What could explain the late emergence of COVID-19 in Africa?

"I was afraid to go to the hospital": A qualitative analysis and ethical implications of the impacts of COVID-19 on the health and medical care of older adults in Ethiopia

Objective

The COVID-19 pandemic has brought severe health consequences among older adults and posed ethical challenges. The aim of this study was to explore the impacts of COVID-19 on the health and medical care of older adults in Ethiopia and associated ethical implications, regardless of older adults' COVID-19 infection status.

Methods

In this qualitative study, we followed an inductive exploratory approach based on reflexive thematic analysis. We conducted semistructured interviews between March 2021 and November 2021 with 20 older adults and 26 health professionals who were selected from healthcare facilities and communities in Ethiopia using purposive and snowball sampling techniques. We audio-recorded, transcribed, translated, and inductively analyzed the interviews using thematic analysis.

Results

Participants reported that the pandemic compromised the accessibility and quality of both COVID and non-COVID healthcare services for older adults, which negatively impacted older adults' health conditions and medical care. Moreover, participants elaborated on the health conditions and care of older patients with COVID-19 and highlighted that older COVID-19 patients often have severe health conditions, do not get adequate COVID-19 care, and may receive lower priority for admission to intensive care units compared to younger patients when resources are limited.

Conclusions

Results of this study showed that practices of COVID-19 care and measures may have led to adverse consequences such as limited availability and access to aged care in Ethiopia, which could have further health consequences on older patients. Our results contribute to a better understanding of ethical issues such as distributive justice and prioritization arising in the healthcare of older patients in times of global pandemic. It is imperative for local and international health policymakers and ethicists to further analyze and address the challenges that compromise the accessibility and continuity of quality care for older persons during a public healthcare crisis.

Genomic surveillance of SARS-CoV-2 in North Africa: 4 years of GISAID data sharing

Objectives

This study aimed to construct geographically, temporally, and epidemiologically representative data sets for SARS-CoV-2 in North Africa, focusing on Variants of Concern (VOCs), Variants of Interest (VOIs), and Variants Under Monitoring (VUMs).

Methods

SARS-CoV-2 genomic sequences and metadata from the EpiCoV database via the Global Initiative on Sharing All Influenza Data platform were analyzed. Data analysis included cases, deaths, demographics, patient status, sequencing technologies, and variant analysis.

Results

A comprehensive analysis of 10,783 viral genomic sequences from six North African countries revealed notable insights. SARS-CoV-2 sampling methods lack standardization, with a majority of countries lacking clear strategies. Over 59% of analyzed genomes lack essential clinical and demographic metadata, including patient age, sex, underlying health conditions, and clinical outcomes, which are essential for comprehensive genomic analysis and epidemiological studies, as submitted to the Global Initiative on Sharing All Influenza Data. Morocco reported the highest number of confirmed COVID-19 cases (1,272,490), whereas Tunisia leads in reported deaths (29,341), emphasizing regional variations in the pandemic's impact. The GRA clade emerged as predominant in North African countries. The lineage analysis showcased a diversity of 190 lineages in Egypt, 26 in Libya, 121 in Tunisia, 90 in Algeria, 146 in Morocco, and 10 in Mauritania. The temporal dynamics of SARS-CoV-2 variants revealed distinct waves driven by different variants.

Conclusions

This study contributes valuable insights into the genomic landscape of SARS-CoV-2 in North Africa, highlighting the importance of genomic surveillance in understanding viral dynamics and informing public health strategies.

Genomic Characterization of SARS-CoV-2 Variants from Clinical Isolates during the COVID-19 Epidemic in Mauritania

The rapid genetic evolution of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) during the coronavirus disease 2019 (COVID-19) pandemic has greatly challenged public health authorities worldwide, including in Mauritania. Despite the presence of the virus in Mauritania, only one study described its genomic variation during the course of the epidemic. The purpose of the present study was to document the genomic pattern of SARS-CoV-2 variants from clinical isolates during the COVID-19 outbreak in Mauritania, from September to November 2021. The whole genomes from 54 SARS-CoV-2 strains detected in nasopharyngeal swabs with a cycle threshold value ≤ 30 were successfully sequenced using next-generation sequencing (NGS) and the Illumina protocol. The mean genome coverage (±standard deviation) was 96.8% (±3.7). The most commonly identified clade was 21J (57.4%), followed by 21D (16.7%), 20A (11.1%), and 20B (9.2%). At the level of lineages, the majority of the samples were Delta variants with the sub-lineage AY.34 (or B.1.617.2.34). Among the 54 SARS-CoV-2 isolates that were successfully sequenced, 33 (61.1%) came from vaccinated individuals, and 21 (38.9%) were from unvaccinated individuals. Several SARS-CoV-2 variants were present in Mauritania between September and November 2021. As Mauritania, like many West African countries, is resource-limited regarding viral genome sequencing facilities, establishment of mutualized sub-regional sequencing platforms will be necessary to ensure continuous monitoring of mutations in viral genomes and track potential reduction in COVID-19 vaccine efficacy, increased transmissibility, and disease severity.

Unravelling Antigenic Cross-Reactions toward the World of Coronaviruses: Extent of the Stability of Shared Epitopes and SARS-CoV-2 Anti-Spike Cross-Neutralizing Antibodies

The human immune repertoire retains the molecular memory of a very great diversity of target antigens (epitopes) and can recall this upon a second encounter with epitopes against which it has previously been primed. Although genetically diverse, proteins of coronaviruses exhibit sufficient conservation to lead to antigenic cross-reactions. In this review, our goal is to question whether pre-existing immunity against seasonal human coronaviruses (HCoVs) or exposure to animal CoVs has influenced the susceptibility of human populations to SARS-CoV-2 and/or had an impact upon the physiopathological outcome of COVID-19. With the hindsight that we now have regarding COVID-19, we conclude that although antigenic cross-reactions between different coronaviruses exist, cross-reactive antibody levels (titers) do not necessarily reflect on memory B cell frequencies and are not always directed against epitopes which confer cross-protection against SARS-CoV-2. Moreover, the immunological memory of these infections is short-term and occurs in only a small percentage of the population. Thus, in contrast to what might be observed in terms of cross-protection at the level of a single individual recently exposed to circulating coronaviruses, a pre-existing immunity against HCoVs or other CoVs can only have a very minor impact on SARS-CoV-2 circulation at the level of human populations.

The striking mimics between COVID-19 and malaria: A review

Objectives

COVID-19 is a transmissible illness triggered by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Since its onset in late 2019 in Wuhan city of China, it continues to spread universally, leading to an ongoing pandemic that shattered all efforts to restrain it. On the other hand, in Africa, the COVID-19 infection may be influenced by malaria coinfection. Hence, in this review article, we aimed to give a comprehensive account of the similarities between COVID-19 and malaria in terms of symptoms, clinical, immunological, and molecular perspectives.

Methodology

In this article, we reviewed over 50 research papers to highlight the multilayered similarities between COVID-19 and malaria infections that might influence the ontology of COVID-19.

Results

Despite the poor health and fragile medical system of many sub-Saharan African countries, they persisted with a statistically significantly low number of COVID-19 cases. This was attributed to many factors such as the young population age, the warm weather, the lack of proper diagnosis, previous infection with malaria, the use of antimalarial drugs, etc. Additionally, population genetics appears to play a significant role in shaping the COVID-19 dynamics. This is evident as recent genomic screening analyses of the angiotensin-converting enzyme 2 (ACE2) and malaria-associated-variants identified 6 candidate genes that might play a role in malaria and COVID-19 incidence and severity. Moreover, the clinical and pathological resemblances between the two diseases have made considerable confusion in the diagnosis and thereafter curb the disease in Africa. Therefore, possible similarities between the diseases in regards to the clinical, pathological, immunological, and genetical ascription were discussed.

Conclusion

Understanding the dynamics of COVID-19 infection in Sub-Saharan Africa and how it is shaped by another endemic disease like malaria can provide insights into how to tailor a successful diagnostic, intervention, and control plans that lower both disease morbidity and mortality.

Space—Time Surveillance of COVID-19 Seasonal Clusters: A Case of Sweden

While COVID-19 is a global pandemic, different countries have experienced different morbidity and mortality patterns. We employ retrospective and prospective space–time permutation analysis on COVID-19 positive records across different municipalities in Sweden from March 2020 to February 2021, using data provided by the Swedish Public Health Agency. To the best of our knowledge, this is the first study analyzing nationwide COVID-19 space–time clustering in Sweden, on a season-to-season basis. Our results show that different municipalities within Sweden experienced varying extents of season-dependent COVID-19 clustering in both the spatial and temporal dimensions. The reasons for the observed differences could be related to the differences in the earlier exposures to the virus, the strictness of the social restrictions, testing capabilities and preparedness. By profiling COVID-19 space–time clusters before the introduction of vaccines, this study contributes to public health efforts aimed at containing the virus by providing plausible evidence in evaluating which epidemiologic interventions in the different regions could have worked and what could have not worked.

Microbial ecology and evolution is key to pandemics: using the coronavirus model to mitigate future public health challenges

Pandemics are global challenges that lead to total disruption of human activities. From the inception of human existence, all pandemics have resulted in loss of human lives. The coronavirus disease caused by SAR-CoV-2 began in China and is now at the global scale with an increase in mortality and morbidity. Numerous anthropogenic activities have been implicated in the emergence and severity of pandemics, including COVID-19. These activities cause changes in microbial ecology, leading to evolution due to mutation and recombination. This review hypothesized that an understanding of these anthropogenic activities would explain the dynamics of pandemics. The recent coronavirus model was used to study issues leading to microbial evolution, towards preventing future pandemics. Our review highlighted anthropogenic activities, including deforestation, mining activities, waste treatment, burning of fossil fuel, as well as international travels as drivers of microbial evolution leading to pandemics. Furthermore, human-animal interaction has also been implicated in pandemic incidents. Our study recommends substantial control of such anthropogenic activities as having been highlighted as ways to reduce the frequency of mutation, reduce pathogenic reservoirs, and the emergence of infectious diseases.

Phylogenetic and genome-wide mutational analysis of SARS-CoV-2 strains circulating in Nigeria: no implications for attenuated COVID-19 outcomes

OBJECTIVES

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of coronavirus disease 2019 (COVID-19). The COVID-19 incidence and mortality rates are low in Nigeria compared to global trends. This research mapped the evolution of SARS-CoV-2 circulating in Nigeria and globally to determine whether the Nigerian isolates are genetically distinct from strains circulating in regions of the world with a high disease burden.

METHODS

Bayesian phylogenetics using BEAST 2.0, genetic similarity analyses, and genomewide mutational analyses were used to characterize the strains of SARS-CoV-2 isolated in Nigeria.

RESULTS

SARS-CoV-2 strains isolated in Nigeria showed multiple lineages and possible introductions from Europe and Asia. Phylogenetic clustering and sequence similarity analyses demonstrated that Nigerian isolates were not genetically distinct from strains isolated in other parts of the globe. Mutational analysis demonstrated that the D614G mutation in the spike protein, the P323L mutation in open reading frame 1b (and more specifically in NSP12), and the R203K/ G204R mutation pair in the nucleocapsid protein were most prevalent in the Nigerian isolates.

CONCLUSION

The SARS-CoV-2 strains in Nigeria were neither phylogenetically nor genetically distinct from virus strains circulating in other countries of the world. Thus, differences in SARS-CoV-2 genomes are not a plausible explanation for the attenuated COVID-19 outcomes in Nigeria.

Performance Evaluation of Lateral Flow Assays for Coronavirus Disease-19 Serology

The coronavirus disease of 2019 (COVID-19) pandemic, caused by infection with the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), has undoubtedly resulted in significant morbidities, mortalities, and economic disruptions across the globe. Affordable and scalable tools to monitor the transmission dynamics of the SARS-CoV-2 virus and the longevity of induced antibodies will be paramount to monitor and control the pandemic as multiple waves continue to rage in many countries. Serologic assays detect humoral responses to the virus, to determine seroprevalence in target populations, or induction of antibodies at the individual level following either natural infection or vaccination. With multiple vaccines rolling out globally, serologic assays to detect anti-SARS-CoV-2 antibodies will be important tools to monitor the development of herd immunity. To address this need, serologic lateral flow assays (LFAs), which can be easily implemented for both population surveillance and home use, will be vital to monitor the evolution of the pandemic and inform containment measures. Such assays are particularly important for monitoring the transmission dynamics and durability of immunity generated by natural infections and vaccination, particularly in resource-limited settings. In this review, we discuss considerations for evaluating the accuracy of these LFAs, their suitability for different use cases, and implementation opportunities.

A new measure of hygiene inequality applied to urban-rural comparison

Access to hygiene services remains one of the most urgent challenges facing countries, especially low-income ones. This has become much more critical in the current context of the COVID-19 pandemic. The WHO/UNICEF Joint Monitoring Program globally monitors access to hygiene service levels. As data are in three parts with a constant sum and a positive value, they are compositional data. Inequality is monitored in disaggregated data; in the urban-rural case, this is done through a simple difference between the urban and rural service levels. However, this simple form of calculation does not take into account the characteristics of the data, which can lead to erroneous interpretations of the results. Therefore, we propose an alternative measure of inequality that uses a ternary diagram and does not infringe on the data properties. The results of the new urban-rural inequality measure show spatial heterogeneity. The highest inequality occurs in Colombia, with a value of 37.1 percentage points, and the lowest in Turkmenistan, with a value of zero. Our results also show that 73 of the 76 countries evaluated have higher basic hygiene services in urban areas than in rural areas. This means that urban households have more availability of a handwashing facility on-premises with soap and water than rural households. Likewise, by subdividing the ternary diagram into ternary parcels, we could group and rank the countries based on hygiene service conditions in a hierarchical order using tripartite information. Finally, our study finds that a multivariate measure of inequality can be important for the public policies of the sector with a general vision, which underscores the value of making evidence-based decisions.

No neutralizing effect of pre-existing tick-borne encephalitis virus antibodies against severe acute respiratory syndrome coronavirus-2: a prospective healthcare worker study

Certain immunizations including vaccination against tick-borne encephalitis virus (TBEV) have been suggested to confer cross-protection against severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). Within a prospective healthcare worker (HCW) cohort, we assessed the potentially protective role of anti-TBEV antibodies against SARS-CoV-2 infection. Among 3352 HCW, those with ≥ 1 previous TBEV vaccination (n = 2018, 60%) showed a reduced risk of SARS-CoV-2 seroconversion (adjusted odds ratio: 0.8, 95% CI: 0.7–1.0, P = 0.02). However, laboratory testing of a subgroup of 26 baseline and follow-up samples did not demonstrate any neutralizing effect of anti-TBEV antibodies against SARS-CoV-2 in live-virus neutralization assay. However, we observed significantly higher anti-TBEV antibody titers in follow-up samples of participants with previous TBEV vaccination compared to baseline, both TBEV neutralizing (p = 0.001) and total IgG (P < 0.0001), irrespective of SARS-CoV-2 serostatus. Based on these data, we conclude that the observed association of previous TBEV vaccination and reduced risk of SARS-CoV-2 infection is likely due to residual confounding factors. The increase in TBEV follow-up antibody titers can be explained by natural TBEV exposure or potential non-specific immune activation upon exposure to various pathogens, including SARS-CoV-2. We believe that these findings, although negative, contribute to the current knowledge on potential cross-immunity against SARS-CoV-2 from previous immunizations.

Economic, Health and Physical Impacts of COVID-19 Pandemic in Sub-Saharan African Regions: A Cross Sectional Survey

PURPOSE

The key preventive measures adopted to minimise the spread of the coronavirus disease (COVID-19) had significant health, economic and physical impacts mostly in developing countries. This study evaluated the health, economic and physical impacts of COVID-19 lockdown measures among sub-Saharan African (SSA) population and associated demographic variations.

METHODS

A total of 1970 respondents took part in this web-based cross-sectional survey during the mandatory lockdown period in most SSA. The dependent variables were health (COVID-19 infection, hospitalisation), socioeconomic (lost job, closed down business) and physical impacts (separated from family) of COVID-19. Univariate and bivariate logistic regression analyses were used to explore the factors associated with each of the dependent variables by the four sub-regions (Southern, Western, Central and East Africa).

RESULTS

The respondents were aged 34.1 ± 11.5 years (range: 18-75 years) and mostly men (1099, 55%). 25.9% (n = 511) reported an impact of COVID-19 pandemic with significant regional variations (p < 0.0005, higher proportion were East 36.2% and Southern Africans 30.3%) but no gender (p = 0.334) and age group variations (p > 0.05). Among Central African respondents, more men than women lost their businesses (45.7% versus 14.3%, p = 0.002) and contracted COVID-19 infections (40.0% versus 18.2%, p = 0.024) during the study period. Multivariable analysis revealed that respondents from East (adjusted odds ratio [AOR] 1.95, 95% confidence interval [CI]: 1.42-2.69), Southern (AOR 1.46, 95% CI: 1.09-1.96) and Central Africa (AOR 1.47, 95% CI: 1.06-2.03) reported significantly higher impact of COVID-19. Those who reported family separation during the lockdown were more likely to be older participants (39-48 years, AOR 2.48, 95% CI: 1.11-5.57).

CONCLUSION

One in four SSA respondents, mostly East and Southern Africans, were adversely affected by the COVID-19 pandemic during the lockdown. Interventions in high-risk populations are needed to reduce the health, socioeconomic and gender disparities in the impacts of COVID-19.

The Determinants of the Low COVID-19 Transmission and Mortality Rates in Africa: A Cross-Country Analysis

Background: More than 1 year after the beginning of the international spread of coronavirus 2019 (COVID-19), the reasons explaining its apparently lower reported burden in Africa are still to be fully elucidated. Few studies previously investigated the potential reasons explaining this epidemiological observation using data at the level of a few African countries. However, an updated analysis considering the various epidemiological waves and variables across an array of categories, with a focus on African countries might help to better understand the COVID-19 pandemic on the continent. Thus, we investigated the potential reasons for the persistently lower transmission and mortality rates of COVID-19 in Africa. Methods: Data were collected from publicly available and well-known online sources. The cumulative numbers of COVID-19 cases and deaths per 1 million population reported by the African countries up to February 2021 were used to estimate the transmission and mortality rates of COVID-19, respectively. The covariates were collected across several data sources: clinical/diseases data, health system performance, demographic parameters, economic indicators, climatic, pollution, and radiation variables, and use of social media. The collinearities were corrected using variance inflation factor (VIF) and selected variables were fitted to a multiple regression model using the R statistical package. Results: Our model (adjusted R-squared: 0.7) found that the number of COVID-19 tests per 1 million population, GINI index, global health security (GHS) index, and mean body mass index (BMI) were significantly associated (P < 0.05) with COVID-19 cases per 1 million population. No association was found between the median life expectancy, the proportion of the rural population, and Bacillus Calmette-Guérin (BCG) coverage rate. On the other hand, diabetes prevalence, number of nurses, and GHS index were found to be significantly associated with COVID-19 deaths per 1 million population (adjusted R-squared of 0.5). Moreover, the median life expectancy and lower respiratory infections rate showed a trend towards significance. No association was found with the BCG coverage or communicable disease burden. Conclusions: Low health system capacity, together with some clinical and socio-economic factors were the predictors of the reported burden of COVID-19 in Africa. Our results emphasize the need for Africa to strengthen its overall health system capacity to efficiently detect and respond to public health crises.

A model of COVID-19 pandemic evolution in African countries

We studied the COVID-19 pandemic evolution in selected African countries. For each country considered, we modeled simultaneously the data of the active, recovered and death cases. In this study, we used a year of data since the first cases were reported. We estimated the time-dependent basic reproduction numbers, R 0 , and the fractions of infected but unaffected populations, to offer insights into containment and vaccine strategies in African countries. We found that R 0 ≤ 4 at the start of the pandemic but has since fallen to R 0 ∼ 1 . The unaffected fractions of the populations studied vary between 1 - 10 % of the recovered cases.

Whole Genome Sequencing of SARS-CoV-2 Strains in COVID-19 Patients From Djibouti Shows Novel Mutations and Clades Replacing Over Time

Since the start of COVID-19 pandemic the Republic of Djibouti, in the horn of Africa, has experienced two epidemic waves of the virus between April and August 2020 and between February and May 2021. By May 2021, COVID-19 had affected 1.18% of the Djiboutian population and caused 152 deaths. Djibouti hosts several foreign military bases which makes it a potential hot-spot for the introduction of different SARS-CoV-2 strains. We genotyped fifty three viruses that have spread during the two epidemic waves. Next, using spike sequencing of twenty-eight strains and whole genome sequencing of thirteen strains, we found that Nexstrain clades 20A and 20B with a typically European D614G substitution in the spike and a frequent P2633L substitution in nsp16 were the dominant viruses during the first epidemic wave, while the clade 20H South African variants spread during the second wave characterized by an increase in the number of severe forms of COVID-19.

Natural Products Modulating Angiotensin Converting Enzyme 2 (ACE2) as Potential COVID-19 Therapies

The 2019 coronavirus disease (COVID-19) is a potentially fatal multisystemic infection caused by the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). Currently, viable therapeutic options that are cost effective, safe and readily available are desired, but lacking. Nevertheless, the pandemic is noticeably of lesser burden in African and Asian regions, where the use of traditional herbs predominates, with such relationship warranting a closer look at ethnomedicine. From a molecular viewpoint, the interaction of SARS-CoV-2 with angiotensin converting enzyme 2 (ACE2) is the crucial first phase of COVID-19 pathogenesis. Here, we review plants with medicinal properties which may be implicated in mitigation of viral invasion either via direct or indirect modulation of ACE2 activity to ameliorate COVID-19. Selected ethnomedicinal plants containing bioactive compounds which may prevent and mitigate the fusion and entry of the SARS-CoV-2 by modulating ACE2-associated up and downstream events are highlighted. Through further experimentation, these plants could be supported for ethnobotanical use and the phytomedicinal ligands could be potentially developed into single or combined preventive therapeutics for COVID-19. This will benefit researchers actively looking for solutions from plant bioresources and help lessen the burden of COVID-19 across the globe.

Plasmodium falciparum malaria drives epigenetic reprogramming of human monocytes toward a regulatory phenotype

In malaria-naïve children and adults, Plasmodium falciparum-infected red blood cells (Pf-iRBCs) trigger fever and other symptoms of systemic inflammation. However, in endemic areas where individuals experience repeated Pf infections over many years, the risk of Pf-iRBC-triggered inflammatory symptoms decreases with cumulative Pf exposure. The molecular mechanisms underlying these clinical observations remain unclear. Age-stratified analyses of uninfected, asymptomatic Malian individuals before the malaria season revealed that monocytes of adults produced lower levels of inflammatory cytokines (IL-1β, IL-6 and TNF) in response to Pf-iRBC stimulation compared to monocytes of Malian children and malaria-naïve U.S. adults. Moreover, monocytes of Malian children produced lower levels of IL-1β and IL-6 following Pf-iRBC stimulation compared to 4-6-month-old infants. Accordingly, monocytes of Malian adults produced more IL-10 and expressed higher levels of the regulatory molecules CD163, CD206, Arginase-1 and TGM2. These observations were recapitulated in an in vitro system of monocyte to macrophage differentiation wherein macrophages re-exposed to Pf-iRBCs exhibited attenuated inflammatory cytokine responses and a corresponding decrease in the epigenetic marker of active gene transcription, H3K4me3, at inflammatory cytokine gene loci. Together these data indicate that Pf induces epigenetic reprogramming of monocytes/macrophages toward a regulatory phenotype that attenuates inflammatory responses during subsequent Pf exposure. Trial Registration: ClinicalTrials.gov NCT01322581.

Atypical respiratory distress in eastern Democratic Republic of the Congo prior to the COVID-19 pandemic. A case report

BACKGROUND

Predictions have been made that Africa would be the most vulnerable continent to the novel Coronavirus disease 2019 (COVID-19). Interestingly, the spread of the disease in Africa seems to have been delayed and initially slower than in many parts of the world. Here we report on two cases of respiratory distress in our region before the official declaration of the disease in December 2019, cases which in the present times would be suspect of COVID-19.

CASE PRESENTATION

These two cases (one 55-year-old man and one 25-year-old woman) of acute respiratory distress secondary to atypical pneumonia were seen in Bukavu, in Eastern Democratic Republic of the Congo (DRC), between September and December 2019. One patient had returned from China and the other had close contacts with travellers from China in the 2 weeks prior to the onset of symptoms. In either case, the aetiology could not be accurately determined. However, the two cases presented a clinical picture (progressive dyspnoea, preceded by dry cough and fever) and laboratory changes (procalcitonin within the normal range, slight inflammation, and lymphopenia) compatible with a viral infection. The chest X-ray series of the first patient showed lesions (reticulations, ground glass, and nodules ≤6 mm) similar to those currently found in COVID-19 patients. In addition, unlike the 25-year-old female patient who had no comorbidity, the 55-year-old male patient who had hypertension as comorbidity, developed a more severe acute respiratory distress which progressed to death.

CONCLUSION

These cases bring to the attention the fact that COVID-19-like syndromes may have already been present in the region months before the official beginning of the pandemic. This also brings to question whether a prior presence of the disease or infections with related virus may account for the delayed and less extensive development of the pandemic in the region.

The COVID-19 pandemic is deepening the health crisis in South Kivu, Democratic Republic of Congo

OBJECTIVE

The outbreak of coronavirus disease 2019 (COVID-19) in South Kivu, Democratic Republic of Congo raised concerns regarding additional morbidity and mortality. Updating these indicators before a second wave is essential in order to prepare for additional help.

METHODS

From mid-May to mid-December 2020, weekly surveys were undertaken in sampled streets from 10 health areas to quantify the use of barrier measures, and interview pedestrians about sickness and deaths in their households. Crude death rates (CDRs) were estimated.

RESULTS

Minimal use or no use of face masks was observed in at least half of the streets. From May to December 2020, the number of suspected cases of COVID-19 increased six-fold (P < 0.05). Of deaths within 30 days preceding the interviews, 20% were considered to be related to COVID-19. The monthly CDRs at the beginning and end of the study were approximately 5 and 25 per 1000 population, respectively (P < 0.05); that is, annual CDRs of 60 and 260 per 1000 population, respectively. Thus, during the first wave, the estimated mortality rate increased by 50% compared with previous years, and increased at least four-fold by the end of 2020.

CONCLUSION

Despite possible overestimations, the excess mortality in South Kivu is extremely concerning. This crisis calls for a rapid response and increased humanitarian assistance.

Introduction into the Marseille geographical area of a mild SARS-CoV-2 variant originating from sub-Saharan Africa: An investigational study

BACKGROUND

In Marseille, France, the COVID-19 incidence evolved unusually with several successive epidemic phases. The second outbreak started in July, was associated with North Africa, and involved travelers and an outbreak on passenger ships. This suggested the involvement of a new viral variant.

METHODS

We sequenced the genomes from 916 SARS-CoV-2 strains from COVID-19 patients in our institute. The patients' demographic and clinical features were compared according to the infecting viral variant.

RESULTS

From June 26th to August 14th, we identified a new viral variant (Marseille-1). Based on genome sequences (n = 89) or specific qPCR (n = 53), 142 patients infected with this variant were detected. It is characterized by a combination of 10 mutations located in the nsp2, nsp3, nsp12, S, ORF3a, ORF8 and N/ORF14 genes. We identified Senegal and Gambia, where the virus had been transferred from China and Europe in February-April as the sources of the Marseille-1 variant, which then most likely reached Marseille through Maghreb when French borders reopened. In France, this variant apparently remained almost limited to Marseille. In addition, it was significantly associated with a milder disease compared to clade 20A ancestor strains, in univariate analysis.

CONCLUSION

Our results demonstrate that SARS-CoV-2 can genetically diversify rapidly, its variants can diffuse internationally and cause successive outbreaks.

The SARS-CoV-2 pandemic: A syndemic perspective

The SARS-CoV-2 pandemic has affected communities, populations, and countries throughout the world. As the SARS-CoV-2 pandemic developed, the extent to which the disease interacted with already existing endemic, non-communicable and infectious diseases became evident, hence deeply influencing health outcomes. Additionally, a synergistic effect has been demonstrated also with socio-economic, cultural, and contextual determinants of health which seem to contribute to poorer health and accumulating social disadvantages. In this essay, using as a starting point the syndemic theory that translates the cumulative and intertwined factors between different epidemics, we argue that the SARS-CoV-2 is a one health issue of a syndemic nature and that the failure to acknowledge this contributes to weakened policy-making processes and public health responses and ineffective health policies and programs.

One hundred thirty-three observed COVID-19 deaths in 10 months: unpacking lower than predicted mortality in Rwanda

The African region was predicted to have worse COVID-19 infection and death rates due to challenging health systems and social determinants of health. However, in the 10 months after its first case, Rwanda recorded 10316 cases and 133 COVID-19-related deaths translating to a case fatality rate (CFR) of 1.3%, which raised the question: why does Rwanda have a low COVID-19 CFR? Here we analysed COVID-19 data and explored possible explanations to better understand the disease burden in the context of Rwanda's infection control strategies.We investigated whether the age distribution plays a role in the observed low CFR in Rwanda by comparing the expected number of deaths for 10-year age bands based on the CFR reported in other countries with the observed number of deaths for each age group. We found that the age-specific CFRs in Rwanda are similar to or, in some older age groups, slightly higher than those in other countries, suggesting that the lower population level CFR reflects the younger age structure in Rwanda, rather than a lower risk of death conditional on age. We also accounted for Rwanda's comprehensive SARS-CoV-2 testing strategies and reliable documentation of COVID-19-related deaths and deduced that these measures may have allowed them to likely identify more asymptomatic or mild cases than other countries and reduced their reported CFR.Overall, the observed low COVID-19 deaths in Rwanda is likely influenced by the combination of effective infection control strategies, reliable identification of cases and reporting of deaths, and the population's young age structure.

Plasmodium falciparum malaria drives epigenetic reprogramming of human monocytes toward a regulatory phenotype

In malaria-naïve children and adults, Plasmodium falciparum -infected red blood cells ( Pf -iRBCs) trigger fever and other symptoms of systemic inflammation. However, in endemic areas where individuals experience repeated Pf infections over many years, the risk of Pf -iRBC-triggered inflammatory symptoms decreases with cumulative Pf exposure. The molecular mechanisms underlying these clinical observations remain unclear. Age-stratified analyses of monocytes collected from uninfected, asymptomatic Malian individuals before the malaria season revealed an inverse relationship between age and Pf -iRBC-inducible inflammatory cytokine (IL-1β, IL-6 and TNF) production, whereas Malian infants and malaria-naïve U.S. adults produced similarly high levels of inflammatory cytokines. Accordingly, monocytes of Malian adults produced more IL-10 and expressed higher levels of the regulatory molecules CD163, CD206, Arginase-1 and TGM2. These observations were recapitulated in an in vitro system of monocyte to macrophage differentiation wherein macrophages re-exposed to Pf -iRBCs exhibited attenuated inflammatory cytokine responses and a corresponding decrease in the epigenetic marker of active gene transcription, H3K4me3, at inflammatory cytokine gene loci. Together these data indicate that Pf induces epigenetic reprogramming of monocytes/macrophages toward a regulatory phenotype that attenuates inflammatory responses during subsequent Pf exposure. These findings also suggest that past malaria exposure could mitigate monocyte-associated immunopathology induced by other pathogens such as SARS-CoV-2.

Author Summary

The malaria parasite is mosquito-transmitted and causes fever and other inflammatory symptoms while circulating in the bloodstream. However, in regions of high malaria transmission the parasite is less likely to cause fever as children age and enter adulthood, even though adults commonly have malaria parasites in their blood. Monocytes are cells of the innate immune system that secrete molecules that cause fever and inflammation when encountering microorganisms like malaria. Although inflammation is critical to initiating normal immune responses, too much inflammation can harm infected individuals. In Mali, we conducted a study of a malaria-exposed population from infants to adults and found that participants' monocytes produced less inflammation as age increases, whereas monocytes of Malian infants and U.S. adults, who had never been exposed to malaria, both produced high levels of inflammatory molecules. Accordingly, monocytes exposed to malaria in the laboratory became less inflammatory when re-exposed to malaria again later, and these monocytes 'turned down' their inflammatory genes. This study helps us understand how people become immune to inflammatory symptoms of malaria and may also help explain why people in malaria-endemic areas appear to be less susceptible to the harmful effects of inflammation caused by other pathogens such as SARS-CoV-2.

SARS-CoV-2 and Plasmodium falciparum common immunodominant regions may explain low COVID-19 incidence in the malaria-endemic belt

Coronavirus disease 2019 (COVID-19) has caused significant morbidity and mortality and new cases are on the rise globally, yet malaria-endemic areas report statistically significant lower incidences. We identified potential shared targets for an immune response to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) by immune determinants' shared identities with P. falciparum using the Immune Epitope Database and Analysis Resource Immune 9.0 browser tool. Probable cross-reactivity is suggested through HLA-A∗02:01 and subsequent CD8+ T-cell activation. The apparent immunodominant epitope conservation between SARS-CoV-2 (N and open reading frame (ORF) 1ab) and P. falciparum thrombospondin-related anonymous protein (TRAP) may underlie the low COVID-19 incidence in the malaria-endemic zone by providing immunity against virus infection to those previously infected with Plasmodium. Additionally, we hypothesize that the shared epitopes which lie within antigens that aid in the establishment of the P. falciparum erythrocyte invasion may be an alternative route for SARS-CoV-2 via the erythrocyte CD147 receptor, although this remains to be proven.