Phylodynamics of SARS-CoV-2 in France, Europe, and the world in 2020.

Although France was one of the most affected European countries by the COVID-19 pandemic in 2020, the dynamics of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) movement within France, but also involving France in Europe and in the world, remain only partially characterized in this timeframe. Here, we analyzed GISAID deposited sequences from January 1 to December 31, 2020 (n = 638,706 sequences at the time of writing). To tackle the challenging number of sequences without the bias of analyzing a single subsample of sequences, we produced 100 subsamples of sequences and related phylogenetic trees from the whole dataset for different geographic scales (worldwide, European countries, and French administrative regions) and time periods (from January 1 to July 25, 2020, and from July 26 to December 31, 2020). We applied a maximum likelihood discrete trait phylogeographic method to date exchange events (i.e., a transition from one location to another one), to estimate the geographic spread of SARS-CoV-2 transmissions and lineages into, from and within France, Europe, and the world. The results unraveled two different patterns of exchange events between the first and second half of 2020. Throughout the year, Europe was systematically associated with most of the intercontinental exchanges. SARS-CoV-2 was mainly introduced into France from North America and Europe (mostly by Italy, Spain, the United Kingdom, Belgium, and Germany) during the first European epidemic wave. During the second wave, exchange events were limited to neighboring countries without strong intercontinental movement, but Russia widely exported the virus into Europe during the summer of 2020. France mostly exported B.1 and B.1.160 lineages, respectively, during the first and second European epidemic waves. At the level of French administrative regions, the Paris area was the main exporter during the first wave. But, for the second epidemic wave, it equally contributed to virus spread with Lyon area, the second most populated urban area after Paris in France. The main circulating lineages were similarly distributed among the French regions. To conclude, by enabling the inclusion of tens of thousands of viral sequences, this original phylodynamic method enabled us to robustly describe SARS-CoV-2 geographic spread through France, Europe, and worldwide in 2020.

Severity of SARS-CoV-2 Omicron variant infection in heart transplant recipients.

SARS-CoV-2 Omicron variant was first detected in France mid-November 2021 in wastewater treatment plants while cases started to increase at the beginning of December. The maximum incidence occurred in mid-January 2022. The Omicron wave spread rapidly throughout France in general population with lower case-fatality rate compared with previous waves. Little is known about infection with Omicron variant in heart transplant (HT) recipients. In this study, we examined incidence and mortality rate of COVID-19 in the general population and among 1,263 HT recipients during the period from June, 2021 to February, 2022, described characteristics of HT recipients infected with SARS-CoV-2 during Omicron (December 1st, 2021-February 7, 2022) and Delta (June 1st- November 30, 2021) periods, and compared hospital course of HT recipients with Omicron and Delta variant infection. Our findings contrast with the reported lower severity for Omicron variant infection compared with Delta variant infection in immunocompetent individuals.

High SARS-CoV-2 seroprevalence among street adolescents in Lomé, Togo, 2021.

BACKGROUND: There is almost no data on the circulation of SARS-CoV-2 among street adolescents. We conducted a study to document the immunization status of street adolescents in Togo against different variants of SARS-CoV-2. METHODS: A cross-sectional study was carried out in 2021 in Lomé, the city with the highest number of COVID 19 cases in Togo (60%). Adolescents aged 13- and 19 years old living on the street were eligible for inclusion. A standardized questionnaire was administered face-to-face to adolescents. A sample of blood was taken and aliquots of plasma were transported to the virology laboratory of the Hôpital Bichat-Claude Bernard (Paris, France). SARS-CoV-2 anti-S and anti-N IgG were measured using chemiluminescent microparticle immunoassay. A quantitative miniaturized and parallel-arranged ELISA assay was used to detect IgG antibodies specifically directed against the different SARS-CoV-2 Variants of Concern (VOC). RESULTS: A total of 299 street adolescents (5.2% female), median age 15 years, interquartile range (14-17 years), were included in this study. The prevalence of SARS-CoV-2 infection was 63.5% (95%CI: 57.8-69.0). Specific-IgG against the ancestral Wuhan strain was developed by 92.0% of subjects. The proportion of patients being immunized against each VOC was 86.8%, 51.1%, 56.3%, 60.0, and 30.5% for the Alpha, Beta, Gamma, Delta, and Omicron VOCs, respectively. CONCLUSION: This study showed a very high prevalence with approximately 2/3 of Togolese street adolescents having antibodies to SARS-CoV-2 due to a previous infection. These results confirm an under-reporting of COVID-19 cases in Togo, questioning the hypothesis of low virus circulation in Togo and even in Africa.

Agreement of respiratory viruses' detection between nasopharyngeal swab and bronchoalveolar lavage in adults admitted for pneumonia: a retrospective study.

OBJECTIVES: The COVID-19 pandemic has highlighted the high diagnostic accuracy of the nasopharyngeal swab (including in intensive care unit (ICU) patients). This study aimed to compare nasopharyngeal swab and bronchoalveolar lavage (BAL) results for non-SARS-CoV-2 viruses in patients with suspected pneumonia. METHODS: A retrospective analysis was performed in one French academic hospital on consecutive adults from 2012 to 2018 and tested nasopharyngeal swab and BAL within 24 hours by using multiplex PCR. The agreement in pathogen detection between nasopharyngeal swab and BAL was evaluated. RESULTS: Patients were primarily men (n = 178/276, 64.5%), with a median age of 60 years (IQR: 51-68 years). Of the 276 patients, 169 (61%) were admitted to the ICU for acute respiratory distress. We detected at least one respiratory virus in 34.4% of the nasopharyngeal swabs (n = 95/276) and 29.0% of BAL (n = 80/276). Two or more viruses were detected in 2.5% of the nasopharyngeal swabs (n = 7/276) and 2.2% of BAL (n = 6/276). Rhinovirus/enteroviruses were the most frequently detected viral group in 10.2% (n = 29/285) of the nasopharyngeal swabs and 9.5% (n = 27/285) of BAL, followed by influenza A, detected in 5.6% (n = 16/285) of the nasopharyngeal swabs and 4.9% (n = 14/285) of BAL. Overall agreement was 83.7% (n = 231/276 (95% CI [78.7%, 87.7%])) (i.e. same pathogen or pathogen combination was identified in the nasopharyngeal swab and BAL for 231 patients). Rhinovirus/enterovirus (n = 29/231) and respiratory syncytial virus (n = 13/231) had the lowest agreement of 62.1% (n = 18/29 (95% CI [42.4%-78.7%])) and 61.5% (n = 8/13 (95% CI [32.3%-84.9%])), respectively). CONCLUSIONS: There was a good agreement between nasopharyngeal swabs and BAL in detecting respiratory viruses among adult patients with suspected pneumonia. However, these data still encourage BAL in the case of a negative nasopharyngeal swab.

Impact of BNT162b2 mRNA anti-SARS-CoV-2 vaccine on interferon-alpha production by plasmacytoid dendritic cells and autoreactive T cells in patients with systemic lupus erythematosus: The COVALUS project.

OBJECTIVE: To evaluate the specific response of SLE patients to BNT162b2 vaccination and its impact on autoimmunity defined as in vivo production of interferon-alpha (IFNα) by plasmacytoid dendritic cells (pDCs) and autoreactive immune responses. METHODS: Our prospective study included SLE patients and healthy volunteers (HV) who received 2 doses of BNT162b2 vaccine 4 weeks apart. Subjects under immunosuppressive drugs or with evidence of prior COVID-19 were excluded. IgG anti-Spike SARS-CoV-2 (anti-S) antibodies, anti-S specific-B cells, anti-S specific T cells, in vivo INF-α production by pDCs, activation marker expression by pDCs and autoreactive anti-nuclear T cells were quantified before first injection, before second injection, and 3 and 6 months after first injection. RESULTS: Vaccinated SLE patients produced significantly lower IgG antibodies and specific B cells against SARS-CoV-2 as compared to HV. In contrast, anti-S T cell response did not significantly differ between SLE patients and HV. Following vaccination, the surface expression of HLA-DR and CD86 and the in vivo production of IFNα by pDCs significantly increased in SLE patients. The boosted expression of HLA-DR on pDCs induced by BNT162b2 vaccine correlated with the overall immune responses against SARS-CoV-2 (anti-S antibodies: r = 0.27 [0.05-0.46], p = 0.02; anti-S B cells: r = 0.19 [-0.03-0.39], p = 0.09); anti-S T cells: r = 0.28 [0.05-0.47], p = 0.016). Eventually, anti-SARS-CoV-2 vaccination was associated with an overall decrease of autoreactive T cells (slope = - 0.00067, p = 0.015). CONCLUSION: BNT162b2 vaccine induces a transient in vivo activation of pDCs in SLE that contributes to the immune responses against SARS-CoV-2. Unexpectedly BNT162b2 vaccine also dampens the pool of circulating autoreactive T cells, suggesting that vaccination may have a beneficial impact on SLE disease.

Dual Monoclonal Antibodies on Sars-Cov-2 Alpha and Delta Variants: Clinical and Virological Efficacy.

Monoclonal antibodies (MAbs) targeting the Spike glycoprotein of SARS-CoV-2 is a key strategy to prevent severe COVID-19. Here, the efficacy of two monoclonal antibody bitherapies against SARS-CoV-2 was assessed on 92 patients at high risk of severe COVID-19 between March and October 2021 (Bichat-Claude Bernard Hospital, Paris, France). Nine patients died despite appropriate management. From 14 days following treatment initiation, we observed a slower viral load decay for patients treated with the bitherapy Bamlanivimab/Etsevimab compared to the Casirivimab/Imdevimab association therapy (P = 0.045). The emergence of several mutations on the Spike protein known to diminish antiviral efficacy was observed from 1 to 3 weeks after infusion. The Q493R mutation was frequently selected, located in a region of joint structural overlap by Bamlanivimab/Etsevimab antibodies. Despite that this study was done on former SARS-CoV-2 variants (Alpha and Delta), the results provide new insights into resistance mechanisms in SARS-CoV-2 antibodies neutralization escape and should be considered for current and novel variants. IMPORTANCE Monoclonal antibody bitherapies (MAbs) are commonly prescribed to treat severe SARS-CoV-2-positive patients, and the rapid growth of resistance mutation emergence is alarming globally. To explore this issue, we conducted both clinical and genomic analyses of SARS-CoV-2 in a series of patients treated in 2021. We first noticed that the two dual therapies prescribed during the study had different kinetics of viral load decay. Rapidly after initiation of the treatments, resistance mutations emerged in the interface between the MAbs and the target Spike glycoprotein, demonstrating the importance to continuously screen the viral genome during treatment course. Taken together, the results highlight that viral mutations may emerge under selective pressure, conferring a putative competitive advantage, and could rapidly spread, as observed for the Omicron variant.

Earlier In Vitro Viral Production With SARS-CoV-2 Alpha Than With Beta, Gamma, B, or A.27 Variants.

Since its emergence in China at the end of 2019, SARS-CoV-2 has rapidly spread across the world to become a global public health emergency. Since then, the pandemic has evolved with the large worldwide emergence of new variants, such as the Alpha (B.1.1.7 variant), Beta (B.1.351 variant), and Gamma (P.1 variant), and some other under investigation such as the A.27 in France. Many studies are focusing on antibody neutralisation changes according to the spike mutations, but to date, little is known regarding their respective replication capacities. In this work, we demonstrate that the Alpha variant provides an earlier replication in vitro, on Vero E6 and A549 cells, than Beta, Gamma, A.27, and historical lineages. This earlier replication was associated with higher infectious titres in cell-culture supernatants, in line with the higher viral loads observed among Alpha-infected patients. Interestingly, Beta and Gamma variants presented similar kinetic and viral load than the other non-Alpha-tested variants.

Efficacy of Severe Acute Respiratory Syndrome Coronavirus-2 Vaccine in Patients With Thoracic Cancer: A Prospective Study Supporting a Third Dose in Patients With Minimal Serologic Response After Two Vaccine Doses.

INTRODUCTION: Coronavirus disease 2019 resulted in a 30% mortality rate in patients with thoracic cancer. Given that patients with cancer were excluded from serum antisevere acute respiratory syndrome coronavirus-2 (SARS-CoV-2) vaccine registration trials, it is still unknown whether they would develop a protective antispike antibody response after vaccination. This prospective vaccine monitoring study primarily aimed to assess humoral responses to the SARS-CoV-2 vaccine in patients with thoracic cancer. METHODS: SARS-CoV-2-spike antibodies were measured using the Abbot Architect SARS-CoV-2 immunoglobulin G immunoassay before the first injection of BNT162b2 mRNA vaccine, at week 4, and 2 to 16 weeks after the second vaccine dose administration. The factors associated with antibody response were analyzed. RESULTS: Overall, 306 patients, with a median age of 67.0 years (interquartile range: 58-74), were vaccinated. Of these, 283 patients received two vaccine doses at 28-day intervals. After a 6.7-month median follow-up, eight patients (2.6%) contracted proven symptomatic SARS-CoV-2 infection, with rapid favorable evolution. Of the 269 serologic results available beyond day 14 after the second vaccine dose administration, 17 patients (6.3%) were still negative (<50 arbitrary units/mL, whereas 34 (11%) were less than 300 arbitrary units/mL (12.5th percentile). In multivariate analysis, only age (p < 0.01) and long-term corticosteroid treatment (p = 0.01) were significantly associated with a lack of immunization. A total of 30 patients received a third vaccine dose, with only three patients showing persistently negative serology thereafter, whereas the others exhibited clear seroconversion. CONCLUSIONS: SARS-CoV2 vaccines were found to be efficient in patients with thoracic cancer, most of them being immunized after two doses. A third shot given to 1% of patients with persistent low antibody titers resulted in an 88% immunization rate.

Emergence of E484K Mutation Following Bamlanivimab Monotherapy among High-Risk Patients Infected with the Alpha Variant of SARS-CoV-2.

An Emergency Use Authorization was issued in the United States and in Europe for a monoclonal antibody monotherapy to prevent severe COVID-19 in high-risk patients. This study aimed to assess the risk of emergence of mutations following treatment with a single monoclonal antibody. Bamlanivimab was administered at a single dose of 700 mg in a one-hour IV injection in a referral center for the management of COVID-19 in France. Patients were closely monitored clinically and virologically with nasopharyngeal RT-PCR and viral whole genome sequencing. Six patients were treated for a nosocomial SARS-CoV-2 infection, all males, with a median age of 65 years and multiple comorbidities. All patients were infected with a B.1.1.7 variant, which was the most frequent variant in France at the time, and no patients had E484 mutations at baseline. Bamlanivimab was infused in the six patients within 4 days of the COVID-19 diagnosis. Four patients had a favorable outcome, one died of complications unrelated to COVID-19 or bamlanivimab, and one kidney transplant patient treated with belatacept died from severe COVID-19 more than 40 days after bamlanivimab administration. Virologically, four patients cleared nasopharyngeal viral shedding within one month after infusion, while two presented prolonged viral excretion for more than 40 days. The emergence of E484K mutants was observed in five out of six patients, and the last patient presented a Q496R mutation potentially associated with resistance. CONCLUSIONS: These results show a high risk of emergence of resistance mutants in COVID-19 patients treated with monoclonal antibody monotherapy.

Impact of the COVID-19 pandemic on the homeless: results from a retrospective closed cohort in France (March-May 2020).

OBJECTIVES: To evaluate severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, hospitalization and fatality rates in residents of homeless shelters run by Samusocial of Paris. METHODS: We conducted a retrospective serological study between July and August 2020 on all residents and staff members of three homeless shelters run by Samusocial of Paris: two centres providing healthcare accommodation (HCA) and one a women's dormitory. We included all adults present in the shelters or who died of a proven SARS-CoV-2 infection during the first wave (March-May). SARS-CoV-2 antibodies were detected in serum samples using the SARS-CoV-2 IgG Architect (Abbott) test. Any participant with a positive PCR or serology was defined as a confirmed SARS-CoV-2 case. RESULTS: We included 100 residents and 83 staff members. The confirmed SARS-CoV-2 rate by PCR or serology was 72/100 (72.0%) for residents and 17/83 (20.5%) for staff members. Women accommodated in the dormitory had the highest infection rate (90.6%). The hospitalization rate in residents was 17/72 (23.6%) and the death rate 4/72 (5.6%). All hospitalizations and deaths occurred among HCA residents. Among the residents of HCA shelters, 34/68 (50%) presented at least two comorbidity factors associated with being at high risk for severe SARS-CoV-2 infection. CONCLUSION: The SARS-CoV-2 infection rate was high in residents of these homeless shelters (10.6% seroprevalence in the Île-de-France region during the first wave). Severe SARS-CoV-2 infection was highly associated with the prevalence of comorbidities. This population should be considered as a priority in vaccination campaigns and in access to individual housing units when at risk.

Contribution of rapid lateral flow assays from capillary blood specimens to the diagnosis of COVID-19 in symptomatic healthcare workers: a pilot study in a university hospital, Paris, France.

BACKGROUND: This study aimed to assess, by rapid tests, the immune status against COVID-19 among Healthcare Workers (HCW) with history of symptoms, and for whom SARS-CoV-2 detection was either not documented or negative. METHODS: Whole blood by finger prick and serum samples were taken from HCW for use with 2 rapid lateral flow tests and an automated immunoassay. RESULTS: Seventy-two HCWs were included, median duration between symptoms onset and serology sampling was 68 days. Anti-SARS-CoV-2 antibodies were detected by rapid test in 11 HCW (15.3%) and confirmed in the 10 with available serum by the automated immunoassay. The frequency of ageusia or anosmia was higher in participants with SARS-CoV-2 antibodies (P = 0.0006 and P = 0.029, respectively). CONCLUSIONS: This study, among symptomatic HCW during the first wave in France, showed that 15% had IgG anti-SARS-CoV-2, a higher seroprevalence than in the general population. Rapid lateral flow tests were highly concordant with automated immunoassay.

Evaluation of three extraction-free SARS-CoV-2 RT-PCR assays: A feasible alternative approach with low technical requirements.

The worldwide demand for SARS-CoV-2 RT-PCR testing resulted in a shortage of diagnostic kits. RNA extraction step constitutes a major bottleneck to perform diagnostic. The aim of this study was to assess performances of different extraction-free SARS-CoV-2 RT-PCR assays compared to a reference RT-PCR assay. The panel of evaluation consisted of 94 samples: 69 positive and 25 negative for SARS-CoV-2 by reference RT-PCR. Three extraction-free RT-PCR assays were assessed: (i) PrimeDirect® Probe RT-qPCR Mix (Takara), (ii) PrimeScript®RT-PCR (Takara), and (iii) SARS-CoV-2 SANSURE®BIOTECH Novel Coronavirus (Sansure). The overall sensitivity of PrimeDirect, PrimeScript and Sansure assays was 55.1 %, 69.6 % and 69.6 %, respectively. The sensitivity increased among samples with Ct<30: 91.9 % (n = 34/37), 89.2 % (n = 33/37) and 94.6 % (n = 35/37) for PrimeDirect, PrimeScript and Sansure assays, respectively. The specificity was 88 %, 100 % and 100 % for PrimeDirect, PrimeScript and Sansure assays, respectively. In the present study, we showed a good sensitivity of extraction-free PCR assays, especially for high viral loads (Ct<30), except PrimeDirect that displayed imperfect sensitivity and specificity. Despite a lower sensitivity for low viral loads, extraction-free reagents can provide a valuable option, cheaper, easier and less reagent consuming for SARS-CoV-2 diagnostic, especially in laboratory with lower experience and equipment for molecular assays.