SARS-CoV-2 infection prevalence and associated factors among primary healthcare workers in France after the third COVID-19 wave.

Data on the SARS-CoV-2 infection among primary health care workers (PHCWs) are scarce but essential to reflect on policy regarding prevention and control measures. We assessed the prevalence of PHCWs who have been infected by SARS-CoV-2 in comparison with modeling from the general population in metropolitan France, and associated factors. A cross-sectional study was conducted among general practitioners (GPs), pediatricians, dental and pharmacy workers in primary care between May and August 2021. Participants volunteered to provide a dried-blood spot for SARS-CoV-2 antibody assessment and completed a questionnaire. The primary outcome was defined as the detection of infection-induced antibodies (anti-nucleocapsid IgG, and for non-vaccinees: anti-Spike IgG and neutralizing antibodies) or previous self-reported infection (positive RT-qPCR or antigenic test, or positive ELISA test before vaccination). Estimates were adjusted using weights for representativeness and compared with prediction from the general population. Poisson regressions were used to quantify associated factors. The analysis included 1612 PHCWs. Weighted prevalences were: 31.7% (95% CI 27.5-36.0) for GPs, 28.7% (95% CI 24.4-33.0) for pediatricians, 25.2% (95% CI 20.6-31.0) for dentists, and 25.5% (95% CI 18.2-34.0) for pharmacists. Estimates were compatible with model predictions for the general population. PHCWs more likely to be infected were: GPs compared to pharmacist assistants (adjusted prevalence ratio [aPR] = 2.26; CI 95% 1.01-5.07), those living in Île-de-France (aPR = 1.53; CI 95% 1.14-2.05), South-East (aPR = 1.57; CI 95% 1.19-2.08), North-East (aPR = 1.81; CI 95% 1.38-2.37), and those having an unprotected contact with a COVID-19 case within the household (aPR = 1.48; CI 95% 1.22-1.80). Occupational factors were not associated with infection. In conclusion, the risk of SARS-CoV-2 exposure for PHCWs was more likely to have occurred in the community rather than at their workplace.

Evidence for some antimicrobial properties of English churchyard lichens.

The emergence of multidrug-resistant bacteria has driven the need for novel antibiotics. Our investigations have focussed on lichens as they naturally produce a wide range of unique and very effective defence chemicals. The aim of this study was to evaluate some of the antimicrobial properties of ten common British churchyard lichens. The lichen material was sampled from ten species, namely Caloplaca flavescens, Diploicia canescens, Cladonia fimbriata, Psilolechia lucida, Lecanora campestris subsp. Campestris, Lecanora sulphurea, Pertusaria amara f.amara, Lepraria incana, Porpidia tuberculosa and Xanthoria calcicola. Crude acetone extracts of these lichens were tested against six bacteria (Escherichia coli, Pseudomonas aeruginosa, Staphylococcus aureus, Salmonela typhimurium, Listeria monocytogenes and Lactobacillus acidophilus ) and two fungi (Trichophyton interdigitale and Aspergillus flavus) by the disc-diffusion susceptibility test method. Extracts of Diploicia canescens, Psilolechia lucida, Lecanora sulphurea, Pertusaria amara and Lepraria incana showed clear inhibition of the Gram-positive bacteria tested (S. aureus, L. monocytogenes, L. plantarum). Diploicia canescens, Pertusaria amara and Lepraria incana extracts also inhibited the dermatophyte fungi tested. The Lepraria incana sample tested here was the only extract that showed activity against any of the Gram-negative bacteria tested; it showed inhibition of Pseudomnas aeruginosa. Overall, our results showed that crude extracts of Diploicia canescens and Pertusaria amara had the most potent antimicrobial activity of all the extracts tested. Our results are in general agreement with published findings elsewhere. The activity of the Porpidia tuberculosa margin sample being different from that of the main colony material was an interesting and new finding reported here for the first time.

Eight Months of Serological Follow-Up of Anti-SARS-CoV-2 Antibodies in France: A Study among an Adult Population.

BACKGROUND: Uncertainties remain regarding the nature and durability of the humoral immune response to severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). AIM: This study investigated immunoglobulin G response and neutralizing activity to evaluate the mean antibody concentrations and response duration induced by each vaccination regimen in a French adult population. METHODS: A study including blood sampling and questionnaires was carried out from November 2020 to July 2021 with three separate follow-up phases. Spike proteins and neutralizing antibodies were quantified using ELISA and a virus-neutralization test. RESULTS: Overall, 295 participants were included. Seroprevalences were 11.5% (n = 34), 10.5% (n = 31), and 68.1% (n = 201) in phases 1, 2, and 3, respectively. Importantly, 5.8% (n = 17) of participants lost their natural antibodies. Antibody response of participants with only a prior infection was 88.2 BAU/mL, significantly lower than those vaccinated, which was 1909.3 BAU/mL (p = 0.04). Moreover, the antibody response of vaccinated participants with a prior infection was higher (3593.8 BAU/mL) than those vaccinated without prior infection (3402.9 BAU/mL) (p = 0.78). Vaccinated participants with or without prior infection had a higher seroneutralization rate (91.0%) than those unvaccinated with prior infection (65.0%). CONCLUSION: These results demonstrated that single infection does not confer effective protection against SARS-CoV-2.

Presence of specific SARS-COV2 antibodies in hemodialysis patients and their caregivers after the first wave of COVID-19.

Hemodialysis (HD) patients are at risk for severe COVID-19 and cannot comply with social distancing. SARS-COV2 seroprevalence in French patients and caregivers after the first wave of COVID-19 is unknown. SeroCOVIDial is a prospective study conducted between June and December 2020. SARS-COV2 seroprevalence was evaluated by a rapid serological test (BIOSYNEX) in HD patients and caregivers, and the presence or not of anti-SARS-COV2 neutralizing or non-neutralizing antibodies in patients was also determined by ELISA and seroneutralization. In June 2020, 451 HD patients and 238 caregivers were included. Overall SARS-COV2 seroprevalence was 8.4% (patients) and 6.7% (caregivers), and was 87.1% (patients) and 90.0% (caregivers) in participants with a previously documented SARS-COV2 infection. Overall seroprevalence reached 13.8% (patients) and 12.6% (caregivers) following the second epidemic wave. During the follow-up, 38 (8.4%) patients died (9 of COVID-19). Among the 44 (10.6%) patients who became infected, only two were seropositive at M0. The levels of anti-SARS-COV2 antibodies decreased over time in patients and caregivers. The BIOSYNEX test showed 82.9% sensitivity and 97.7% specificity. Prevalence of anti-SARS-COV2 antibodies was low in HD patients and caregivers after the first epidemic wave but rose after the second wave. A rapid serological test showed good performances and could be useful for future monitoring of anti-SARS-COV2 antibodies.

Seroprevalence of SARS-CoV-2 IgG Antibodies and Factors Associated with SARS-CoV-2 IgG Neutralizing Activity among Primary Health Care Workers 6 Months after Vaccination Rollout in France.

We aimed to investigate the immunoglobulin G response and neutralizing activity against severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) among primary health care workers (PHCW) in France and assess the association between the neutralizing activity and several factors, including the coronavirus disease 2019 (COVID-19) vaccination scheme. A cross-sectional survey was conducted between 10 May 2021 and 31 August 2021. Participants underwent capillary blood sampling and completed a questionnaire. Sera were tested for the presence of antibodies against the nucleocapsid (N) protein and the S-1 portion of the spike (S) protein and neutralizing antibodies. In total, 1612 PHCW were included. The overall seroprevalences were: 23.6% (95% confidence interval (CI) 21.6-25.7%) for antibodies against the N protein, 94.7% (93.6-95.7%) for antibodies against the S protein, and 81.3% (79.4-83.2%) for neutralizing antibodies. Multivariate regression analyses showed that detection of neutralizing antibodies was significantly more likely in PHCW with previous SARS-CoV-2 infection than in those with no such history among the unvaccinated (odds ratio (OR) 16.57, 95% CI 5.96-59.36) and those vaccinated with one vaccine dose (OR 41.66, 95% CI 16.05-120.78). Among PHCW vaccinated with two vaccine doses, the detection of neutralizing antibodies was not significantly associated with previous SARS-CoV-2 infection (OR 1.31, 95% CI 0.86-2.07), but was more likely in those that received their second vaccine dose within the three months before study entry than in those vaccinated more than three months earlier (OR 5.28, 95% CI 3.51-8.23). This study highlights that previous SARS-CoV-2 infection and the time since vaccination should be considered when planning booster doses and the design of COVID-19 vaccine strategies.

Trends in social exposure to SARS-Cov-2 in France. Evidence from the national socio-epidemiological cohort-EPICOV.

BACKGROUND: We aimed to study whether social patterns of exposure to SARS-CoV-2 infection changed in France throughout the year 2020, in light to the easing of social contact restrictions. METHODS: A population-based cohort of individuals aged 15 years or over was randomly selected from the national tax register to collect socio-economic data, migration history, and living conditions in May and November 2020. Home self-sampling on dried blood was proposed to a 10% random subsample in May and to all in November. A positive anti-SARS-CoV-2 ELISA IgG result against the virus spike protein (ELISA-S) was the primary outcome. The design, including sampling and post-stratification weights, was taken into account in univariate and multivariate analyses. RESULTS: Of the 134,391 participants in May, 107,759 completed the second questionnaire in November, and respectively 12,114 and 63,524 were tested. The national ELISA-S seroprevalence was 4.5% [95%CI: 4.0%-5.1%] in May and 6.2% [5.9%-6.6%] in November. It increased markedly in 18-24-year-old population from 4.8% to 10.0%, and among second-generation immigrants from outside Europe from 5.9% to 14.4%. This group remained strongly associated with seropositivity in November, after controlling for any contextual or individual variables, with an adjusted OR of 2.1 [1.7-2.7], compared to the majority population. In both periods, seroprevalence remained higher in healthcare professions than in other occupations. CONCLUSION: The risk of Covid-19 infection increased among young people and second-generation migrants between the first and second epidemic waves, in a context of less strict social restrictions, which seems to have reinforced territorialized socialization among peers.

Acceptance, efficacy, and safety of COVID-19 vaccination in older patients with cancer.

PURPOSE: The COVID-19 vaccination campaign began in December 2020, in France, and primarily targeted the oldest people. Our study aimed to determine the level of acceptance of vaccination in a population of older patients with cancer. METHODS: From January 2021, we offered vaccination with the BNT162b2 COVID-19 vaccine to all patients 70 years and older referred to our geriatric oncology center in Marseille University Hospital (AP-HM) for geriatric assessment before initiation of an oncological treatment. Objectives were to evaluate acceptance rate of COVID-19 vaccination and to assess vaccine safety, reactogenicity, and efficacy two months after the first dose. RESULTS: Between January 18, 2021 and May 7, 2021, 150 older patients with cancer were offered vaccination after a geriatric assessment. The majority were men (61.3%), with a mean age of 81 years. The two most frequent primary tumors were digestive (29.4%) and thoracic (18%). The vaccine acceptance rate was 82.6% and the complete vaccination rate (2 doses) reached 75.3%. Among the vaccinated patients, 15.9% reported mild side effects after the first dose and 23.4% after the second dose, mostly arm pain and fatigue. COVID-19 cases were observed in 5.1% of vaccinated patients compared with 16.7% in unvaccinated patients. Of the 22 vaccinated patients who agreed to have their serum tested, 15 had antibodies against the spike protein at day 21 after the first dose. CONCLUSION: Our study showed a high acceptance rate of COVID-19 vaccination, with good tolerance in this frail population. These results highlight the benefits of organizing vaccination campaigns at the very beginning of oncological management in older patients. CLINICAL TRIAL REGISTRATION: This study was registered May 23, 2019 in ClinicalTrials.gov (NCT03960593).

Heterogeneous SARS-CoV-2 humoral response after COVID-19 vaccination and/or infection in the general population.

Assessment of the intensity, dynamics and determinants of the antibody response after SARS-CoV-2 infection or vaccination in the general population is critical to guide vaccination policies. This study characterized the anti-spike IgG titers in 13,971 participants included in a French multicohort population-based serological survey on COVID-19 between April and October 2020 and followed-up with serological testing between May and October 2021. Eight follow-up profiles were defined depending on SARS-CoV-2 infection (0, 1 or 2) and COVID-19 vaccination (0, 1, 2 or 3). The anti-spike titer was lower in adults with no vaccination even in case of infection or reinfection, while it was higher in adults with infection followed by vaccination. The anti-spike titer was negatively correlated with age in vaccinated but uninfected adults, whereas it was positively correlated with age in unvaccinated but infected adults. In adults with 2 vaccine injections and no infection, the vaccine protocol, age, gender, and time since the last vaccine injection were independently associated with the anti-spike titer. The decrease in anti-spike titer was much more rapid in vaccinated than in infected subjects. These results highlight the strong heterogeneity of the antibody response against SARS-CoV-2 in the general population depending on previous infection and vaccination.

A simple reverse genetics method to generate recombinant coronaviruses.

Engineering recombinant viruses is a pre-eminent tool for deciphering the biology of emerging viral pathogens such as the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). However, the large size of coronavirus genomes renders the current reverse genetics methods challenging. Here, we describe a simple method based on "infectious subgenomic amplicons" (ISA) technology to generate recombinant infectious coronaviruses with no need for reconstruction of the complete genomic cDNA and apply this method to SARS-CoV-2 and also to the feline enteric coronavirus. In both cases we rescue wild-type viruses with biological characteristics similar to original strains. Specific mutations and fluorescent red reporter genes can be readily incorporated into the SARS-CoV-2 genome enabling the generation of a genomic variants and fluorescent reporter strains for in vivo experiments, serological diagnosis, and antiviral assays. The swiftness and simplicity of the ISA method has the potential to facilitate the advance of coronavirus reverse genetics studies, to explore the molecular biological properties of the SARS-CoV-2 variants, and to accelerate the development of effective therapeutic reagents.

A Cross-Sectional Study of Exposure Factors Associated with Seropositivity for SARS-CoV-2 Antibodies during the Second Epidemic Wave among a Sample of the University of Corsica (France).

This study aimed to estimate the seroprevalence of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection within the staff and student populations of the University of Corsica (France) during the second wave of the epidemic. METHODS: A cross-sectional survey was conducted from 23 November 2020 to 31 January 2021. The participants underwent blood sampling using a fingerstick procedure and completed an anonymized questionnaire. Sera were tested for the presence of anti-SARS-CoV-2 IgG (ELISA-S) and, if positive, with an in-house virus neutralization test (VNT). RESULTS: A total of 418 persons were included in the study. The overall seroprevalence was 12.8% (95% confidence interval (CI), 9.8-16.6%). A total of 15 (31%) of the 49 individuals who had a positive ELISA-S also had a positive VNT. Seropositivity was associated with living at the city campus during the week and on weekends (OR = 3.74 [1.40-12.00]), using public transportation/carpooling (OR = 2.00 [1.01-4.02]), and being in contact with a person who tested positive for SARS-CoV-2 (OR = 2.32 [1.20-4.40]). The main symptoms associated with seropositivity were "having had an acute respiratory infection" (OR = 3.05 [1.43-6.43]) and "experiencing loss of smell" (OR = 16.4 [5.87-50.7]). CONCLUSION: These results could be useful for SARS-CoV-2 prevention and control on university campuses.

Determining the best window for BNT162b2 mRNA vaccination for SARS-CoV-2 in patients with multiple sclerosis receiving anti-CD20 therapy.

We studied the serologic response to the BNT162b2 mRNA vaccine at four weeks after the second dose in patients with RRMS treated with rituximab with extended-interval dosing (n = 26). At four weeks, 73% of patients were seropositive. No patient without B cells at the first dose (n = 4) was seropositive. Four of seven (57%) patients with B-cell proportion >0% and ≤5% were seropositive. All patients with B-cell proportion >5% (n = 15) were seropositive. In all patients, quantitative ELISA measures after vaccination were correlated with B-cell counts measured before vaccination. In patients receiving rituximab, seropositivity after BNT162b2 mRNA vaccination emerged only after B-cell repopulation.

Long-Term Infectivity of Chikungunya Virus Stored in the Dark at 4°C.

We call into question the established dogma that viruses with envelopes and RNA genomes have limited stability by demonstrating the staggering long-term viability, ∼2 years, of chikungunya virus when stored in liquid environments at +4°C in the dark. We contend that our understanding of the infectivity of a variety of enveloped viruses requires a new approach to identify under standardized conditions the primary determinants of their viability.

Emergence of dengue virus serotype 2 in Mauritania and molecular characterization of its circulation in West Africa.

The number of sporadic and epidemic dengue fever cases have reportedly been increasing in recent years in some West African countries, such as Senegal and Mali. The first epidemic of laboratory-confirmed dengue occurred in Nouakchott, the capital city of Mauritania situated in the Saharan desert, in 2014. On-site diagnosis of dengue fever was established using a rapid diagnostic test for dengue. In parallel, the presence of Aedes aegypti mosquitoes in the city was confirmed. The initial diagnosis was confirmed by RT-PCR, which showed that all samples from the 2014 dengue epidemic in Nouakchott were dengue virus serotype 2 (DENV-2). The whole genome or envelope protein gene of these strains, together with other DENV-2 strains obtained from travelers returning from West African countries to France between 2016 and 2019 (including two Mauritanian strains in 2017 and 2018), were sequenced. Phylogenetic analysis suggested a recent emergence of an epidemic strain from the cosmopolitan genotype belonging to West African cosmopolitan lineage II, which is genetically distinct from African sylvatic genotype. The origin of this DENV-2 lineage is still unknown, but our data seem to suggest a recent and rapid dispersion of the epidemic strain throughout the region. More complete genome sequences of West African DENV-2 are required for a better understanding of the dynamics of its circulation. Arboviral surveillance and outbreak forecasting are urgently needed in West Africa.

Spike and neutralizing antibodies response to COVID-19 vaccination in haemodialysis patients.

BACKGROUND: Humoral response to the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) vaccines needs to be evaluated in the fragile population of patients on maintenance haemodialysis (HD). METHODS: We analysed the antibody response to the spike (S) antigen of SARS-CoV-2 before and after each dose of the messenger RNA (mRNA) Comirnaty vaccine (BNT162b2; BioNTech & Pfizer) in patients from a single dialysis centre and detected the presence of neutralizing antibodies (Nabs). RESULTS: Among the 90 vaccinated HD patients (mean age 69 years, 61% male), 19 (21%) had a history of SARS-CoV-2 infection. A seroconversion with anti-S immunoglobulin G antibodies (Sabs) was documented in 20% of patients after the first dose (early responders) and in 77% after the second dose, while 23% were non-responders. Cardiac disease, cirrhosis and gamma globulin levels were independently predictive of the absence of seroconversion. Nabs were detected in 15.4% of early responders after the first dose and in 84.6% of early responders and 57.9% of late responders after the second dose. Sab titres after the second dose were higher in patients with Nab than without Nab {598 [interquartile range (IQR) 246-882]) versus 134 [IQR 61-390]; P < 0.0001}. All patients with a history of SARS-CoV-2 infection developed both Sabs and Nabs and their titres for Sabs and Nabs were higher than in late responders. CONCLUSIONS: Most HD patients develop a substantial humoral response against SARS-CoV2, with Nabs, following the mRNA vaccine. Whether this immunity persists over time and is able to efficiently protect patients from coronavirus disease 2019 remains to be determined.

Impact of the Second Epidemic Wave of SARS-CoV-2: Increased Exposure of Young People.

We aimed to use serological surveillance based on serial cross-sectional sampling of residual sera obtained from clinical laboratories to compare the differences in age and sex profiles of infected persons in the first and second waves of SARS-CoV-2 in Corsica, France. Residual sera were obtained, including samples from individuals of all ages collected for routine screening or clinical management by clinical laboratories. All the sera collected were tested for the presence of anti-SARS-CoV-2 IgG using a kit for semi-quantitative detection of IgG antibodies against the S1 domain of the viral spike protein (ELISA-S). Samples that were borderline and positive in ELISA-S were tested with an in-house virus neutralization test. During the second-wave period, we collected between 6 November, 2020 and 12 February, 2021, 4,505 sera from patients aged 0-101 years (60.4% women). The overall weighted seroprevalence of residual sera collected during the second-wave period [8.04% (7.87-9.61)] was significantly higher than the overall weighted seroprevalence estimated at the end of the first wave between 16 April and 15 June, 2020 [5.46% (4.37-7.00)] (p-value = 0.00025). Ninety-eight (30.1%) of the 326 samples tested in the VNT assay had a positive neutralization antibody titer. Estimated seroprevalence increased significantly for men [odds ratio (OR) OR = 1.80 (1.30-2.54); p-value = 0.00026] and for people under 30 years of age [OR = 2.17 (1.46-3.28); p-value = 0.000032]. This increase was observed in young adults aged 20-29 years among whom antibody frequencies were around four-fold higher than those observed at the end of the first wave. In conclusion, our seroprevalence estimates, including the proportion of the participants who had produced neutralizing antibodies, indicate that in February, 2021 the population of Corsica was still far from being protected against SARS-Cov-2 by "herd immunity."

Antibody status and cumulative incidence of SARS-CoV-2 infection among adults in three regions of France following the first lockdown and associated risk factors: a multicohort study.

BACKGROUND: We aimed to estimate the seropositivity to anti-SARS-CoV-2 antibodies in May-June 2020 after the first lockdown period in adults living in three regions in France and to identify the associated risk factors. METHODS: Between 4 May 2020 and 23 June 2020, 16 000 participants in a survey on COVID-19 from an existing consortium of three general adult population cohorts living in the Ile-de-France (IDF) or Grand Est (GE) (two regions with high rate of COVID-19) or in the Nouvelle-Aquitaine (NA) (with a low rate) were randomly selected to take a dried-blood spot for anti-SARS-CoV-2 antibodies assessment with three different serological methods (ClinicalTrial Identifier #NCT04392388). The primary outcome was a positive anti-SARS-CoV-2 ELISA IgG result against the spike protein of the virus (ELISA-S). Estimates were adjusted using sampling weights and post-stratification methods. Multiple imputation was used to infer the cumulative incidence of SARS-CoV-2 infection with adjustments for imperfect tests accuracies. RESULTS: The analysis included 14 628 participants, 983 with a positive ELISA-S. The weighted estimates of seropositivity and cumulative incidence were 10.0% [95% confidence interval (CI): 9.1%, 10.9%] and 11.4% (95% CI: 10.1%, 12.8%) in IDF, 9.0% (95% CI: 7.7%, 10.2%) and 9.8% (95% CI: 8.1%, 11.8%) in GE and 3.1% (95% CI: 2.4%, 3.7%) and 2.9% (95% CI: 2.1%, 3.8%) in NA, respectively. Seropositivity was higher in younger participants [odds ratio (OR) = 1.84 (95% CI: 1.79, 6.09) in <40 vs 50-60 years old and OR = 0.56 (95% CI: 0.42, 0.74) in ≥70 vs 50-60 years old)] and when at least one child or adolescent lived in the same household [OR = 1.30 (95% CI: 1.11, 1.53)] and was lower in smokers compared with non-smokers [OR = 0.71 (95% CI: 0.57, 0.89)]. CONCLUSIONS: Seropositivity to anti-SARS-CoV-2 antibodies in the French adult population was ≤10% after the first wave. Modifiable and non-modifiable risk factors were identified.

Emergence of Indian lineage of ECSA chikungunya virus in Djibouti, 2019.

The chikungunya virus (CHIKV) originated from Africa and has spread worldwide. Since 2017, multiple chikungunya outbreaks have been reported in the Horn of Africa, without molecular characterization. In November 2019, an autochthonous acute chikungunya infection was diagnosed in a French patient living in Djibouti, marking the re-emergence of the virus in the country. The strain was isolated and fully sequenced. Phylogenetic analysis revealed that the Djiboutian strain belongs to the Indian lineage of the Eastern/Central/South African (ECSA) genotype. Two mutations highly increasing the virus's fitness in Aedes aegypti, the sole vector present in Djibouti city, were identified.