Shifting Patterns of Influenza Circulation during the COVID-19 Pandemic, Senegal

Historically low levels of seasonal influenza circulation were reported during the first years of the COVID-19 pandemic and were mainly attributed to implementation of nonpharmaceutical interventions. In tropical regions, influenza’s seasonality differs largely, and data on this topic are scarce. We analyzed data from Senegal’s sentinel syndromic surveillance network before and after the start of the COVID-19 pandemic to assess changes in influenza circulation. We found that influenza shows year-round circulation in Senegal and has 2 distinct epidemic peaks: during January–March and during the rainy season in August–October. During 2021–2022, the expected January–March influenza peak completely disappeared, corresponding to periods of active SARS-CoV-2 circulation. We noted an unexpected influenza epidemic peak during May–July 2022. The observed reciprocal circulation of SARS-CoV-2 and influenza suggests that factors such as viral interference might be at play and should be further investigated in tropical settings

Analysis of contact tracing data showed contribution of asymptomatic and non-severe infections to the maintenance of SARS-CoV-2 transmission in Senegal

Abstract During the COVID-19 pandemic in Senegal, contact tracing was done to identify transmission clusters, their analysis allowed to understand their dynamics and evolution. In this study, we used information from the surveillance data and phone interviews to construct, represent and analyze COVID-19 transmission clusters from March 2, 2020, to May 31, 2021. In total, 114,040 samples were tested and 2153 transmission clusters identified. A maximum of 7 generations of secondary infections were noted. Clusters had an average of 29.58 members and 7.63 infected among them; their average duration was 27.95 days. Most of the clusters (77.3%) are concentrated in Dakar, capital city of Senegal. The 29 cases identified as super-spreaders, i.e., the indexes that had the most positive contacts, showed few symptoms or were asymptomatic. Deepest transmission clusters are those with the highest percentage of asymptomatic members. The correlation between proportion of asymptomatic and degree of transmission clusters showed that asymptomatic strongly contributed to the continuity of transmission within clusters. During this pandemic, all the efforts towards epidemiological investigations, active case-contact detection, allowed to identify in a short delay growing clusters and help response teams to mitigate the spread of the disease

Cross-Reactivity of SARS-CoV-2 Laboratory Diagnostics to Endemic Diseases in Africa: A Diagnostic Accuracy Study

Background: Serology is a great tool to assess the level of immunity against SARS-CoV-2 in settings with limited access to molecular diagnostics. However, African populations displays a particular immunological profile with massive circulation of infectious agents from different aetiologies that can affect assays performance.Methods: We evaluated the OMEGA Diagnostics COVID-19 ELISA-IgG and the ID Screen® SARS-CoV-2-N IgG Indirect in Senegal using a panel of 636 blood samples covering several African-endemic diseases and healthy donors to determine test sensitivity and specificity. The sensitivity panel of sera includes 461 serum samples collected from 91 patients hospitalized for COVID-19 disease. COVID-19 cases were confirmed by qRT-PCR and samples were collected on an interval of three days until viral clearance. In addition, 272 sera obtained from COVID-19 negative individuals were selected from a well-documented biobank of sera collected before the COVID-19 outbreak.Finding: High-cross reactivity have been found in individuals with a history of exposure to Chikungunya, HIV, malaria (Plasmodium falciparum), rheumatoid factor as well as healthy donors with respective specificities of 55%, 41.8%, 70%, 70% and 75%. ELISA experiments with commercial assays targeting either SARS-CoV-2 Nucleocapsid protein and Spike 2 protein or nucleocapsid protein only suggest that cross-reactivity might be directed against Spike 2 protein and not Nucleocapsid protein. Further samples characterisation reveals that anti-malaria IgG is the leading cause of such poor specificities, but exposure to other diseases contributed as well.Interpretation: We anticipate that COVID-19 seroprevalence can be biased if assays are not contextualized. Since malaria is endemic in African settings, we propose that a particular attention must be given in serological surveillance of COVID-19 or anti-SARS-CoV-2 antibodies quantification as vaccines are being rolled out

Seroprevalence of anti-SARS-CoV-2 antibodies in Senegal: a national population-based cross-sectional survey, between October and November 2020

Posté le 17 septembre 2021.Background: Senegal reported the first COVID-19 case on March 2, 2020. A nationwide cross-sectional epidemiological survey was conducted to capture the true extent of COVID-19 exposure.Methods: Multi-stage random cluster sampling of households was carried out between October 24 and November 26, 2020, at the end of the first wave of COVID-19 transmission. Anti-SARS-CoV-2 antibodies (IgG and/or IgM) were screened using three distinct ELISA assays. Adjusted prevalence for the survey design were calculated for each test separately, and thereafter combined. Crude, adjusted prevalence based on tests performances and weighted prevalence by sex-age strata were estimated to assess the seroprevalence.Findings: Of the 1,463 participants included in this study, 58·8% were women and the mean age of participants was 29·2 years (range 0·25–82·0). The national seroprevalence was estimated at 28 . 4% (95% CI: 26·1-30·8). There was substantial regional variability. Four regions recorded the highest seroprevalence: Ziguinchor (56·7%), Sedhiou (48·0%), Dakar (44·0%) and Kaolack (32·7%) whereas, Louga (11·1%) and Matam (11·2%), located in the Center-North, were less impacted in our analysis. All age groups were impacted and the prevalence of SARS-CoV-2 was comparable in symptomatic and asymptomatic groups. We estimated 4,744,392 SARS-CoV-2 (95% CI: 4,360,164 – 5,145,327) potential infected in Senegal compared to 16,089 COVID-19 RT-PCR laboratory-confirmed cases reported at the time of the survey.Interpretation: These results provide an estimate of SARS-CoV-2 virus dissemination in the Senegalese population. Preventive and control measures need to be reinforced in the country and especially in the south border regions

Seroprevalence of anti-SARS-CoV-2 antibodies in Senegal: a national population-based cross-sectional survey, between October and November 2020

Posté le 17 septembre 2021.International audienceObjectivesA nationwide cross-sectional epidemiological survey was conducted to capture the true extent of coronavirus disease 2019 (COVID-19) exposure in Senegal.MethodsMulti-stage random cluster sampling of households was performed between October and November 2020, at the end of the first wave of COVID-19 transmission. Anti-severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) antibodies were screened using three distinct ELISA assays. Adjusted prevalence rates for the survey design were calculated for each test separately, and thereafter combined. Crude and adjusted prevalence rates based on test performance were estimated to assess the seroprevalence. As some samples were collected in high malaria endemic areas, the relationship between SARS-CoV-2 seroreactivity and antimalarial humoral immunity was also investigated.ResultsOf the 1463 participants included in this study, 58.8% were female and 41.2% were male; their mean age was 29.2 years (range 0.20–84.8.0 years). The national seroprevalence was estimated at 28.4% (95% confidence interval 26.1–30.8%). There was substantial regional variability. All age groups were impacted, and the prevalence of SARS-CoV-2 was comparable in the symptomatic and asymptomatic groups. An estimated 4 744 392 (95% confidence interval 4 360 164–5 145 327) were potentially infected with SARS-CoV-2 in Senegal, while 16 089 COVID-19 RT-PCR laboratory-confirmed cases were reported by the national surveillance. No correlation was found between SARS-CoV-2 and Plasmodium seroreactivity.ConclusionsThese results provide a better estimate of SARS-CoV-2 dissemination in the Senegalese population. Preventive and control measures need to be reinforced in the country and especially in the south border regions

Spatial distribution of COVID-19 positive cases at district level.

Spatial distribution of COVID-19 positive cases at district level.</p

Epidemiological parameters comparison according to different periods.

Epidemiological parameters comparison according to different periods.</p

Heatmap of symptom frequency and histogram of asymptomatic patients by age group.

A. Heatmap of symptom frequency by age group. Symptoms are listed in rows and age groups in columns. Values in cells indicate the frequency of patients from the corresponding age group manifesting the corresponding symptom. The more the red color is accentuated, the more the symptom is frequent. The blue box targets the "cough" symptom, one of the most involved symptoms in transmission due to the dispersed micro-droplets. This symptom is less frequent in young patients (most active sub-population) compared to adult (less active sub-population). B. Histogram of asymptomatic patients by age group. Black vertical bars represent the standard errors.</p

Confirmed COVID-19 cases according to their travel history.

A. Histogram of COVID-19 cases with and without travel history. Dates of onset are represented in the x-axis and number of tested cases on the y-axis. Grey part of the bars represents cases without travel history, black bars cases circulated inside Senegal, green bars cases from the rest of the world, red bars cases from Europe and blue bars cases from other African countries. B. Country’s origin of imported COVID-19 cases.</p

Univariate and multivariate risk factors analysis according to "symptomatic/asymptomatic" status for Period 2 (from June 26 to October 31^st, 2020).

(DOCX)</p