Dynamics of SARS-CoV-2 lineages in French Guiana in 2020-2021: 4 epidemic waves with cross-influences from Europe and South America.

Since the first cases of SARS-CoV-2 infection in Wuhan in December 2019, this RNA virus gave rise to different viral lineages with different virological, epidemiological and immunological properties. Here we describe the dynamics of circulation of SARS-CoV-2 lineages in an Amazonian South American French overseas territory, French Guiana (FG). The data analyzed are based on the general epidemic course, and genomic surveillance data come from whole genome sequencing (WGS) as well as typing PCRs. From March 2020 to October 2021, four COVID-19 epidemic waves were observed in FG with an evolution of viral lineages influenced by virus introductions from continental France and above all by land-based introductions from neighbouring countries. The third epidemic wave from March to June 2021 was driven by a predominant Gamma introduced from Brazil and a less frequent Alpha introduced from France. This coexistence was completely substituted by Delta that initiated the fourth epidemic wave.

COVID-19 epidemic in remote areas of the French Amazon, March 2020 to May 2021: Another reality.

BACKGROUND: French Guiana (FG) is an ultra-peripheral European region in the Amazon, and the COVID-19 epidemic has had very different kinetics from both its giant neighbors, Brazil or mainland France. METHODS: This study summarized the epidemics of COVID-19 in FG. RESULTS: The tropical climate, multiethnicity, and remoteness of the population forced healthcare providers to accordingly adapt the management of the epidemic. Incidence and mortality have been lower than that in Europe and Latin America due to a combination of prevalence of the youth in the population and highly developed healthcare system. CONCLUSIONS: Currently, vaccine hesitancy hinders the rapid expansion of vaccine coverage.

COVID-19 epidemic in remote areas of the French Amazon, March 2020 to May 2021: Another reality

ABSTRACT Background: French Guiana (FG) is an ultra-peripheral European region in the Amazon, and the COVID-19 epidemic has had very different kinetics from both its giant neighbors, Brazil or mainland France. Methods: This study summarized the epidemics of COVID-19 in FG. Results: The tropical climate, multiethnicity, and remoteness of the population forced healthcare providers to accordingly adapt the management of the epidemic. Incidence and mortality have been lower than that in Europe and Latin America due to a combination of prevalence of the youth in the population and highly developed healthcare system. Conclusions: Currently, vaccine hesitancy hinders the rapid expansion of vaccine coverage.

The Epidemiology of COVID 19 in the Amazon and the Guianas: Similarities, Differences, and International Comparisons.

Background: The COVID 19 epidemic submerged many health systems in the Amazon. The objective of the present study was to focus on the epidemic curves of the COVID 19 epidemic in different centers, and to look at testing and mortality data. Methods: Publicly available datasets were used. The log10 of the daily cumulated number of cases starting from the day the territory reached 100 cumulated cases was plotted to compare the magnitude, shape and slope of the different curves. The maximum daily testing efforts were plotted for each territory in relation to the maximum daily number of diagnoses. The case fatality rate was computed by dividing the number of COVID 19 deaths by the number of confirmed cases. Results: In the Amazonian regions in general the speed of growth was generally lower than in Europe or the USA, or Southern Brazil. Whereas, countries like South Korea or New Zealand "broke" the curve relatively rapidly the log linear trajectory seemed much longer with signs of a decline in growth rate as of early July 2020. After a very slow start, French Guiana had the lowest slope when compared to other Amazonian territories with significant epidemics. The Amazonian states of Roraima, Amazonas, Parà, and Amapà had among the highest number of cases and deaths per million inhabitants in the world. French Guiana had significantly fewer deaths relative to its number of confirmed cases than other Amazonian territories. French Guiana had a late epidemic surge with intense testing scale-up often exceeding 4,000 persons tested daily per million inhabitants. Brazil was an outlier with low daily testing levels in relation to the number of daily diagnoses. Conclusions: There were marked heterogeneities mortality rates suggesting that socioeconomic, political factors, and perhaps ethnic vulnerability led to striking outcome differences in this Amazonian context.

Evaluating the impact of curfews and other measures on SARS-CoV-2 transmission in French Guiana.

While general lockdowns have proven effective to control SARS-CoV-2 epidemics, they come with enormous costs for society. It is therefore essential to identify control strategies with lower social and economic impact. Here, we report and evaluate the control strategy implemented during a large SARS-CoV-2 epidemic in June-July 2020 in French Guiana that relied on curfews, targeted lockdowns, and other measures. We find that the combination of these interventions coincided with a reduction in the basic reproduction number of SARS-CoV-2 from 1.7 to 1.1, which was sufficient to avoid hospital saturation. We estimate that thanks to the young demographics, the risk of hospitalisation following infection was 0.3 times that of metropolitan France and that about 20% of the population was infected by July. Our model projections are consistent with a recent seroprevalence study. The study showcases how mathematical modelling can be used to support healthcare planning in a context of high uncertainty.

Dengue serosurvey after a 2-month long outbreak in Nîmes, France, 2015: was there more than met the eye?

BackgroundClusters of dengue cases have recently become more frequent in areas of southern France colonised by the vector mosquito Aedes albopictus. In July 2015, a 2-month outbreak of dengue virus serotype 1 (DENV-1) was reported in Nîmes. Aim: We conducted a serosurvey in the affected area at the end of the vector activity period to determine the true extent of dengue transmission. Methods: We collected capillary blood from consenting household members, and information on their medical and travel histories, and exposure to mosquito bites. Recent infections were identified using IgM and IgG anti-DENV ELISA, followed, when positive, by plaque reduction neutralisation tests on serum against DENV 1-4 and West Nile virus. The prevalence estimator was calibrated on reference demographic data. We quantified the spatial clustering of dengue cases within the affected community and inferred the transmission tree. Results: The study participation rate was 39% (564/1,431). Three of 564 participants tested positive for DENV-1 infection (after marginal calibration, 0.41%; 95% confidence interval: 0.00-0.84). The spatial analysis showed that cases were clustered at the household level. Most participants perceived the presence of mosquitos as abundant (83%) and reported frequent mosquito bites (57%). We incidentally identified six past West Nile virus infections (0.9%; 95% CI: 0.2-1.6). Conclusion: This serosurvey confirms the potential for arboviral diseases to cause outbreaks - albeit limited for now - in France and Europe.

Do alcohol-based hand rubs reduce the incidence of acute diarrhea during military deployments? A prospective randomized trial.

BACKGROUND: Acute diarrhea remains a public health concern in armed forces deployed in tropical areas where access to water and soap is limited. This study aims to assess the effectiveness of alcohol-based hand rubs (ABHR) on incidence of diarrhea in poor hygiene conditions. METHOD: A prospective randomized trial was conducted between November 2014 and January 2015 among French military troops deployed in Africa to compare a group of soldiers receiving usual hand hygiene recommendations (control group), to a group of soldiers who received ABHR in addition to usual hand hygiene recommendations (intervention group). Data on diarrhea and hygiene behaviors were collected using self-questionnaires. The incidence rate of diarrhea episodes in groups was compared. RESULTS: Participation rate was 59% (236/400). The proportion of individuals who used ABHR was 97% in the intervention group and 62% in the control group. The overall incidence rate of diarrheal episodes was observed to be in the region of 60 per 100 persons-month without any significant difference between groups after adjustment on confounding factors (p = 0.93). Handwashing with soap was used on average 4 times a day in the control group and twice a day in the intervention group (p = 0.93). It was the only significant protective factor for diarrhea (p < 10-3). CONCLUSION: Our results support that supplying soap and good quality water should be a priority on the field.

Autochthonous dengue outbreak in Nîmes, South of France, July to September 2015.

In August and September 2015, seven locally acquired cases of dengue virus type 1 (DENV-1) were detected in Nîmes, south of France, where Aedes albopictus has been established since 2011. Epidemiological and entomological investigations allowed to steer vector control measures to contain transmission. An imported case from French Polynesia with onset fever on 4 July was identified as primary case. This outbreak occurred from 8 August to 11 September in a 300 m radius area. Six sprayings to control mosquitos were performed in the affected area. We describe the first considerable dengue outbreak in mainland France where only sporadic cases of autochthonous dengue were recorded previously (2010, 2013 and 2014). The 69 day-period between the primary case and the last autochthonous case suggests multiple episodes of mosquito infections. The absence of notification of autochthonous cases during the month following the primary case's symptoms onset could be explained by the occurrence of inapparent illness. Recurrence of cases every year since 2013, the size of the 2015 outbreak and continuing expansion of areas with presence of Ae. albopictus highlight the threat of arboviral diseases in parts of Europe. Thus, European guidelines should be assessed and adjusted to the current context.

Dengue: etiology of acute febrile illness in Abidjan, Côte d'Ivoire, in 2011-2012.

BACKGROUND: The burden of dengue in Africa is not well understood. A prospective study was conducted in Abidjan, Côte d'Ivoire from December 2011 to December 2012 to estimate the proportion of dengue and malaria cases among febrile patients during a period when dengue was not known to be circulating in the region, and to describe the clinical and virological characteristics of laboratory-diagnosed dengue cases. METHODS: Blood samples were taken from febrile patients (body temperature ≥ 38°C) at two study sites. Patients with fever lasting more than 7 days, with fever of known origin and with jaundice were excluded. Thick blood film tests, ELISA for anti-dengue IgM and reverse transcription-PCR (RT-PCR) were performed. RESULTS: A total of 812 patients were enrolled (51.7% male [48.3% female]; 46.4% aged <10 years) of whom 796 (98.0%) provided IgM ELISA and RT-PCR data, and 807 (99.4%) had thick blood film results. Three (0.4%) patients had laboratory-diagnosed dengue (one with DENV-3 serotype), none of whom were diagnosed clinically, and 234 (28.8%) had confirmed malaria. CONCLUSIONS: This study suggests that dengue virus circulates in Abidjan outside an epidemic and that there should be an increase in awareness of dengue as a possible diagnosis in cases of undifferentiated fever. These results stress the importance of implementing laboratory capacity to assess dengue burden in Africa.