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

COVID-19 inflammatory signature in a Mozambican cohort: unchanged red blood series and reduced levels of IL-6 and other proinflammatory cytokines

BACKGROUND

Alterations in haematological, biochemical parameters and cytokine levels, were reported in patients with COVID-19, however, there is an underrepresentation of the African population, which could provide evidence for understanding SARS-CoV-2 pathogenesis and useful tools for clinical management of cases. In this study, we aimed to determine the haematological, biochemical and cytokine profile in Mozambican individuals with SARS-CoV-2.

METHODS

A cohort of 85 Mozambican individuals with RT-PCR SARS-CoV-2 results, was stratified into negative, asymptomatic, mild, moderate, and severe categories. Haematological, biochemical and cytokines measurement were performed on samples from the study participants. Principal component analysis (PCA) was performed to identify similar patterns among the study cases. Comparisons between groups were performed using the Kruskal-Wallis test. Receiver operating characteristic (ROC) and area under the curve (AUC) analysis were conducted to evaluate the ability of these parameters to distinguish severe from non-severe cases of SARS-CoV-2 infection.

RESULTS

SARS-CoV-2 infection was associated with a significant (p < 0.05) decrease in peripheral blood absolute counts of total lymphocytes and eosinophils, below the reference values along with no abnormal change (p > 0.05) in red blood cell count, haemoglobin, platelets and other red series parameters. At the serum level, SARS-CoV-2 infection was associated with an increase in serum levels of C-reactive protein (C-RP) and glucose above the reference values and to a significant reduction a significant (p < 0.05) reduction in levels of interferon-gamma (INF-γ), Tumour Necrosis Factor alfa (TNF-α) and the interleukin 1 beta (IL-1β) and IL-6 in severe cases, when compared to negative cases. Haematological, biochemical and cytokine profiles segregate severe from non-severe cases of COVID-19 with an excellent performance of C-RP (AUC = 0.95; p < 0.001) and good performance of lymphocytes (AUC = 0.88; p < 0.001) and IL-15 (AUC = 0.86; p < 0.001).

CONCLUSION

The lack of variation in red and platelet series, coupled with a decrease in the levels of classical pro-inflammatory in severe cases, deviates from what has been reported in other contexts suggesting, that there may be peculiarities in COVID-19 manifestation within the context of this study population. Furthermore, these results identify parameters with potential for clinical management of COVID-19 and therefore good resource allocation, particularly for severe cases.

Humoral Immunity Profiling to Pandemic and Bat-Derived Coronavirus Variants: A Geographical Comparison

Dynamic pathogen exposure may impact the immunological response to SARS-CoV-2 (SCV2). One potential explanation for the lack of severe SCV2-related morbidity and mortality in Southeast Asia is prior exposure to related betacoronaviruses. Recent discoveries of SCV2-related betacoronaviruses from horseshoe bats (Rhinolophus sinicus) in Thailand, Laos, and Cambodia suggest the potential for bat-to-human spillover exposures in the region. In this work, serum antibodies to protein constructs from SCV2 and a representative bat coronavirus isolated in Cambodia (RshSTT182) are measured in pre-pandemic Cambodian human sera using ELISA assays. Of 293 Cambodian samples tested (N = 131 with acute malaria, n = 162 with acute undifferentiated febrile illness), 32 (10.9%) are seropositive for SCV2 based on established Spike and receptor-binding domain (RBD) cutoffs. Within SCV2 seropositive samples, 16 (50%) have higher antibody levels to antigens from the representative virus RshSTT182 versus SCV2 antigens; competitive binding ELISA assays demonstrate inhibition of reactivity to SCV2 Spike after pre-incubation with RshSTT182 Spike. Surrogate virus neutralization tests demonstrate that 8/30 (26.7%) SCV2 ELISA positive pre-pandemic Cambodian samples have neutralizing activity against SCV2, while 14/30 (46.7%) have activity against other SCV2-related betacoronaviruses. These data suggest that exposure to related betacoronaviruses may elicit cross-reactive immunity to SCV2 prior to the global pandemic.

Insights into parasites and COVID-19 co-infections in Iran: a systematic review

BACKGROUND

It is well-documented that using immunosuppressive drugs such as corticosteroids or cytokine blockers in treating coronavirus disease 2019 (COVID-19) increases the risk of co-infections. Here we systematically summarized the cases of COVID-19-associated parasitic infections (CAPIs) in Iran.

METHODS

From 19 February 2020 to 10 May 2023, all studies on Iranian patients suffering from CAPIs were collected from several databases using a systematic search strategy.

RESULTS

Of 540 records, 11 studies remained for data extraction. In this research, most of the studies were related to Lophomonas and Toxoplasma. Of 411 cases of CAPIs, toxoplasmosis (385 [93.7%]) had the highest rate of infection among Iranian patients, followed by blastocystosis (15 [3.6%]), fascioliasis (4 [0.97%]), leishmaniasis (3 [0.7%]), lophomoniasis (3 [0.7%]) and strongyloidiasis (1 [0.2%]). In general, Blastocystis enhanced diarrhoea in patients with COVID-19. Lophomonas, Toxoplasma and Strongyloides increased the severity of COVID-19, but Fasciola decreased its intensity. Patients with a history of cutaneous leishmaniasis showed mild symptoms of COVID-19. Also, patients with a prior history of hydatid cysts were not affected by COVID-19.

CONCLUSIONS

Due to the similar symptoms of some parasitic diseases and COVID-19 and immunosuppressive treatment regimens in these patients that may cause the reactivation or recurrence of parasitic infections, early diagnosis and treatment are required.

Impact of latent toxoplasmosis on pneumonic and non-pneumonic COVID-19 patients with estimation of relevant oxidative stress biomarkers

Susceptibility to COVID-19, the most devastating global pandemic, appears to vary widely across different population groups. Exposure to toxoplasmosis has been proposed as a theory to explain the diversity of these populations. The aim of the present study was to investigate the possible association between latent toxoplasmosis and COVID-19 and its probable correlation with markers of oxidative stress, C-reactive protein (CRP) and ferritin. In a case-control study, blood samples were collected from 91 confirmed (48 non-pneumonic; NP, and 43 pneumonic; P) COVID-19 patients and 45 healthy controls. All participants were tested for IgG anti-Toxoplasma gondii antibodies and oxidative stress markers (nitric oxide [NO], superoxide dismutase [SOD] and reduced glutathione [GSH]), and CRP and serum ferritin levels were determined. In COVID-19 patients, IgG anti-T. gondii antibodies were found in 54% compared to 7% in the control group, with the difference being statistically significant (P ˂ 0.001). However, no significant correlation was found between the severity of COVID-19 and latent T. gondii infection. Latent toxoplasmosis had a strong influence on the risk of COVID-19. NO and SOD levels were significantly increased in COVID-19 patients, while GSH levels decreased significantly in them compared to control subjects (P ˂ 0.001 for both values). CRP and ferritin levels were also significantly elevated in P COVID-19 patients infected with toxoplasmosis. This is the first study to look at the importance of oxidative stress indicators in co-infection between COVID-19 and T. gondii. The high prevalence of latent toxoplasmosis in COVID-19 suggests that T. gondii infection can be considered a strong indicator of the high risk of COVID-19.

Cutaneous Leishmaniasis Hampers COVID-19: A Controlled Cross-Sectional Study in High-Burden Endemic Areas of Iran

INTRODUCTION

Emerging infectious diseases such as SARS-CoV-2 can cause pandemics and create a critical risk for humans. In a previous pilot study, we reported that the immunological responses induced by cutaneous leishmaniasis (CL) could decrease the incidence and severity of COVID-19. In this large-scale case-control study, we assessed the possible relationship between mortality and morbidity of COVID-19 in healed CL persons suffering scars compared to cases without CL history.

METHODS

This controlled cross-sectional study was conducted between July 2020 and December 2022 in the endemic and high-burden areas of CL in southeastern Iran. In the study, 1400 previous CL cases with scars and 1,521,329 subjects who had no previous CL were analyzed. We used R 4.0.2 to analyze the data. Firth's bias reduction approach corresponding to the penalization of likelihood logistic regression by Jeffreys was also employed to influence the variables in the dataset. Also, a Bayesian ordinal logistic regression model was performed to explore the COVID-19 severity in both case and referent groups.

RESULTS

The occurrence and severity rate of COVID-19 in CL scar cases are significantly less than in the non-CL control group, while in the CL scar subjects, patients with critical conditions and mortality were not observed. The morbidity (OR = 0.11, CI 0.06-0.20 and P < 0.001) and severity of COVID-19 in previous cases with CL scars were significantly diminished than that in the control group (credible interval - 2.57, - 1.62).

CONCLUSIONS

The results represented a durable negative relationship between cured CL and COVID-19 incidence and severity. Additional studies seem necessary and should be designed to further validate the true impact and underlying mechanistic action of CL on COVID-19.

Climate and COVID-19 transmission: a cross-sectional study in Africa

The role of climate in the Coronavirus disease 2019 (COVID-19) transmission appears to be controversial, as reported in earlier studies. In Africa, the subject is poorly documented. In this study, over the period from January 1st, 2020 to September 31, 2022, the daily variations in cumulative confirmed cases of COVID-19 for each African country (54 countries) are modelled through time-series-based approaches and using meteorological factors as covariates. It is suggested from the findings that climate plays a role in COVID-19 transmission since at least one meteorological factor is found to be significant in 32 countries. In decreasing order, the most often occurring meteorological factors are dewpoint temperature, relative and absolute humidity, average temperature and solar radiation. Most of these factors show a lagged effect with confirmed cases (between 0 and 28 days). Also, some meteorological factors exhibit contrasting effects on COVID-19 transmission, resulting in both positive and negative association with cumulative cases, therefore highlighting the complex nature of the interplay between climate and COVID-19 transmission.

Development and comparative evaluation of SARS-CoV-2 S-RBD and N based ELISA tests in various African endemic settings

Management of the COVID-19 pandemic relies on molecular diagnostic methods supported by serological tools. Herein, we developed S-RBD- and N- based ELISA assays useful for infection rate surveillance as well as the follow-up of acquired protective immunity against SARS-CoV-2. ELISA assays were optimized using COVID-19 Tunisian patients' sera and prepandemic controls. Assays were further validated in 3 African countries with variable endemic settings. The receiver operating curve was used to evaluate the assay performances. The N- and S-RBD-based ELISA assays performances, in Tunisia, were very high (AUC: 0.966 and 0.98, respectively, p < 0.0001). Cross-validation analysis showed similar performances in different settings. Cross-reactivity, with malaria infection, against viral antigens, was noticed. In head-to-head comparisons with different commercial assays, the developed assays showed high agreement. This study demonstrates, the added value of the developed serological assays in low-income countries, particularly in ethnically diverse populations with variable exposure to local endemic infectious diseases.

Clinical profile and Predictors of Outcomes of Hospitalized Patients with Laboratory-Confirmed Severe Acute Respiratory Syndrome Coronavirus 2 in Nigeria: A Retrospective Analysis of 13 High Burden States in Nigeria

Background

The majority of global COVID deaths have occurred in developed countries. Not much is known about the clinical outcomes for the patients admitted with COVID in Nigeria. We thus described the clinical characteristics, outcomes, and predictors of outcomes of hospitalized Nigerian COVID-19 patients.

Methodology

We performed multilevel and mixed effects regression, Kaplan-Meir survival, and Cox proportionate hazards analyses to evaluate factors associated with death in patients admitted for COVID-19 in 13 high-burden states of Nigeria between 25th February 2020 and 30th August 2021.

Results

Of the 3462 patients (median age, 40 years (interquartile range 28 years 54 years), 2,990(60.6%) were male and, 213(6.15%) of them died while on admission. Male sex (adjusted odds ratio [aOR], 1.78 [95% confidence interval {CI}, 1.23-2.56]), age group 45-65 years (OR, 3.93 [95% CI, 1.29-12.02]), age group 66-75 years (aOR, 5.37 [95% CI, 1.68-17.14]), age group > 75 years (aOR, 6.81 [95% CI, 2.04-22.82]), chronic cardiac disease (aOR, 3.07 [95% CI, 1.20-7.86]), being diabetic (aOR, 2.16 [95% CI, 1.41-3.31]), and having chronic kidney disease (OR, 11.01 [95% CI, 2.74-44.24]),were strongly associated with increased odds of death. Having concurrent malaria (aOR, 0.45 [95% CI, 0.16-1.28]), use of Azithromycin for treatment (aOR, 0.33 [95% CI, 0.19-0.54]), and use of Chloroquine/Hydroxychloroquine for treatment (aOR, 0.07 [95% CI, 0.03-0.14]) were significantly associated with decreased odds of death.

Conclusions

The cumulative probability of death of male patients, diabetics, hypertensives, and patients with CKD was higher than that of female patients and those without those comorbidities while concurrent malaria and use of chloroquine/hydroxychloroquine in the treatment regimen were associated with a decreased risk of dying in patients treated in our isolation centers.

Cross-reactivity of SARS-CoV-2 with other pathogens, especially dengue virus: A historical perspective

Dengue is a vector-borne viral disease caused by a Flavivirus whereas the COVID-19 pandemic was caused by a highly contagious virus, SARS-CoV-2 belonging to the family Coronaviridae. However, COVID-19 severity was observably less in dengue-endemic countries and vice versa especially during the active years of the pandemic (2019-2021). We observed that dengue virus (DENV) antibodies (Abs) could cross-react with SARS-CoV-2 spike antigen. This resulted in SARS-CoV-2 false positivity by rapid Ab test kits. DENV Abs binding to SARS-CoV-2 receptor-binding domain (and the reverse scenario), as revealed by docking studies further validated DENV and SARS-CoV-2 cross-reactivity. Finally, SARS-CoV-2 Abs were found to cross-neutralize DENV1 and DENV2 in virus neutralization test (VNT). Abs to other pathogens like Plasmodium were also cross-reactive but non-neutralizing for SARS-CoV-2. Here, we analyze the existing data on SARS-CoV-2 cross-reactivity with other pathogens, especially dengue to assess its impact on health (cross-protection?) and differential sero-diagnosis/surveillance.

Population-based assessment of the burden of COVID-19 infection in African countries: a first-year report card and public health implications

Background

The COVID-19 pandemic constitutes a global health threat and poses a major burden on the African continent. We assessed the real-world burden of COVID-19 infection in African Union (AU) member states to determine the distributional patterns of epidemiological measures during the first 1 year of the pandemic.

Methods

This retrospective cross-sectional study utilized COVID-19 data from publicly available data repositories of the African Center for Disease Control and Prevention and Our World in Data for the period February 2020 to January 2021. AU member states were classified into low, medium, and high burdens based on COVID-19 morbidity. We conducted descriptive and inferential analyses of COVID-19-reported cases, deaths, recoveries, active cases, COVID-19 tests, and epidemiological measures that included morbidity and mortality rates, case fatality rate (CFR), and case ratios.

Results

A total of 3.21 million cases were reported during the 1-year period, with 2.6 million recoveries, 536,784 cases remaining active, and 77,486 deaths. Most countries (49.1%, n = 26) in AU experienced a low burden of COVID-19 infection compared to 28.3% (n = 15) with medium burden and 22.6% (n = 12) with high burden. AU nations with a high burden of the disease were mainly in the northern and southern regions. South Africa recorded the highest number of cases (1.31 million), followed by Morocco with 457,625 and Tunisia with 175,065 cases. Correspondently, death tolls for these countries were 36,467, 7888, and 5528 deaths, respectively. Of the total COVID-19 tests performed (83.8 million) during the first 1 year, 62.43% were from high-burden countries. The least testing occurred in the medium-burden (18.42%) countries. The overall CFR of AU was 2.21%. A morbidity rate of 327.52/105 population and mortality rate of 5.96/105 population were recorded during the first 1-year period with significant variations (p < 0.0001) across burden levels. Continental morbidity and mortality rates of 17,359/105 and 315.933/105 populations were recorded with significant correlation (r = 0.863, p < 0.0001) between them and variations across selected epidemiological measures by COVID-19 burden levels.

Conclusion

Understanding the true burden of the disease in AU countries is important for establishing the impact of the pandemic in the African continent and for intervention planning, preparedness, and deployment of resources during COVID-19 surges and future pandemics.

Prevalence of SARS-CoV-2 and co-infection with malaria during the first wave of the pandemic (the Burkina Faso case)

Africa accounts for 1.5% of the global coronavirus disease 2019 (COVID-19) cases and 2.7% of deaths, but this low incidence has been partly attributed to the limited testing capacity in most countries. In addition, the population in many African countries is at high risk of infection with endemic infectious diseases such as malaria. Our aim is to determine the prevalence and circulation of SARS-CoV-2 variants, and the frequency of co-infection with the malaria parasite. We conducted serological tests and microscopy examinations on 998 volunteers of different ages and sexes in a random and stratified population sample in Burkina-Faso. In addition, nasopharyngeal samples were taken for RT-qPCR of SARS-CoV-2 and for whole viral genome sequencing. Our results show a 3.2 and a 2.5% of SARS-CoV-2 seroprevalence and PCR positivity; and 22% of malaria incidence, over the sampling period, with marked differences linked to age. Importantly, we found 8 cases of confirmed co-infection and 11 cases of suspected co-infection mostly in children and teenagers. Finally, we report the genome sequences of 13 SARS-CoV-2 isolates circulating in Burkina Faso at the time of analysis, assigned to lineages A.19, A.21, B.1.1.404, B.1.1.118, B.1 and grouped into clades; 19B, 20A, and 20B. This is the first population-based study about SARS-CoV-2 and malaria in Burkina Faso during the first wave of the pandemic, providing a relevant estimation of the real prevalence of SARS-CoV-2 and variants circulating in this Western African country. Besides, it highlights the non-negligible frequency of co-infection with malaria in African communities.

Toxoplasmosis and symptoms severity in patients with COVID-19 in referral centers in Northern Iran

Toxoplasmosis has been categorized as one of the long-lasting protozoan parasitic infections. It affects almost one-third of the world's population. In recent years, several documented studies have elucidated that infected individuals have a remarkably higher incidence of distinct health problems and show various adverse effects. In the PCR-positive COVID-19 patients in Gonbad-e-Kavus, Kalaleh, and Minoodasht counties in the northern part of Iran from June 2021 to December 2021, we sought to investigate any potential relationships between the severity of COVID-19 symptoms and acute and latent toxoplasmosis caused by Toxoplasma gondii (T. gondii). Whole blood samples of 161 COVID-19 patients with positive PCR. The samples were centrifuged to separate serum and screened for two important antibodies against T. gondii (IgM and IgG) by using ELISA kits for human anti-T. gondii IgM and IgG. Anti-T. gondii IgM and IgG antibodies were detected in 8/161 (5.0%) and 42/161 (26.1%) COVID-19 patients, respectively. No significant relationships were found between Toxoplasma IgM and IgG results with clinical signs, age, sex, contact with animals, comorbidities, and also the mortality rate of people with COVID-19. These findings showed that acute and latent toxoplasmosis infections are common among patients with COVID-19; however, no significant associations were found between toxoplasma infections and the symptoms of COVID-19. Therefore, toxoplasmosis is not considered a risk factor for COVID-19.

Global SARS-CoV-2 seroprevalence from January 2020 to April 2022: A systematic review and meta-analysis of standardized population-based studies

BACKGROUND

Our understanding of the global scale of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) infection remains incomplete: Routine surveillance data underestimate infection and cannot infer on population immunity; there is a predominance of asymptomatic infections, and uneven access to diagnostics. We meta-analyzed SARS-CoV-2 seroprevalence studies, standardized to those described in the World Health Organization's Unity protocol (WHO Unity) for general population seroepidemiological studies, to estimate the extent of population infection and seropositivity to the virus 2 years into the pandemic.

METHODS AND FINDINGS

We conducted a systematic review and meta-analysis, searching MEDLINE, Embase, Web of Science, preprints, and grey literature for SARS-CoV-2 seroprevalence published between January 1, 2020 and May 20, 2022. The review protocol is registered with PROSPERO (CRD42020183634). We included general population cross-sectional and cohort studies meeting an assay quality threshold (90% sensitivity, 97% specificity; exceptions for humanitarian settings). We excluded studies with an unclear or closed population sample frame. Eligible studies-those aligned with the WHO Unity protocol-were extracted and critically appraised in duplicate, with risk of bias evaluated using a modified Joanna Briggs Institute checklist. We meta-analyzed seroprevalence by country and month, pooling to estimate regional and global seroprevalence over time; compared seroprevalence from infection to confirmed cases to estimate underascertainment; meta-analyzed differences in seroprevalence between demographic subgroups such as age and sex; and identified national factors associated with seroprevalence using meta-regression. We identified 513 full texts reporting 965 distinct seroprevalence studies (41% low- and middle-income countries [LMICs]) sampling 5,346,069 participants between January 2020 and April 2022, including 459 low/moderate risk of bias studies with national/subnational scope in further analysis. By September 2021, global SARS-CoV-2 seroprevalence from infection or vaccination was 59.2%, 95% CI [56.1% to 62.2%]. Overall seroprevalence rose steeply in 2021 due to infection in some regions (e.g., 26.6% [24.6 to 28.8] to 86.7% [84.6% to 88.5%] in Africa in December 2021) and vaccination and infection in others (e.g., 9.6% [8.3% to 11.0%] in June 2020 to 95.9% [92.6% to 97.8%] in December 2021, in European high-income countries [HICs]). After the emergence of Omicron in March 2022, infection-induced seroprevalence rose to 47.9% [41.0% to 54.9%] in Europe HIC and 33.7% [31.6% to 36.0%] in Americas HIC. In 2021 Quarter Three (July to September), median seroprevalence to cumulative incidence ratios ranged from around 2:1 in the Americas and Europe HICs to over 100:1 in Africa (LMICs). Children 0 to 9 years and adults 60+ were at lower risk of seropositivity than adults 20 to 29 (p < 0.001 and p = 0.005, respectively). In a multivariable model using prevaccination data, stringent public health and social measures were associated with lower seroprevalence (p = 0.02). The main limitations of our methodology include that some estimates were driven by certain countries or populations being overrepresented.

CONCLUSIONS

In this study, we observed that global seroprevalence has risen considerably over time and with regional variation; however, over one-third of the global population are seronegative to the SARS-CoV-2 virus. Our estimates of infections based on seroprevalence far exceed reported Coronavirus Disease 2019 (COVID-19) cases. Quality and standardized seroprevalence studies are essential to inform COVID-19 response, particularly in resource-limited regions.

Assessing the impact of non-pharmaceutical interventions (NPIs) and BCG vaccine cross-protection in the transmission dynamics of SARS-CoV-2 in eastern Africa

OBJECTIVE

The outbreak of the novel coronavirus disease 2019 (COVID-19) is still affecting African countries. The pandemic presents challenges on how to measure governmental, and community responses to the crisis. Beyond health risks, the socio-economic implications of the pandemic motivated us to examine the transmission dynamics of COVID-19 and the impact of non-pharmaceutical interventions (NPIs). The main objective of this study was to assess the impact of BCG vaccination and NPIs enforced on COVID-19 case-death-recovery counts weighted by age-structured population in Ethiopia, Kenya, and Rwanda. We applied a semi-mechanistic Bayesian hierarchical model (BHM) combined with Markov Chain Monte Carlo (MCMC) simulation to the age-structured pandemic data obtained from the target countries.

RESULTS

The estimated mean effective reproductive number (Rt) for COVID-19 was 2.50 (C1: 1.99-5.95), 3.51 (CI: 2.28-7.28) and 3.53 (CI: 2.97-5.60) in Ethiopia, Kenya and Rwanda respectively. Our results indicate that NPIs such as lockdowns, and curfews had a large effect on reducing Rt. Current interventions have been effective in reducing Rt and thereby achieve control of the epidemic. Beyond age-structure and NPIs, we found no significant association between COVID-19 and BCG vaccine-induced protection. Continued interventions should be strengthened to control transmission of SARS-CoV-2.

Spike protein of SARS-CoV-2 variants: a brief review and practical implications

The scientific community has been alarmed by the possible immunological evasion, higher infectivity, and severity of disease caused by the newest variants of SARS-CoV-2. The spike protein has an important role in the cellular invasion of viruses and is the target of several vaccines and therapeutic resources, such as monoclonal antibodies. In addition, some of the most relevant mutations in the different variants are on the spike (S) protein gene sequence that leads to structural alterations in the predicted protein, thus causing concern about the protection mediated by vaccines against these new strains. The present review highlights the most recent knowledge about COVID-19 and vaccines, emphasizing the different spike protein structures of SARS-CoV-2 and updating the reader about the emerging viral variants and their classifications, the more common viral mutations described and their distribution in Brazil. It also compiles a table with the most recent knowledge about all of the Omicron spike mutations.

Prophylactic effect of cutaneous leishmaniasis against COVID-19: a case-control field assessment

INTRODUCTION

We assessed the potential relationship between COVID-19 and laboratory-confirmed cutaneous leishmaniasis (CL)-registered cases with a history of scarring, compared with volunteer participants without history of CL.

METHODS

This case-control retrospective study was conducted in southeastern Iran with a high anthroponotic cutaneous leishmaniasis (ACL) burden.

RESULTS

Overall, n=1010 CL cases (n=479 male, n=531 female) were evaluated for infection with SARS-CoV-2. In the CL case group, 2 men and 1 woman (0.3% in total) had a mild form of COVID-19 disease; none were hospitalized or died. In contrast, of n=2020 participants without history of CL, n=57 (2.9%) contracted laboratory-confirmed COVID-19, including mild (66.7%), hospitalized (26.3%), critical (3.5%) and fatal (3.5%). There was a strong negative association between CL infection and COVID-19. The burden of COVID-19 in CL-cured participants significantly reduced the morbidity (odds ratio: 0.12; CI: 0.03-0.30; P <0.001) and mortality (percentile: -4.10, -0.02).

CONCLUSION

Participants with a history of CL scar had significantly reduced incidence of COVID-19 morbidity and mortality. The cross-protection mediated by CL may retard COVID-19 in endemic countries. However, further longitudinal studies are needed to explore the potential profile and duration of this protection offered by CL against COVID-19.

Understanding the COVID-19 pandemic prevalence in Africa through optimal feature selection and clustering: evidence from a statistical perspective

The COVID-19 pandemic, which outbroke in Wuhan (China) in December 2019, severely hit almost all sectors of activity in the world as a consequence of the restrictive measures imposed. Two years later, Africa still emerges as the least affected continent by the pandemic. This study analyzed COVID-19 prevalence across African countries through country-level variables prior to clustering. Using Spearman-rank correlation, multicollinearity analysis and univariate filtering, 9 country-level variables were identified from an initial set of 34 variables. These variables relate to socioeconomic status, population structure, healthcare system and environment and the climatic setting. A clustering of the 54 African countries is further carried out through the use of agglomerative hierarchical clustering (AHC) method, which generated 3 distinctive clusters. Cluster 1 (11 countries) is the most affected by COVID-19 (median of 63,508.6 confirmed cases and 946.5 deaths per million) and is composed of countries with the highest socioeconomic status. Cluster 2 (27 countries) is the least affected (median of 4473.7 confirmed cases and 81.2 deaths per million), and mainly features countries with the least socioeconomic features and international exposure. Cluster 3 (16 countries) is intermediate in terms of COVID-19 prevalence (median of 2569.3 confirmed cases and 35.7 deaths per million) and features countries the least urbanized and geographically close to the equator, with intermediate international exposure and socioeconomic features. These findings shed light on the main features of COVID-19 prevalence in Africa and might help refine effectively coping management strategies of the ongoing pandemic.

Supplementary Information

The online version contains supplementary material available at 10.1007/s10668-022-02646-3.

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.

SARS-CoV-2 infection in Africa: a systematic review and meta-analysis of standardised seroprevalence studies, from January 2020 to December 2021

INTRODUCTION

Estimating COVID-19 cumulative incidence in Africa remains problematic due to challenges in contact tracing, routine surveillance systems and laboratory testing capacities and strategies. We undertook a meta-analysis of population-based seroprevalence studies to estimate SARS-CoV-2 seroprevalence in Africa to inform evidence-based decision making on public health and social measures (PHSM) and vaccine strategy.

METHODS

We searched for seroprevalence studies conducted in Africa published 1 January 2020-30 December 2021 in Medline, Embase, Web of Science and Europe PMC (preprints), grey literature, media releases and early results from WHO Unity studies. All studies were screened, extracted, assessed for risk of bias and evaluated for alignment with the WHO Unity seroprevalence protocol. We conducted descriptive analyses of seroprevalence and meta-analysed seroprevalence differences by demographic groups, place and time. We estimated the extent of undetected infections by comparing seroprevalence and cumulative incidence of confirmed cases reported to WHO.

PROSPERO

CRD42020183634.

RESULTS

We identified 56 full texts or early results, reporting 153 distinct seroprevalence studies in Africa. Of these, 97 (63%) were low/moderate risk of bias studies. SARS-CoV-2 seroprevalence rose from 3.0% (95% CI 1.0% to 9.2%) in April-June 2020 to 65.1% (95% CI 56.3% to 73.0%) in July-September 2021. The ratios of seroprevalence from infection to cumulative incidence of confirmed cases was large (overall: 100:1, ranging from 18:1 to 954:1) and steady over time. Seroprevalence was highly heterogeneous both within countries-urban versus rural (lower seroprevalence for rural geographic areas), children versus adults (children aged 0-9 years had the lowest seroprevalence)-and between countries and African subregions.

CONCLUSION

We report high seroprevalence in Africa suggesting greater population exposure to SARS-CoV-2 and potential protection against COVID-19 severe disease than indicated by surveillance data. As seroprevalence was heterogeneous, targeted PHSM and vaccination strategies need to be tailored to local epidemiological situations.

Global dynamics of SARS-CoV-2/malaria model with antibody immune response

Coronavirus disease 2019 (COVID-19) is a new viral disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Malaria is a parasitic disease caused by Plasmodium parasites. In this paper, we explore a within-host model of SARS-CoV-2/malaria coinfection. This model consists of seven ordinary differential equations that study the interactions between uninfected red blood cells, infected red blood cells, free merozoites, uninfected epithelial cells, infected epithelial cells, free SARS-CoV-2 particles, and antibodies. We show that the model has bounded and nonnegative solutions. We compute all steady state points and derive their existence conditions. We use appropriate Lyapunov functions to confirm the global stability of all steady states. We enhance the reliability of the theoretical results by performing numerical simulations. The steady states reflect the monoinfection and coinfection with malaria and SARS-CoV-2. The shared immune response reduces the concentrations of malaria merozoites and SARS-CoV-2 particles in coinfected patients. This response reduces the severity of SARS-CoV-2 infection in this group of patients.

Using outbreak data to estimate the dynamic COVID-19 landscape in Eastern Africa

Background

The emergence of COVID-19 as a global pandemic presents a serious health threat to African countries and the livelihoods of its people. To mitigate the impact of this disease, intervention measures including self-isolation, schools and border closures were implemented to varying degrees of success. Moreover, there are a limited number of empirical studies on the effectiveness of non-pharmaceutical interventions (NPIs) to control COVID-19. In this study, we considered two models to inform policy decisions about pandemic planning and the implementation of NPIs based on case-death-recovery counts.

Methods

We applied an extended susceptible-infected-removed (eSIR) model, incorporating quarantine, antibody and vaccination compartments, to time series data in order to assess the transmission dynamics of COVID-19. Additionally, we adopted the susceptible-exposed-infectious-recovered (SEIR) model to investigate the robustness of the eSIR model based on case-death-recovery counts and the reproductive number (R₀). The prediction accuracy was assessed using the root mean square error and mean absolute error. Moreover, parameter sensitivity analysis was performed by fixing initial parameters in the SEIR model and then estimating R₀, β and γ.

Results

We observed an exponential trend of the number of active cases of COVID-19 since March 02 2020, with the pandemic peak occurring around August 2021. The estimated mean R₀ values ranged from 1.32 (95% CI, 1.17–1.49) in Rwanda to 8.52 (95% CI: 3.73–14.10) in Kenya. The predicted case counts by January 16/2022 in Burundi, Ethiopia, Kenya, Rwanda, South Sudan, Tanzania and Uganda were 115,505; 7,072,584; 18,248,566; 410,599; 386,020; 107,265, and 3,145,602 respectively. We show that the low apparent morbidity and mortality observed in EACs, is likely biased by underestimation of the infected and mortality cases.

Conclusion

The current NPIs can delay the pandemic pea and effectively reduce further spread of COVID-19 and should therefore be strengthened. The observed reduction in R₀ is consistent with the interventions implemented in EACs, in particular, lockdowns and roll-out of vaccination programmes. Future work should account for the negative impact of the interventions on the economy and food systems.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12879-022-07510-3.

SARS-CoV-2: Molecular Structure, Pathogenesis, Potential Therapeutic Targets, and Immune Response of the Infected Subject

Background

The pathogenic mechanisms and immune response of COVID-19 are far from clear. Through a documentary review of literature, the authors describe virological and molecular aspects of SARS-CoV-2, the intimate mechanisms of cell infection, and potential therapeutic targets. They also analyze the characteristics of immune response of the infected subject.

Objectives

Objectives of this study are to describe the state of knowledge on virological data, molecular and physiopathogenic mechanisms of SARS-CoV-2, with a view to a better understanding of the therapeutic targets, as well as the immune response of the infected subject. Methodology. This documentary review is a compilation of several meta-analyses, consistent with the methodology described in the PRISMA statement on literature data on SARS-CoV-2, published between March 22 and August 14, 2020 (Moher et al.). The search engines used for the selection of articles were as follows: PubMed, Google Scholar, Global Health, and WHO reports. Papers of interest were those addressing virological and molecular data on SARS-CoV-2, therapeutic aspects of COVID-19, and immunity of the infected subject. Of the 617 eligible papers, 417 could be retained after removing the duplicates. Ultimately, only 50 articles were retained for final evaluation. The data collected allowed the development of a two-armed model around the physiopathological aspects and potential therapeutic targets, as well as aspects of host immunity, respectively. The model was then compared to data from the HIV literature.

Conclusion

Reported data could contribute to a better understanding of molecular mechanisms of cellular infection by SARS-CoV-2 as well as to a more easy explanation of the action of pharmacological agents used for the treatment, while elucidating intimate mechanisms of the immunity of infected subject.

Seroreactivity of the Severe Acute Respiratory Syndrome Coronavirus 2 Recombinant S Protein, Receptor-Binding Domain, and Its Receptor-Binding Motif in COVID-19 Patients and Their Cross-Reactivity With Pre-COVID-19 Samples From Malaria-Endemic Areas

Despite the global interest and the unprecedented number of scientific studies triggered by the COVID-19 pandemic, few data are available from developing and low-income countries. In these regions, communities live under the threat of various transmissible diseases aside from COVID-19, including malaria. This study aims to determine the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) seroreactivity of antibodies from COVID-19 and pre-COVID-19 samples of individuals in Mali (West Africa). Blood samples from COVID-19 patients (n = 266) at Bamako Dermatology Hospital (HDB) and pre-COVID-19 donors (n = 283) from a previous malaria survey conducted in Dangassa village were tested by ELISA to assess IgG antibodies specific to the full-length spike (S) protein, the receptor-binding domain (RBD), and the receptor-binding motif (RBM436-507). Study participants were categorized by age, gender, treatment duration for COVID-19, and comorbidities. In addition, the cross-seroreactivity of samples from pre-COVID-19, malaria-positive patients against the three antigens was assessed. Recognition of the SARS-CoV-2 proteins by sera from COVID-19 patients was 80.5% for S, 71.1% for RBD, and 31.9% for RBM (p < 0.001). While antibody responses to S and RBD tended to be age-dependent, responses to RBM were not. Responses were not gender-dependent for any of the antigens. Higher antibody levels to S, RBD, and RBM at hospital entry were associated with shorter treatment durations, particularly for RBD (p < 0.01). In contrast, higher body weights negatively influenced the anti-S antibody response, and asthma and diabetes weakened the anti-RBM antibody responses. Although lower, a significant cross-reactive antibody response to S (21.9%), RBD (6.7%), and RBM (8.8%) was detected in the pre-COVID-19 and malaria samples. Cross-reactive antibody responses to RBM were mostly associated (p < 0.01) with the absence of current Plasmodium falciparum infection, warranting further study.

An Imported Case of Afebrile Plasmodium falciparum Malaria Infection from Tanzania in a Returning Traveler to the Republic of Korea following an Earlier COVID-19 Infection

Malaria is well-known as one of the most common causes of fever among travelers returning from endemic areas such as tropical African countries. However, afebrile Plasmodium falciparum malaria has rarely been reported in a returning traveler with no prior history of malaria infection. Here, we report an imported case of afebrile P. falciparum malaria infection from Tanzania in a returning traveler to the Republic of Korea, following an earlier COVID-19 infection without previous history of malaria infection. Our case suggests the hypothesis that severe symptoms of P. falciparum malaria infection might be prevented by cross- immunity from previous COVID-19 infection.

Malaria Epidemiology and COVID-19 Pandemic: Are They Interrelated?

Coronavirus disease 2019 (COVID-19) is a systemic disease, impacting multiple organs in the human body. But COVID-19 also impacts other diseases of relevance to public and planetary health. To understand and respond to the COVID-19 pandemic, we need an intersectional conceptual lens and systems thinking. For example, the strain on health care systems due to COVID-19 has adversely impacted global malaria elimination programs. With many epidemiological, clinical, and biological parallels documented, we examined in this study the scenario of malaria and COVID-19 syndemic in India. The disruptive influence of COVID-19 on the National Framework for Malaria Elimination (NFME), impact of unintended chemoprophylaxis, population genetic influences, and the shifting patterns of epidemiology are compared. Importantly, a time series analysis forecasted the burden of malaria increasing in the upcoming years. Although reported malaria cases showed a decline in 2020 compared to the previous years, an increase in cases was documented in 2021, with nine states reporting an increase up to July 2021. Pandemics often cause crosscutting disruptions in health care. Reshaping the priorities of the malaria elimination program and a diligent implementation of the priorities in the NFME would, therefore, be well-advised: (1) vector control, (2) antimalarial therapy recommendations, (3) monitoring drug resistance, (4) prevention of the spread of asymptomatic disease-causing low-density transmission, and (5) large-scale testing measures. In conclusion, the findings from the present study inform future comparative studies in other world regions to better understand the broader, systemic, temporal, and spatial impacts of the COVID-19 pandemic on existing and future diseases across public health systems and services.

Impact of COVID-19 and malaria Coinfection on Clinical Outcomes: A Retrospective Cohort Study

Objectives

Despite the possibility of concurrent infection with COVID-19 and malaria, little is known about the clinical course of coinfected patients. We analysed the clinical outcomes of patients with concurrent COVID-19 and malaria infection.

Methods

We conducted a retrospective cohort study that assessed prospectively collected data of all patients who were admitted between May and December 2020 to the Universal COVID-19 treatment center (UCTC), Khartoum, Sudan. UCTC compiled demographic, clinical, laboratory (including testing for malaria), and outcome data in all patients with confirmed COVID-19 hospitalized at that clinic. The primary outcome was all-cause mortality during the hospital stay. We built proportional hazard Cox models with malaria status as the main exposure and stepwise adjustment for age, sex, cardiovascular comorbidities, diabetes, and hypertension.

Results

We included 591 patients with confirmed COVID-19 diagnosis who were also tested for malaria. Mean (SD) age was 58 (16.2) years, 446/591 (75.5%) were males. Malaria was diagnosed in 270/591 (45.7%) patients. Most malaria patients were infected by Plasmodium falciparum (140/270; 51.9%), while 121/270 (44.8%) were coinfected with Plasmodium falciparum and Plasmodium vivax. Median follow-up was 29 days. Crude mortality rates were 10.71 and 5.87 per 1000 person-days for patients with and without concurrent malaria, respectively. In the fully adjusted Cox model, patients with concurrent malaria and COVID-19 had a greater mortality risk (hazard ratio 1.43, 95% confidence interval 1.21-1.69).

Discussion

Coinfection with COVID-19 and malaria is associated with increased all-cause in-hospital mortality compared to monoinfection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2).

The Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) Pandemic: Are Africa's Prevalence and Mortality Rates Relatively Low?

Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), the cause of coronavirus disease 19 (COVID-19), has been rapidly spreading since December 2019, and within a few months, it turned out to be a global pandemic. The disease affects primarily the lungs, but its pathogenesis spreads to other organs as well. However, its mortality rates vary, and in the majority of infected people, there are no serious consequences. Many factors including advanced age, preexisting health conditions, and genetic predispositions are believed to exacerbate outcomes of COVID-19. The virus contains several structural proteins including the spike (S) protein with subunits for binding, fusion, and internalization into host cells following interaction with host cell receptors and proteases (ACE2 and TMPRSS2, respectively) to cause the subsequent pathology. Although the pandemic has spread into all countries, most of Africa is thought of as having relatively less prevalence and mortality. Several hypotheses have been forwarded as reasons for this and include warmer weather conditions, vaccination with BCG (i.e., trained immunity), and previous malaria infection. From genetics or metabolic points of view, it has been proposed that most African populations could be protected to some degree because they lack some genetic susceptibility risk factors or have low-level expression of allelic variants, such as ACE2 and TMPRSS2 that are thought to be involved in increased infection risk or disease severity. The frequency of occurrence of α-1 antitrypsin (an inhibitor of a tissue-degrading protease, thereby protecting target host tissues including the lung) deficiency is also reported to be low in most African populations. More recently, infections in Africa appear to be on the rise. In general, there are few studies on the epidemiology and pathogenesis of the disease in African contexts, and the overall costs and human life losses due to the pandemic in Africa will be determined by all factors and conditions interacting in complex ways.

Immunomodulatory Potential of Non-Classical HLA-G in Infections including COVID-19 and Parasitic Diseases

Human Leukocyte Antigen-G (HLA-G), a polymorphic non-classical HLA (HLA-Ib) with immune-regulatory properties in cancers and infectious diseases, presents both membrane-bound and soluble (sHLA-G) isoforms. Polymorphism has implications in host responses to pathogen infections and in pathogenesis. Differential expression patterns of HLA-G/sHLA-G or its polymorphism seem to be related to different pathological conditions, potentially acting as a disease progression biomarker. Pathogen antigens might be involved in the regulation of both membrane-bound and sHLA-G levels and impact immune responses during co-infections. The upregulation of HLA-G in viral and bacterial infections induce tolerance to infection. Recently, sHLA-G was found useful to identify the prognosis of Coronavirus disease 2019 (COVID-19) among patients and it was observed that the high levels of sHLA-G are associated with worse prognosis. The use of pathogens, such as Plasmodium falciparum, as immune modulators for other infections could be extended for the modulation of membrane-bound HLA-G in COVID-19-infected tissues. Overall, such information might open new avenues concerning the effect of some pathogens such as parasites in decreasing the expression level of HLA-G to restrict pathogenesis in some infections or to influence the immune responses after vaccination among others.

COVID-19, Cation Dysmetabolism, Sialic Acid, CD147, ACE2, Viroporins, Hepcidin and Ferroptosis: A Possible Unifying Hypothesis

Background: iron and calcium dysmetabolism, with hyperferritinemia, hypoferremia, hypocalcemia and anemia have been documented in the majority of COVID-19 patients at later/worse stages. Furthermore, complementary to ACE2, both sialic acid (SA) molecules and CD147 proved relevant host receptors for SARS-CoV-2 entry, which explains the viral attack to multiple types of cells, including erythrocytes, endothelium and neural tissue. Several authors advocated that cell ferroptosis may be the core and final cell degenerative mechanism. Methods: a literature research was performed in several scientific search engines, such as PubMed Central, Cochrane Library, Chemical Abstract Service. More than 500 articles were retrieved until mid-December 2021, to highlight the available evidence about the investigated issues. Results: based on COVID-19 literature data, we have highlighted a few pathophysiological mechanisms, associated with virus-based cation dysmetabolism, multi-organ attack, mitochondria degeneration and ferroptosis. Our suggested elucidated pathological sequence is: a) spike protein subunit S1 docking with sialylated membrane glycoproteins/receptors (ACE2, CD147), and S2 subunit fusion with the lipid layer; b) cell membrane morpho-functional changes due to the consequent electro-chemical variations and viroporin action, which induce an altered ion channel function and intracellular cation accumulation; c) additional intracellular iron concentration due to a deregulated hepcidin-ferroportin axis, with higher hepcidin levels. Viral invasion may also affect erythrocytes/erythroid precursors, endothelial cells and macrophages, through SA and CD147 receptors, with relative hemoglobin and iron/calcium dysmetabolism. AB0 blood group, hemochromatosis, or environmental elements may represent possible factors which affect individual susceptibility to COVID-19.     Conclusions: our literature analysis confirms the combined role of SA molecules, ACE2, CD147, viroporins and hepcidin in determining the cation dysmetabolism and final ferroptosis in the cells infected by SARS-CoV-2. The altered ion channels and electrochemical gradients of the cell membrane have a pivotal role in the virus entry and cell dysmetabolism, with subsequent multi-organ immune-inflammatory degeneration and erythrocyte/hemoglobin alterations.

COVID-19, Cation Dysmetabolism, Sialic Acid, CD147, ACE2, Viroporins, Hepcidin and Ferroptosis: A Possible Unifying Hypothesis

Background: iron and calcium dysmetabolism, with hyperferritinemia, hypoferremia, hypocalcemia and anemia have been documented in the majority of COVID-19 patients at later/worse stages. Furthermore, complementary to ACE2, both sialic acid (SA) molecules and CD147 proved relevant host receptors for SARS-CoV-2 entry, which explains the viral attack to multiple types of cells, including erythrocytes, endothelium and neural tissue. Several authors advocated that cell ferroptosis may be the core and final cell degenerative mechanism. Methods: a literature research was performed in several scientific search engines, such as PubMed Central, Cochrane Library, Chemical Abstract Service. More than 500 articles were retrieved until mid-December 2021, to highlight the available evidence about the investigated issues. Results: based on COVID-19 literature data, we have highlighted a few pathophysiological mechanisms, associated with virus-based cation dysmetabolism, multi-organ attack, mitochondria degeneration and ferroptosis. Our suggested elucidated pathological sequence is: a) spike protein subunit S1 docking with sialylated membrane glycoproteins/receptors (ACE2, CD147), and S2 subunit fusion with the lipid layer; b) cell membrane morpho-functional changes due to the consequent electro-chemical variations and viroporin action, which induce an altered ion channel function and intracellular cation accumulation; c) additional intracellular iron concentration due to a deregulated hepcidin-ferroportin axis, with higher hepcidin levels. Viral invasion may also affect erythrocytes/erythroid precursors, endothelial cells and macrophages, through SA and CD147 receptors, with relative hemoglobin and iron/calcium dysmetabolism. AB0 blood group, hemochromatosis, or environmental elements may represent possible factors which affect individual susceptibility to COVID-19.     Conclusions: our literature analysis confirms the combined role of SA molecules, ACE2, CD147, viroporins and hepcidin in determining the cation dysmetabolism and final ferroptosis in the cells infected by SARS-CoV-2. The altered ion channels and electrochemical gradients of the cell membrane have a pivotal role in the virus entry and cell dysmetabolism, with subsequent multi-organ immune-inflammatory degeneration and erythrocyte/hemoglobin alterations.

Low incidence of COVID-19 case severity and mortality in Africa; Could malaria co-infection provide the missing link?

Background

Despite reports of malaria and coronavirus diseases 2019 (COVID-19) co-infection, malaria-endemic regions have so far recorded fewer cases of COVID-19 and deaths from COVID-19, indicating a probable protection from the poor outcome of COVID-19 by malaria. On the contrary, other evidence suggests that malaria might contribute to the death caused by COVID-19. Hence, this paper reviewed existing evidence hypothesizing poor outcome or protection of COVID-19 patients when co-infected with malaria.

Methods

PRISMA guidelines for systematic review were employed in this study. Published articles from December 2019 to May 2021on COVID-19 and malaria co-infection and outcome were systematically searched in relevant and accessible databases following a pre-defined strategy. Studies involving human, in vivo animal studies, and in vitro studies were included.

Results

Twenty three (23) studies were included in the review out of the 3866 records identified in the selected scientific databases. Nine (9) papers reported on co-infection of COVID-19 and malaria. Five (5) papers provided information about synergism of malaria and COVID-19 poor prognosis, 2 papers reported on syndemic of COVID-19 and malaria intervention, and 7 studies indicated that malaria protects individuals from COVID-19.

Conclusions

Low incidence of COVID-19 in malaria-endemic regions supports the hypothesis that COVID-19 poor prognosis is prevented by malaria. Although further studies are required to ascertain this hypothesis, cross-immunity and common immunodominant isotopes provide strong evidence to support this hypothesis. Also, increase in co-inhibitory receptors and atypical memory B cells indicate synergy between COVID-19 and malaria outcome, though, more studies are required to make a definite conclusion.

Low incidence and mortality rate of COVID-19 in malaria endemic regions

There have been reports of malaria and COVID-19 co-infection

Malaria could be the link for the reported low incidence of COVID-19 in Africa

Cross immunity and common immunodominant epitopes between Malaria and COVID-19, and antimalaria drugs could be the reason for observed low fatality and incidence rate of COVID-19 in malaria endemic regions.

Malaria infection and deaths could increase amid the COVID-19 pandemic due to interrupted malaria control interventions.

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.

The Pandemic Experience in Southeast Asia: Interface Between SARS-CoV-2, Malaria, and Dengue

Southeast Asia (SEA) emerged relatively unscathed from the first year of the global SARS-CoV-2 pandemic, but as of July 2021 the region is experiencing a surge in case numbers primarily driven by Alpha (B.1.1.7) and subsequently the more transmissible Delta (B.1.617.2) variants. While initial disease burden was mitigated by swift government responses, favorable cultural and societal factors, the more recent rise in cases suggests an under-appreciation of prior prevalence and over-appreciation of possible cross-protective immunity from exposure to endemic viruses, and highlights the effects of vaccine rollout at varying tempos and of variable efficacy. This burgeoning crisis is further complicated by co-existence of malaria and dengue in the region, with implications of serological cross-reactivity on interpretation of SARS-CoV-2 assays and competing resource demands impacting efforts to contain both endemic and pandemic disease.

COVID-19 risk perception among residents of seven sub-Saharan African countries: socio-demographic correlates and predicted probabilities

Introduction

as the COVID-19 pandemic rages on, sub-Saharan Africa remains at high risk given the poor adherence to pandemic control protocols. Misconceptions about the contagion may have given rise to adverse risk behaviours across population groups. This study evaluates risk perception among 2,244 residents of seven countries in sub-Saharan Africa (Botswana, Kenya, Malawi, Nigeria, Tanzania, Zambia and Zimbabwe) in relation to socio-demographic determinants.

Methods

an online survey was conducted via social media platforms to a random sample of participants. Risk perception was evaluated across six domains: loss of income, food scarcity, having a relative infected, civil disorder, criminal attacks, or losing a friend or relative to COVID-19. A multivariable ordinal logistic regression was conducted to assess socio-demographic factors associated with the perceived risk of being affected by COVID-19.

Results

595 (27%) respondents did not consider themselves to be at risk, while 33% perceived themselves to be at high risk of being affected by the pandemic with respect to the six domains evaluated. Hospital-based workers had the highest proportional odds (3.5; 95%CI: 2.3-5.6) high perceived risk. Teenage respondents had the highest predictive probability (54.6%; 95% CI: 36.6-72.7%) of perceiving themselves not to be at risk of being affected by COVID-19, while Zambia residents had the highest predictive probability (40.7%; 95% CI: 34.3-47.0%) for high-risk perception.

Conclusion

this study reveals the need to increase awareness of risks among socio-demographic groups such as younger people and the unemployed. Targeted risk communication strategies will create better risk consciousness, as well as adherence to safety measures.

Low COVID-19 impact in Africa: The multifactorial Nexus

Africa has defied predictions of being the worst hit by the novel coronavirus disease (COVID-19), caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, which has devastated Europe, the Americas, and some Asian countries. However, with a current second and third wave of the COVID-19 pandemic across other continents, pertinent​ questions have arisen regarding the lower disease severity and seemingly better outcomes in most African countries. Several factors have been proposed as discussed in this review including, underreporting, quick lockdown measures, effective public health intervention, younger population structure, cross-immunity and experience from fighting previous epidemics, such as the Ebola virus outbreak, previous infections or vaccinations, genetic predisposition, and tropical climate. We have discussed the implications of these factors on the magnitude of the outbreak and the better-than-expected outcomes observed in Africa. In addition, other potential factors like vitamin-D deficiency and chronic non-communicable diseases could predispose non-African regions to severe COVID-19 outcome. Therefore, this review further advocates for research to understand the precise mechanisms responsible for the pandemic’s relatively mild impact in Africa and proposed recommendations to prevent an infection surge.

The Conundrum of Low COVID-19 Mortality Burden in sub-Saharan Africa: Myth or Reality?

The demographic age structure of sub-Saharan Africa contributes significantly to the low morbidity and mortality of COVID-19 compared to other regions in the world.

COVID-19: Mechanistic Model of the African Paradox Supports the Central Role of the NF-κB Pathway

The novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has expanded into a global pandemic, with more than 220 million affected persons and almost 4.6 million deaths by 8 September 2021. In particular, Europe and the Americas have been heavily affected by high infection and death rates. In contrast, much lower infection rates and mortality have been reported generally in Africa, particularly in the sub-Saharan region (with the exception of the Southern Africa region). There are different hypotheses for this African paradox, including less testing, the young age of the population, genetic disposition, and behavioral and epidemiological factors. In the present review, we address different immunological factors and their correlation with genetic factors, pre-existing immune status, and differences in cytokine induction patterns. We also focus on epidemiological factors, such as specific medication coverage, helminth distribution, and malaria endemics in the sub-Saharan region. An analysis combining different factors is presented that highlights the central role of the NF-κB signaling pathway in the African paradox. Importantly, insights into the interplay of different factors with the underlying immune pathological mechanisms for COVID-19 can provide a better understanding of the disease and the development of new targets for more efficient treatment strategies.

Peptides of H. sapiens and P. falciparum that are predicted to bind strongly to HLA-A*24:02 and homologous to a SARS-CoV-2 peptide

AIM

This study is looking for a common pathogenicity between SARS-CoV-2 and Plasmodium species, in individuals with certain HLA serotypes.

METHODS

1. Tblastx searches of SARS-CoV-2 are performed by limiting searches to five Plasmodium species that infect humans. 2. Aligned sequences in the respective organisms' proteomes are searched with blastp. 3. Binding predictions of the identified SARS-CoV-2 peptide to HLA supertype representatives are performed. 4. Blastp searches of predicted epitopes that bind strongly to the identified HLA allele are performed by limiting searches to H. sapiens and Plasmodium species, separately. 5. Peptides with minimum 60% identity to the predicted epitopes are found in results. 6. Peptides among those, which bind strongly to the same HLA allele, are predicted. 7. Step-4 is repeated by limiting searches to H. sapiens, followed by the remaining steps until step-7, for peptides sourced by Plasmodium species after step-6.

RESULTS

SARS-CoV-2 peptide with single letter amino acid code CFLGYFCTCYFGLFC has the highest identity to P. vivax. Its YFCTCYFGLF part is predicted to bind strongly to HLA-A*24:02. Peptides in the human proteome both homologous to YFCTCYFGLF and with a strong binding affinity to HLA-A*24:02 are YYCARRFGLF, YYCHCPFGVF, and YYCQQYFFLF. Such peptides in the Plasmodium species' proteomes are FFYTFYFELF, YFVACLFILF, and YFPTITFHLF. The first one belonging to P. falciparum has a homologous peptide (YFYLFSLELF) in the human proteome, which also has a strong binding affinity to the same HLA allele.

CONCLUSION

Immune responses to the identified-peptides with similar sequences and strong binding affinities to HLA-A*24:02 can be related to autoimmune response risk in individuals with HLA-A*24:02 serotypes, upon getting infected with SARS-CoV-2 or P. falciparum.

Impact of COVID-19 on Tuberculosis Case Detection and Treatment Outcomes in Sierra Leone

The COVID-19 pandemic has adversely affected tuberculosis (TB) care delivery in high burden countries. We therefore conducted a retrospective study to assess the impact of COVID-19 on TB case detection and treatment outcomes at the Chest Clinic at Connaught Hospital in Freetown, Sierra Leone. Overall, 2300 presumptive cases were tested during the first three quarters of 2020 (intra-COVID-19) versus 2636 in 2019 (baseline), representing a 12.7% decline. Testing declined by 25% in women, 20% in children and 81% in community-initiated referrals. Notwithstanding, laboratory-confirmed TB cases increased by 37.0% and treatment success rate was higher in 2020 (55.6% vs. 46.7%, p = 0.002). Multivariate logistic regression analysis found that age < 55 years (aOR 1.74, 95% CI (1.80, 2.56); p = 0.005), new diagnosis (aOR 1.69, 95% CI (1.16, 2.47); p = 0.007), pulmonary TB (aOR 3.17, 95% CI (1.67, 6.04); p < 0.001), HIV negative status (aOR 1.60, 95%CI (1.24, 2.06); p < 0.001) and self-administration of anti-TB drugs through monthly dispensing versus directly observed therapy (DOT) (aOR 1.56, 95% CI (1.21, 2.03); p = 0.001) independently predicted treatment success. These findings may have policy implications for DOTS in this setting and suggest that more resources are needed to reverse the negative impact of the COVID-19 pandemic on TB program activities in Sierra Leone.

Understanding COVID-19 in Africa

In this Comment article, Sofonias Tessema and John Nkengasong provide an overview of the current state of the COVID-19 pandemic in Africa and the challenges posed by the triple burden of emerging, endemic and non-communicable diseases.

Predicted structural mimicry of spike receptor-binding motifs from highly pathogenic human coronaviruses

•

Potential coronavirus spike protein mimicry revealed by structural comparison.

•

Human and non-human protein potential interactions with virus identified.

•

Predicted structural mimicry corroborated by protein–protein docking.

•

Epitope-based alignments may help guide vaccine efforts.

Viruses often encode proteins that mimic host proteins in order to facilitate infection. Little work has been done to understand the potential mimicry of the SARS-CoV-2, SARS-CoV, and MERS-CoV spike proteins, particularly the receptor-binding motifs, which could be important in determining tropism and druggability of the virus. Peptide and epitope motifs have been detected on coronavirus spike proteins using sequence homology approaches; however, comparing the three-dimensional shape of the protein has been shown as more informative in predicting mimicry than sequence-based comparisons. Here, we use structural bioinformatics software to characterize potential mimicry of the three coronavirus spike protein receptor-binding motifs. We utilize sequence-independent alignment tools to compare structurally known protein models with the receptor-binding motifs and verify potential mimicked interactions with protein docking simulations. Both human and non-human proteins were returned for all three receptor-binding motifs. For example, all three were similar to several proteins containing EGF-like domains: some of which are endogenous to humans, such as thrombomodulin, and others exogenous, such as Plasmodium falciparum MSP-1. Similarity to human proteins may reveal which pathways the spike protein is co-opting, while analogous non-human proteins may indicate shared host interaction partners and overlapping antibody cross-reactivity. These findings can help guide experimental efforts to further understand potential interactions between human and coronavirus proteins.

T cell epitopes of SARS-CoV-2 spike protein and conserved surface protein of Plasmodium malariae share sequence homology

Since its emergence in late 2019, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been spreading remarkably fast worldwide. Effective countermeasures require the rapid development of data and tools to monitor its spread and better understand immunogenic profile. However, limited information is available about the tools and target of the immune responses to SARS-CoV-2. In this study, we excogitated a new approach for analyzing phylogenetic relationships by using the whole prototype proteome sequences. Phylogenetic analysis on the whole prototype proteome sequences showed that SARS-CoV-2 was a direct descendant of Bat-CoV and was closely related to Pangolin-CoV, Bat-SL-CoV, and SARS-CoV. The pairwise comparison of SARS-CoV-2 with Bat-CoV showed an unusual replacement of the motif consisting of seven amino acids (NNLDSKV) within the spike protein of SARS-CoV-2. The replaced motif in the spike protein of SARS-CoV-2 was found in 12 other species, including a conserved surface protein of a malaria-causing pathogen, Plasmodium malariae. We further identified the T and B cell epitope sequence homology of SARS-CoV-2 spike protein with conserved surface protein of P. malariae using the Immune Epitope Database and Analysis Resource (IEDB). The shared immunodominant epitopes may provide immunity against SARS-CoV-2 infection to those previously infected with P. malariae.

Coronavirus infection: An immunologists' perspective

Coronavirus infections are frequent viral infections in several species. As soon as the severe acute respiratory syndrome (SARS) appeared in the early 2000s, most of the research focused on pulmonary disease. However, disorders in immune response and organ dysfunctions have been documented. Elderly individuals with comorbidities exhibit worse outcomes in all the coronavirus that cause SARS. Disease severity in SARS-CoV-2 infection is related to severe inflammation and tissue injury, and effective immune response against the virus is still under analysis. ACE2 receptor expression and polymorphism, age, gender and immune genetics are factors that also play an essential role in patients' clinical features and immune responses and have been partially discussed. The present report aims to review the physiopathology of SARS-CoV-2 infection and propose new research topics to understand the complex mechanisms of viral infection and viral clearance.

How Genetics Might Explain the Unusual Link Between Malaria and COVID-19

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-associated coronavirus disease 2019 (COVID-19) pandemic has been the subject of a large number of studies in recent times. Here, starting from the evidence that in Italy, the areas with the lowest number of COVID-19 cases were those with the highest incidence of malaria in the early 1900's, we explore possible inverse relationships between malaria and COVID-19. Indeed, some genetic variants, which have been demonstrated to give an advantage against malaria, can also play a role in the incidence and severity of SARS-CoV-2 infections (e.g., the ACE2 receptor). To verify this scientific hypothesis, we here use public data from whole-genome sequencing (WGS) experiments to extrapolate the genetic information of 46 world populations with matched COVID-19 data. In particular, we focus on 47 genes, including ACE2 and genes which have previously been reported to play a role in malaria. Only common variants (>5%) in at least 30% of the selected populations were considered, and, for this subset, we correlate the intra-population allele frequency with the COVID-19 data (cases/million inhabitants), eventually pinpointing meaningful variants in 6 genes. This study allows us to distinguish between positive and negative correlations, i.e., variants whose frequency significantly increases with increasing or decreasing COVID-19 cases. Finally, we discuss the possible molecular mechanisms associated with these variants and advance potential therapeutic options, which may help fight and/or prevent COVID-19.

Less Severe Cases of COVID-19 in Sub-Saharan Africa: Could Co-infection or a Recent History of Plasmodium falciparum Infection Be Protective?

Sub-Saharan Africa has generally experienced few cases and deaths of coronavirus disease 2019 (COVID-19). In addition to other potential explanations for the few cases and deaths of COVID-19 such as the population socio-demographics, early lockdown measures and the possibility of under reporting, we hypothesize in this mini review that individuals with a recent history of malaria infection may be protected against infection or severe form of COVID-19. Given that both the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and Plasmodium falciparum (P. falciparum) merozoites bind to the cluster of differentiation 147 (CD147) immunoglobulin, we hypothesize that the immunological memory against P. falciparum merozoites primes SARS-CoV-2 infected cells for early phagocytosis, hence protecting individuals with a recent P. falciparum infection against COVID-19 infection or severity. This mini review therefore discusses the potential biological link between P. falciparum infection and COVID-19 infection or severity and further highlights the importance of CD147 immunoglobulin as an entry point for both SARS-CoV-2 and P. falciparum into host cells.

HLA, Immune Response, and Susceptibility to COVID-19

The severe acute respiratory syndrome caused by Coronavirus 2 (SARS-CoV-2) that appeared in December 2019 has precipitated the global pandemic Coronavirus Disease 2019 (COVID-19). However, in many parts of Africa fewer than expected cases of COVID-19, with lower rates of mortality, have been reported. Individual human leukocyte antigen (HLA) alleles can affect both the susceptibility and the severity of viral infections. In the case of COVID-19 such an analysis may contribute to identifying individuals at higher risk of the disease and the epidemiological level to understanding the differences between countries in the epidemic patterns. It is also recognized that first antigen exposure influences the consequence of subsequent exposure. We thus propose a theory incorporating HLA antigens, the "original antigenic sin (OAS)" effect, and presentation of viral peptides which could explain with differential susceptibility or resistance to SARS-CoV-2 infections.