deficient civil registration systems. Registration: AEA RCT Registry, #0008065 (14 September 2021).

Respiratory viruses in rural Zambia before and during the COVID-19 pandemic

OBJECTIVES

With the emergence of the COVID-19 pandemic, restrictions were implemented globally to control the virus. Data on respiratory pathogens in sub-Saharan Africa during the COVID-19 pandemic are scarce. This analysis was conducted to evaluate patterns of respiratory pathogens in rural Zambia before and during the first year of the pandemic.

METHODS

Surveillance was established in December 2018 at Macha Hospital in southern Zambia. Patients with respiratory symptoms in the outpatient and inpatient clinics were recruited. Nasopharyngeal samples were collected and tested for respiratory pathogens. The prevalence of respiratory symptoms and pathogens was evaluated and compared in the first (December 10, 2018-December 9, 2019) and second (December 10, 2019-November 30, 2020) years of surveillance.

RESULTS

Outpatient visits and admissions for respiratory illness significantly decreased from the first to second year, especially among children. SARS-CoV-2 was not detected from any participants in Year 2. Among outpatients and inpatients with respiratory symptoms, the prevalence of respiratory syncytial virus and influenza viruses decreased from the first to second year. In contrast, the prevalence of rhinovirus/enterovirus, metapneumovirus and parainfluenza virus increased.

CONCLUSIONS

The epidemiology of respiratory viruses in rural Zambia changed during the first year of the COVID-19 pandemic, suggesting that public health interventions may have had an impact on the introduction and circulation of respiratory pathogens in this area.

SARS-CoV-2 infection and antibody seroprevalence in routine surveillance patients, healthcare workers and general population in Kita region, Mali: an observational study 2020-2021

OBJECTIVE

To estimate the degree of SARS-CoV-2 transmission among healthcare workers (HCWs) and general population in Kita region of Mali.

DESIGN

Routine surveillance in 12 health facilities, HCWs serosurvey in five health facilities and community serosurvey in 16 villages in or near Kita town, Mali.

SETTING

Kita region, western Mali; local health centres around the central (regional) referral health centre.

PARTICIPANTS

Patients in routine surveillance, HCWs in local health centres and community members of all ages in populations associated with study health centres.

MAIN OUTCOME MEASURES

Seropositivity of ELISA test detecting SARS-CoV-2-specific total antibodies and real-time RT-PCR confirmed SARS-CoV-2 infection.

RESULTS

From 2392 routine surveillance samples, 68 (2.8%, 95% CI: 2.2% to 3.6%) tested positive for SARS-CoV-2 by RT-PCR. The monthly positivity rate was 0% in June-August 2020 and gradually increased to 6% by December 2020 and 6.2% by January 2021, then declined to 5.5%, 3.3%, 3.6% and 0.8% in February, March, April and May 2021, respectively. From 397 serum samples collected from 113 HCWs, 175 (44.1%, 95% CI: 39.1% to 49.1%) were positive for SARS-CoV-2 antibodies. The monthly seroprevalence was around 10% from September to November 2020 and increased to over 40% from December 2020 to May 2021. For community serosurvey in December 2020, overall seroprevalence of SARS-CoV-2 antibodies was 27.7%. The highest age-stratified seroprevalence was observed in participants aged 60-69 years (45.5%, 95% CI: 32.3% to 58.6%). The lowest was in children aged 0-9 years (14.0%, 95% CI: 7.4% to 20.6%).

CONCLUSIONS

SARS-CoV-2 in rural Mali is much more widespread than assumed by national testing data and particularly in the older population and frontline HCWs. The observation is contrary to the widely expressed view, based on limited data, that COVID-19 infection rates were lower in 2020-2021 in West Africa than in other settings.

Using Google Health Trends to investigate COVID-19 incidence in Africa

The COVID-19 pandemic has caused over 500 million cases and over six million deaths globally. From these numbers, over 12 million cases and over 250 thousand deaths have occurred on the African continent as of May 2022. Prevention and surveillance remains the cornerstone of interventions to halt the further spread of COVID-19. Google Health Trends (GHT), a free Internet tool, may be valuable to help anticipate outbreaks, identify disease hotspots, or understand the patterns of disease surveillance. We collected COVID-19 case and death incidence for 54 African countries and obtained averages for four, five-month study periods in 2020–2021. Average case and death incidences were calculated during these four time periods to measure disease severity. We used GHT to characterize COVID-19 incidence across Africa, collecting numbers of searches from GHT related to COVID-19 using four terms: ‘coronavirus’, ‘coronavirus symptoms’, ‘COVID19’, and ‘pandemic’. The terms were related to weekly COVID-19 case incidences for the entire study period via multiple linear and weighted linear regression analyses. We also assembled 72 variables assessing Internet accessibility, demographics, economics, health, and others, for each country, to summarize potential mechanisms linking GHT searches and COVID-19 incidence. COVID-19 burden in Africa increased steadily during the study period. Important increases for COVID-19 death incidence were observed for Seychelles and Tunisia. Our study demonstrated a weak correlation between GHT and COVID-19 incidence for most African countries. Several variables seemed useful in explaining the pattern of GHT statistics and their relationship to COVID-19 including: log of average weekly cases, log of cumulative total deaths, and log of fixed total number of broadband subscriptions in a country. Apparently, GHT may best be used for surveillance of diseases that are diagnosed more consistently. Overall, GHT-based surveillance showed little applicability in the studied countries. GHT for an ongoing epidemic might be useful in specific situations, such as when countries have significant levels of infection with low variability. Future studies might assess the algorithm in different epidemic contexts.

Examining the Implementation of Digital Health to Strengthen the COVID-19 Pandemic Response and Recovery and Scale up Equitable Vaccine Access in African Countries

The COVID-19 pandemic has profoundly impacted the world, having taken the lives of over 6 million individuals. Accordingly, this pandemic has caused a shift in conversations surrounding the burden of diseases worldwide, welcoming insights from multidisciplinary fields including digital health and artificial intelligence. Africa faces a heavy disease burden that exacerbates the current COVID-19 pandemic and limits the scope of public health preparedness, response, containment, and case management. Herein, we examined the potential impact of transformative digital health technologies in mitigating the global health crisis with reference to African countries. Furthermore, we proposed recommendations for scaling up digital health technologies and artificial intelligence-based platforms to tackle the transmission of the SARS-CoV-2 and enable equitable vaccine access. Challenges related to the pandemic are numerous. Rapid response and management strategies-that is, contract tracing, case surveillance, diagnostic testing intensity, and most recently vaccine distribution mapping-can overwhelm the health care delivery system that is fragile. Although challenges are vast, digital health technologies can play an essential role in achieving sustainable resilient recovery and building back better. It is plausible that African nations are better equipped to rapidly identify, diagnose, and manage infected individuals for COVID-19, other diseases, future outbreaks, and pandemics.

Examining the Implementation of Digital Health to Strengthen the COVID-19 Pandemic Response and Recovery and Scale up Equitable Vaccine Access in African Countries

The COVID-19 pandemic has profoundly impacted the world, having taken the lives of over 6 million individuals. Accordingly, this pandemic has caused a shift in conversations surrounding the burden of diseases worldwide, welcoming insights from multidisciplinary fields including digital health and artificial intelligence. Africa faces a heavy disease burden that exacerbates the current COVID-19 pandemic and limits the scope of public health preparedness, response, containment, and case management. Herein, we examined the potential impact of transformative digital health technologies in mitigating the global health crisis with reference to African countries. Furthermore, we proposed recommendations for scaling up digital health technologies and artificial intelligence–based platforms to tackle the transmission of the SARS-CoV-2 and enable equitable vaccine access. Challenges related to the pandemic are numerous. Rapid response and management strategies—that is, contract tracing, case surveillance, diagnostic testing intensity, and most recently vaccine distribution mapping—can overwhelm the health care delivery system that is fragile. Although challenges are vast, digital health technologies can play an essential role in achieving sustainable resilient recovery and building back better. It is plausible that African nations are better equipped to rapidly identify, diagnose, and manage infected individuals for COVID-19, other diseases, future outbreaks, and pandemics.

A fast extraction-free isothermal LAMP assay for detection of SARS-CoV-2 with potential use in resource-limited settings

Background

To retain the spread of SARS-CoV-2, fast, sensitive and cost-effective testing is essential, particularly in resource limited settings (RLS). Current standard nucleic acid-based RT-PCR assays, although highly sensitive and specific, require transportation of samples to specialised laboratories, trained staff and expensive reagents. The latter are often not readily available in low- and middle-income countries and this may significantly impact on the successful disease management in these settings. Various studies have suggested a SARS-CoV-2 loop mediated isothermal amplification (LAMP) assay as an alternative method to RT-PCR.

Methods

Four previously published primer pairs were used for detection of SARS-CoV-2 in the LAMP assay. To determine optimal conditions, different temperatures, sample input and incubation times were tested. Ninety-three extracted RNA samples from St. George's Hospital, London, 10 non-extracted nasopharyngeal swab samples from Great Ormond Street Hospital for Children, London, and 92 non-extracted samples from Queen Elisabeth Central Hospital (QECH), Malawi, which have previously been tested for SARS-Cov-2 by quantitative reverse-transcription RealTime PCR (qRT-PCR), were analysed in the LAMP assay.

Results

In this study we report the optimisation of an extraction-free colourimetric SARS-CoV-2 LAMP assay and demonstrated that a lower limit of detection (LOD) between 10 and 100 copies/µL of SARS-CoV-2 could be readily detected by a colour change of the reaction within as little as 30 min. We further show that this assay could be quickly established in Malawi, as no expensive equipment is necessary. We tested 92 clinical samples from QECH and showed the sensitivity and specificity of the assay to be 86.7% and 98.4%, respectively. Some viral transport media, used routinely to stabilise RNA in clinical samples during transportation, caused a non-specific colour-change in the LAMP reaction and therefore we suggest collecting samples in phosphate buffered saline (which did not affect the colour) as the assay allows immediate sample analysis on-site.

Conclusion

SARS-CoV-2 LAMP is a cheap and reliable assay that can be readily employed in RLS to improve disease monitoring and management.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12985-022-01800-7.

SARS-CoV-2 seroprevalence and associated risk factors in periurban Zambia: a population-based study

BACKGROUND

We nested a seroprevalence survey within the TREATS (Tuberculosis Reduction through Expanded Antiretroviral Treatment and Screening) project. We aimed to measure the seroprevalence of SARS-CoV-2 infection and investigate associated risk factors in one community (population ∼27,000) with high prevalence of TB/HIV in Zambia.

METHODS

The study design was cross-sectional. A random sample of 3592 individuals aged ≥15 years enrolled in the TREATS TB-prevalence survey were selected for antibody testing. Randomly selected blocks of residence were visited between October 2020 and March 2021. Antibodies against SARS-CoV-2 were detected using Abbott- ARCHITECT SARS-CoV-2 IgG assay.

RESULTS

A total of 3035/3526 (86.1%) individuals had a blood sample taken. Antibody testing results were available for 2917/3035 (96.1%) participants. Overall, 401/2977 (13.5%) individuals tested positive for IgG antibodies. Seroprevalence was similar by sex (12.7% men vs 14.0% women) and was lowest in the youngest age group 15-19 years (9.7%) and similar in ages 20 years and older (∼15%). We found no evidence of an association between seroprevalence and HIV-status or TB. There was strong evidence (p <0.001) of variation by time of enrollment, with prevalence varying from 2.8% (95% CI 0.8-4.9) among those recruited in December 2020 to 33.7% (95% CI 27.7-39.7) among those recruited in mid-February 2021.

CONCLUSION

Seroprevalence was 13.5% but there was substantial variation over time, with a sharp increase to approximately 35% toward the end of the second epidemic wave.

Assessing the burden of COVID-19 in developing countries: systematic review, meta-analysis and public policy implications

INTRODUCTION

The infection fatality rate (IFR) of COVID-19 has been carefully measured and analysed in high-income countries, whereas there has been no systematic analysis of age-specific seroprevalence or IFR for developing countries.

METHODS

We systematically reviewed the literature to identify all COVID-19 serology studies in developing countries that were conducted using representative samples collected by February 2021. For each of the antibody assays used in these serology studies, we identified data on assay characteristics, including the extent of seroreversion over time. We analysed the serology data using a Bayesian model that incorporates conventional sampling uncertainty as well as uncertainties about assay sensitivity and specificity. We then calculated IFRs using individual case reports or aggregated public health updates, including age-specific estimates whenever feasible.

RESULTS

In most locations in developing countries, seroprevalence among older adults was similar to that of younger age cohorts, underscoring the limited capacity that these nations have to protect older age groups.Age-specific IFRs were roughly 2 times higher than in high-income countries. The median value of the population IFR was about 0.5%, similar to that of high-income countries, because disparities in healthcare access were roughly offset by differences in population age structure.

CONCLUSION

The burden of COVID-19 is far higher in developing countries than in high-income countries, reflecting a combination of elevated transmission to middle-aged and older adults as well as limited access to adequate healthcare. These results underscore the critical need to ensure medical equity to populations in developing countries through provision of vaccine doses and effective medications.

Mean generation function model in AIDS epidemic estimation

Background

Since the first case of HIV infection was reported in China in 1985, the incidence and mortality of AIDS have been increasing rapidly, which has caused serious damage to the life and health of people in China and all over the world. Therefore, it is of great significance to study the technique for predicting AIDS morbidity and mortality. The purpose of this research is to explore the applicability of the mean generation function model (MGFM) in the early warning of AIDS morbidity and mortality, to predict its prevalence trend, to enrich the prediction techniques and methods of AIDS research and to provide suggestions for AIDS transmission control.

Methods

In this research, the MGFM was applied to predict the incidence and mortality of AIDS in China. AIDS incidence and mortality data in China from 2008 to 2019 were used to construct the prediction model.

Results

The MGFM can predict the annual incidence and mortality of AIDS. The model constructed in this research predicted that the incidence and mortality of AIDS in China will continue to increase from 2020 to 2023.

Conclusion

The mean birth function model was an effective method to monitor and predict the changing trend of AIDS incidence and mortality in China.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12911-022-01825-6.