Introduction into the Marseille geographical area of a mild SARS-CoV-2 variant originating from sub-Saharan Africa (original) (raw)
Serologic response to SARS-CoV-2 in an African population
Scientific African, 2021
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AAS Open Research
Following the coronavirus outbreaks described as severe acute respiratory syndrome (SARS) in 2003 and the Middle East respiratory syndrome (MERS) in 2012, the world has again been challenged by yet another corona virus, named severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). SARS-CoV-2 infections were first detected in a Chinese Province in December 2019 and then declared a pandemic by the World Health Organization in March 2020. An infection caused by SARS-CoV-2 may result in asymptomatic, uncomplicated or fatal coronavirus disease 2019 (COVID-19). Fatal disease has been linked with the uncontrolled “cytokine storm” manifesting with complications mostly in people with underlying cardiovascular and pulmonary disease conditions. The severity of COVID-19 disease and the associated mortality has been disproportionately lower in terms of number of cases and deaths in Africa and also Asia in comparison to Europe and North America. Also, persons of colour residing in Europe an...
Variation in SARS-CoV-2 outbreaks across sub-Saharan Africa
Nature Medicine, 2021
Extended Data Fig. 10 | Transmission climate-dependency and sensitivity to R 0max and R 0min value selection. Transmission (R 0) declines with increasing specific humidity from R 0max to R 0min. Three exemplar cities with low, intermediate, and high average specific humidity are shown across rows (Windhoek, Antananarivo, and Lome, respectively). a-c, Proportion of the population infected (I/N) over time for the specified R 0min and R 0max values. d, Variation in peak size and timing when 1.0 < R 0min < 1.5.
Spatiotemporal prevalence of COVID-19 and SARS-CoV-2 variants in Africa
The coronavirus disease 2019 (COVID-19) pandemic has caused significant public health and socioeconomic crises across Africa; however, the prevalent patterns of COVID-19 and the circulating characteristics of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants in the continent remain insufficiently documented. Methods: In this study, national data on case numbers, infection incidences, mortality rates, the circulation of SARS-CoV-2 variants, and key health indexes were collected from various official and professional sources between January 2020 and December 2023 were analyzed with SaTScan and geographically weighted regression (GWR). The prevalent profiles and circulating features of SARS-CoV-2 across the African continent, including its five regions and all African countries, were analyzed. Four major waves of the epidemic were observed. The first wave was closely associated with the introduction of the early SARS-CoV-2 strain while the subsequent waves were linked to the emergence of specific variants, including variants of concern (VOCs) Alpha, Beta, variants of interest (VOIs) Eta (second wave), VOC Delta (third wave), and VOC Omicron (fourth wave). SaTScan analysis identified four large spatiotemporal clusters that affected various countries. A significant number of countries (50 out of 56) reported their first cases during February 2020 and March 2020, predominantly involving individuals with confirmed cross-continental travel histories, mainly from Europe. In total, 12 distinct SARS-CoV-2 VOCs and VOIs were identified, with the most prevalent being VOCs Omicron, Delta, Beta, Alpha, and VOI Eta. Unlike the dominance of VOC Delta during the third wave and Omicron during the fourth wave, VOC Alpha was relatively rare in the Southern regions but more common in the other four regions. At the same time, Beta predominated in the Southern region and Eta in the Western region during the second wave. Additionally, relatively higher COVID-19 case incidences and mortalities were reported in the Southern and Northern African regions. Spearman rank correlation and geographically weighted regression (GWR) analyses of COVID-19 incidences against health indexes in 52 African countries indicate that countries with higher national health expenditures and better personnel indexes tended to report higher case incidences. Discussion: This study offers a detailed overview of the COVID-19 pandemic in Africa. Strengthening the capacity of health institutions across African countries is essential for the timely detection of new SARS-CoV-2 variants and,
Dynamic and features of SARS-CoV-2 infection in Gabon
Scientific Reports
In a context where SARS-CoV-2 population-wide testing is implemented, clinical features and antibody response in those infected have never been documented in Africa. Yet, the information provided by analyzing data from population-wide testing is critical to understand the infection dynamics and devise control strategies. We described clinical features and assessed antibody response in people screened for SARS-CoV-2 infection. We analyzed data from a cohort of 3464 people that we molecularly screened for SARS-CoV-2 infection in our routine activity. We recorded people SARS-CoV-2 diagnosis, age, gender, blood types, white blood cells (WBC), symptoms, chronic disease status and time to SARS-CoV-2 RT-PCR conversion from positive to negative. We calculated the age-based distribution of SARS-CoV-2 infection, analyzed the proportion and the spectrum of COVID-19 severity. Furthermore, in a nested sub-study, we screened 83 COVID-19 patients and 319 contact-cases for anti-SARS-CoV-2 antibodie...
Detection of a SARS-CoV-2 variant of concern in South Africa
Nature
Epidemic dynamics in South Africa The second wave of the SARS-CoV-2 epidemic in South Africa began around October 2020, weeks after a trough in daily recorded cases following the first peak 19 (Fig. 1a). The country-wide estimated effective reproduction number (R e) increased to above 1 at the end of October (indicating a growing epidemic), which coincided with a steady rise in daily cases. At the peak of the national epidemic in the middle of July, there were over 13,000
Influencing factors of SARS-Cov2 spread in Africa
2020
After the warnings launched by the World Health Organization (WHO), the spotlights are currently turned towards African countries. What might happen to Africa, where most countries have weak health care systems, including inadequate surveillance and laboratory capacity, scarcity of public health human resources, and limited financial means [2]. Nevertheless, to better manage this multidimensional crisis, the challenge is not only about the availability of health infrastructures, but also how to considerate other factors that may modify the course of the disease by either accelerating or rather limiting the spread of the virus, such as geographical, socio-economical, and even political factors.
The evolution of SARS-CoV-2 testing in Africa: Observations from the first 1 million cases
2021
The coronavirus disease 2019 (COVID-19) is a communicable respiratory disease in humans caused by a new strain of coronavirus named severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), first reported in Wuhan City, China, in December 2019. [1] Most infected people develop mild to moderate symptoms that include fever, dry cough, tiredness, diarrhoea, headache, loss of taste or smell and difficulty breathing or shortness of breath, among others reported in the literature. [2] Early in the outbreak, the World Health Organization (WHO) recognised the central role of identification of cases through laboratory testing in the response by highlighting it as an integral part of the strategic preparedness and response plan for COVI9-19. [3] Reverse transcriptase polymerase chain reaction (RT-PCR)-based tests that detect SARS-CoV-2 RNA have been the gold standard for detection and confirmation of diagnosis, and become positive 1-3 days before onset of symptoms, with the highest viral load on the day of onset of symptoms. [4] The rapid spread of the virus around the world led to the declaration of COVID-19 as a public health emergency of international concern in January 2020, and a global pandemic on 11 March. [5,6] The first COVID-19 case in Africa was reported in Egypt on 14 February, and by 14 May all African countries had reported at least one case of COVID-19. [7] By 5 August, the African continent recorded its 1 millionth case, approximately 6 months after the first reported case (Fig. 1). South Africa (SA) has contributed the highest number of cases on the continent, followed by Egypt and Nigeria, making it the country with the 10th-highest caseload in the world (Fig. 1).
The Lancet Infectious Diseases, 2022
Background By August, 2021, South Africa had been affected by three waves of SARS-CoV-2; the second associated with the beta variant and the third with the delta variant. Data on SARS-CoV-2 burden, transmission, and asymptomatic infections from Africa are scarce. We aimed to evaluate SARS-CoV-2 burden and transmission in one rural and one urban community in South Africa. Methods We conducted a prospective cohort study of households in Agincourt, Mpumalanga province (rural site) and Klerksdorp, North West province (urban site) from July, 2020 to August, 2021. We randomly selected households for the rural site from a health and sociodemographic surveillance system and for the urban site using GPS coordinates. Households with more than two members and where at least 75% of members consented to participate were eligible. Midturbinate nasal swabs were collected twice a week from household members irrespective of symptoms and tested for SARS-CoV-2 using real-time RT-PCR (RT-rtPCR). Serum was collected every 2 months and tested for anti-SARS-CoV-2 antibodies. Main outcomes were the cumulative incidence of SARS-CoV-2 infection, frequency of reinfection, symptomatic fraction (percent of infected individuals with ≥1 symptom), the duration of viral RNA shedding (number of days of SARS-CoV-2 RT-rtPCR positivity), and the household cumulative infection risk (HCIR; number of infected household contacts divided by the number of susceptible household members). Findings 222 households (114 at the rural site and 108 at the urban site), and 1200 household members (643 at the rural site and 557 at the urban site) were included in the analysis. For 115 759 nasal specimens from 1200 household members (follow-up 92•5%), 1976 (1•7%) were SARS-CoV-2-positive on RT-rtPCR. By RT-rtPCR and serology combined, 749 of 1200 individuals (62•4% [95% CI 58•1-66•4]) had at least one SARS-CoV-2 infection episode, and 87 of 749 (11•6% [9•4-14•2]) were reinfected. The mean infection episode duration was 11•6 days (SD 9•0; range 4-137). Of 662 RT-rtPCR-confirmed episodes (>14 days after the start of follow-up) with available data, 97 (14•7% [11•9-17•9]) were symptomatic with at least one symptom (in individuals aged <19 years, 28 [7•5%] of 373 episodes symptomatic; in individuals aged ≥19 years, 69 [23•9%] of 289 episodes symptomatic). Among 222 households, 200 (90•1% [85•3-93•7]) had at least one SARS-CoV-2-positive individual on RT-rtPCR or serology. HCIR overall was 23•9% (195 of 817 susceptible household members infected [95% CI 19•8-28•4]). HCIR was 23•3% (20 of 86) for symptomatic index cases and 23•9% (175 of 731) for asymptomatic index cases (univariate odds ratio [OR] 1•0 [95% CI 0•5-2•0]). On multivariable analysis, accounting for age and sex, low minimum cycle threshold value (≤30 vs >30) of the index case (OR 5•3 [2•3-12•4]) and beta and delta variant infection (vs Wuhan-Hu-1, OR 3•3 [1•4-8•2] and 10•4 [4•1-26•7], respectively) were associated with increased HCIR. People living with HIV who were not virally supressed (≥400 viral load copies per mL) were more likely to develop symptomatic illness when infected with SAR-CoV-2 (OR 3•3 [1•3-8•4]), and shed SARS-CoV-2 for longer (hazard ratio 0•4 [95% CI 0•3-0•6]) compared with HIV-uninfected individuals. Interpretation In this study, 565 (85•3%) SARS-CoV-2 infections were asymptomatic and index case symptom status did not affect HCIR, suggesting a limited role for control measures targeting symptomatic individuals. Increased household transmission of beta and delta variants was likely to have contributed to successive waves of SARS-CoV-2 infection, with more than 60% of individuals infected by the end of follow-up.
Limited spread of a rare spike E484K-harboring SARS-CoV-2 in Marseille, France
Archives of Virology, 2022
We detected SARS-CoV-2 of PANGO lineage R.1 with the spike substitution E484K in three patients. Eleven other sequences in France and 8,831 worldwide were available from GISAID, 92% originating from Japan. The three genome sequences from our institute were phylogenetically closest to another from Guinea-Conakry, where one of the patients had travelled. These viruses did not exhibit any unusual features in cell culture. Spike structural predictions indicated a 1.3-time higher transmissibility index than for the globally spread B.1.1.7 variant but also an affinity loss for gangliosides that might have slowed dissemination. The spread of new SARS-CoV-2 mutants/variants is still not well understood and therefore difficult to predict, and this hinders implementation of effective preventive measures, including adapted vaccines.
Background: The current COVID-19 pandemic affects the entire world population and has serious health, economic and social consequences. Assessing the prevalence of COVID-19 through population-based serological surveys is essential to monitor the progression of the epidemic, especially in African countries where the extent of SARS-CoV-2 spread remains unclear. Methods: A two-stage cluster population-based SARS-CoV-2 seroprevalence survey was conducted in Bobo-Dioulasso and in Ouagadougou, Burkina Faso, Fianarantsoa, Madagascar and Kumasi, Ghana between February and June 2021. IgG seropositivity was determined in 2,163 households with a specificity improved SARS-CoV-2 Enzyme-linked Immunosorbent Assay. Population seroprevalence was evaluated using a Bayesian logistic regression model that accounted for test performance and age, sex and neighbourhood of the participants. Results: Seroprevalence adjusted for test performance and population characteristics were 55.7% [95% Credible Interval (CrI) 49•0; 62•8] in Bobo-Dioulasso, 37•4% [95% CrI 31•3; 43•5] in Ouagadougou, 41•5% [95% CrI 36•5; 47•2] in Fianarantsoa, and 41•2% [95% CrI 34•5; 49•0] in Kumasi. Within the study population, less than 6% of participants performed a test for acute SARS-CoV-2 infection since the onset of the pandemic. Conclusions: High exposure to SARS-CoV-2 was found in the surveyed regions albeit below the herd immunity threshold and with a low rate of previous testing for acute infections. Despite the high seroprevalence in our study population, the duration of protection from naturally acquired immunity remains unclear and new virus variants
Journal of Medical Virology, 2021
The rapid spread of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variant of concern with higher infectivity has already resulted in the enormous increase in infection cases worldwide. We report an unrecognized introduction of the variant B.1.1.7 in Gabon in December 2020, which was the initial phase of the variant introduction to Africa. The B.1.1.7 variant was also detected in a hospitalized patient in January 2021, indicating a rapid spread of the variant in Gabon since its first detection. Phylogenetic analysis revealed that the detected B.1.1.7 variants originated from the distinct regions, strongly suggesting that the B.1.1.7 variant had been repeatedly introduced to Gabon since December 2020. These results provide insights on the This is an open access article under the terms of the Creative Commons Attribution-NonCommercial-NoDerivs License, which permits use and distribution in any medium, provided the original work is properly cited, the use is non-commercial and no modifications or adaptations are made.
Journal of Public Health in Africa
In Cameroon, COVID-19 infection spread rapidly and nationwide, with up to 721 deaths reported. To the best of our knowledge, no study reported the on-theground data using a large patients’ dataset to give a comprehensive knowledge on COVID-19 pandemic in Cameroon. The objective of this study was to shade lights on the epidemiological, virological and clinical features of COVID-19 in the Cameroonian context. An observational study was conducted among symptomatic and asymptomatic individuals tested for SARS-CoV-2 by PCR on nasopharyngeal samples from April 22nd, 2020 to January 5th, 2021. Out of 14119 individuals (59.8% male), overall SARS-CoV-2 positivity was 12.7% (from 7.9% in <10 years to 17.3% in >60 years, p<0.001). The positivity rate of symptomatic individuals was 36.1% versus 9.8% among asymptomatic ones, p<0.001. Age group ≤10 [aOR (95%CI): 0.515 (0.338-0.784), p=0.002] and being symptomatic [aOR (95% CI): 5.108 (4.521-5.771), p<0.001] were predictors of SARS-...
Seroprevalence of SARS-CoV-2 antibodies in Republic of Congo, February 2022
Epidemiology and Infection, 2022
In resource-limited countries, the lack of widespread screening masks the true situation of COVID-19. We conducted this study to assess SARS-CoV-2 spread by detection of specific antibodies and to determine associated factors. A population-based cross-sectional study was conducted. Subjects were tested for the presence of two antibodies (IgM and IgG) specific to SARS-CoV-2. Data collection was done using a smartphone with the KoboCollect application. Prevalence of antibodies was estimated with 95% confidence intervals. Logistic regression was used to determine factors associated with positive serological test. A total of 9,094 persons were tested in 4,340 households. The mean age was 30.18 ± 18.65 years, 46.5% male. The overall seroprevalence (prevalence, 95% CI) of SARS-CoV-2 antibodies was (48.2% [47.2%-49.2%]). Being vaccinated, having been in contact with a COVID-19 patient, being older than 50 years, living in a union, having secondary education and having tertiary education were factors independently associated with the likelihood of having anti-sars-CoV-2. We estimate in February 2022 that 48% persons had antibodies against the COVID-19 virus, more among those vaccinated. Vaccination intensification in low prevalence departments will reduce the risk of new outbreaks. 10 July 2022, there are 552,504,624 cases and 6,347,816 deaths, representing a case fatality rate of 1.1%. The hecatomb predicted in Africa due to health system failure never occurred, as the Africa Centres for Disease Control and Prevention (Africa CDC) reported 11,994,754 cases of COVID-19 in the continent, including 255,127 deaths for a case-fatality rate of 2.1% until 1 August 2021 [2]. Polymerase chain reaction (PCR) for detection of viral nucleic acid in upper and lower respiratory tract specimens is the gold standard for clinical diagnosis of COVID-19, but its supply is limited in African countries [3, 4]. In this context, the number of positive cases based on PCR diagnosis does not predict the level of SARS-CoV-2 circulation in the population. In the case of a new coronavirus, the initial seroprevalence in the population is assumed to be negligible, due to the new origin of the virus. Therefore, monitoring of antibody seropositivity in a population may allow conclusions to be drawn about the extent of infection and the cumulative incidence of infection in the population. Studies conducted regarding the circulation of SARS-CoV-2 in some African countries revealed prevalence ranging from 19.1% to 65.0% in the general population [5-16] and 4.0% to 63.0% in specific populations [17-24]. Results of a recent study using a meta-analysis of proportions show that the overall seroprevalence of anti-SARS-CoV-2 antibodies in Africa was 16.0% (95% confidence interval [CI]: 13.1-18.9%) in the period 2020-2021 [25]. Based on these statistics, it is safe to say that the virus has spread widely in African countries, in contrast to the estimations published by governments [2].
2021
At the end of 2020, the Network for Genomic Surveillance in South Africa (NGS-SA) detected a SARS-CoV-2 variant of concern (VOC) in South Africa (501Y.V2 or PANGO lineage B.1.351)1. 501Y.V2 is associated with increased transmissibility and resistance to neutralizing antibodies elicited by natural infection and vaccination2,3. 501Y.V2 has since spread to over 50 countries around the world and has contributed to a significant resurgence of the epidemic in southern Africa. In order to rapidly characterize the spread of this and other emerging VOCs and variants of interest (VOIs), NGS-SA partnered with the Africa Centres for Disease Control and Prevention and the African Society of Laboratory Medicine through the Africa Pathogen Genomics Initiative to strengthen SARS-CoV-2 genomic surveillance across the region.
Spreading of SARS-CoV-2 in West Africa and assessment of risk factors
Epidemiology and Infection, 2020
Although the African continent is, for the moment, less impacted than the rest of the world, it still faces the risk of a spread of COVID-19. In this study, we have conducted a systematic review of the information available in the literature in order to provide an overview of the epidemiological and clinical features of COVID-19 pandemic in West Africa and of the impact of risk factors such as comorbidities, climatic conditions and demography on the pandemic. Burkina Faso is used as a case study to better describe the situation in West Africa. The epidemiological situation of COVID-19 in West Africa is marked by a continuous increase in the numbers of confirmed cases. This geographic area had on 29 July 2020, 131 049 confirmed cases by polymerase chain reaction, 88 305 recoveries and 2102 deaths. Several factors may influence the SARS-CoV-2 circulation in Africa: (i) comorbidities: diabetes mellitus and high blood pressure could lead to an increase in the number of severe cases of S...