Using the near real-time effective reproduction number rt as an early-warning tool for seasonal bronchiolitis and influenza-like illness epidemics.

Background: Yearly bronchiolitis and influenza-like illness epidemics in France often involve high morbidity and mortality, which severely impacts healthcare. Epidemics are declared by the French National Institute of Public Health based on syndromic surveillance of primary care and emergency departments (ED), using statistics-based alarms. Although the effective reproduction number (Rt) is used to monitor the dynamics of epidemics, it has never been used as an early warning tool for bronchiolitis or influenza-like illness epidemics in France.

Impact of the Omicron variant on SARS-CoV-2 reinfections in France, March 2021 to February 2022.

Since the first reports in summer 2020, SARS-CoV-2 reinfections have raised concerns about the immunogenicity of the virus, which will affect SARS-CoV-2 epidemiology and possibly the burden of COVID-19 on our societies in the future. This study provides data on the frequency and characteristics of possible reinfections, using the French national COVID-19 testing database. The Omicron variant had a large impact on the frequency of possible reinfections in France, which represented 3.

Impact of the lockdown on the burden of COVID-19 in outpatient care in France, spring 2020.

Background: To limit the spread of SARS-CoV-2 several countries implemented measures to reduce the number of contacts such as a national lockdown. We estimated the impact of the first lockdown on the burden of COVID-19 in the community in France.

Methods: Physicians participating in the French Sentinelles network reported the number of patients with an acute respiratory infection (ARI) seen in consultation and performed nasopharyngeal swabs in a sample of these patients (first patient of the week).

Estimation of influenza-attributable burden in primary care from season 2014/2015 to 2018/2019, France.

Influenza viruses cause seasonal epidemics whose intensity varies according to the circulating virus type and subtype. We aim to estimate influenza-like illness (ILI) incidence attributable to influenza viruses in France from October 2014 to May 2019. Physicians participating in the French Sentinelles network reported the number of patients with ILI seen in consultation and performed nasopharyngeal swabs in a sample of these patients.

Underdetection of cases of COVID-19 in France threatens epidemic control.

As countries in Europe gradually relaxed lockdown restrictions after the first wave, test-trace-isolate strategies became critical to maintain the incidence of coronavirus disease 2019 (COVID-19) at low levels. Reviewing their shortcomings can provide elements to consider in light of the second wave that is currently underway in Europe. Here we estimate the rate of detection of symptomatic cases of COVID-19 in France after lockdown through the use of virological and participatory syndromic surveillance data coupled with mathematical transmission models calibrated to regional hospitalizations.

Innate and Adaptive Anti-SIV Responses in Macaque Semen: Implications for Infectivity and Risk of Transmission.

HIV-1 infection is transmitted primarily by sexual exposure, with semen being the principal contaminated fluid. However, HIV-specific immune response in semen has been understudied. We investigated specific parameters of the innate, cellular, and humoral immune response that may affect semen infectivity in macaques infected with SIVmac251.

First cases of coronavirus disease 2019 (COVID-19) in France: surveillance, investigations and control measures, January 2020.

A novel coronavirus (severe acute respiratory syndrome coronavirus 2, SARS-CoV-2) causing a cluster of respiratory infections (coronavirus disease 2019, COVID-19) in Wuhan, China, was identified on 7 January 2020. The epidemic quickly disseminated from Wuhan and as at 12 February 2020, 45,179 cases have been confirmed in 25 countries, including 1,116 deaths. Strengthened surveillance was implemented in France on 10 January 2020 in order to identify imported cases early and prevent secondary transmission.

Comparative Analysis of Eleven Healthcare-Associated Outbreaks of Middle East Respiratory Syndrome Coronavirus (Mers-Cov) from 2015 to 2017.

Since its emergence in 2012, 2,260 cases and 803 deaths due to Middle East respiratory syndrome coronavirus (MERS-CoV) have been reported to the World Health Organization. Most cases were due to transmission in healthcare settings, sometimes causing large outbreaks. We analyzed epidemiologic and clinical data of laboratory-confirmed MERS-CoV cases from eleven healthcare-associated outbreaks in the Kingdom of Saudi Arabia and the Republic of Korea between 2015-2017.

Nonhuman primate models for cell-associated simian immunodeficiency virus transmission: the need to better understand the complexity of HIV mucosal transmission.

Nonhuman primates are extensively used to assess strategies to prevent infection from sexual exposure to human immunodeficiency virus (HIV) and to study mechanisms of mucosal transmission. However, although semen represents one of the most important vehicles for the virus, the vast majority of preclinical challenge studies have used cell-free simian immunodeficiency virus (SIV) or simian/human immunodeficiency virus (SHIV) viral particles inoculated as diluted culture supernatants. Semen is a complex body fluid containing many factors that may facilitate or decrease HIV infectiousness.

Semen CD4+ T cells and macrophages are productively infected at all stages of SIV infection in macaques.

The mucosal events of HIV transmission have been extensively studied, but the role of infected cells present in the genital and rectal secretions, and in the semen, in particular, remains a matter of debate. As a prerequisite to a thorough in vivo investigation of the early transmission events through infected cells, we characterized in detail by multi-parameter flow cytometry the changes in macaque seminal leukocytes during SIVmac251 infection, focusing on T cells, macrophages and dendritic cells. Using immunocytofluorescence targeting SIV proteins and real-time quantitative PCR targeting SIV DNA, we investigated the nature of the infected cells on sorted semen leukocytes from macaques at different stages of infection.

Captured retroviral envelope syncytin gene associated with the unique placental structure of higher ruminants.

Syncytins are envelope genes of retroviral origin that have been co-opted for a role in placentation and likely contribute to the remarkable diversity of placental structures. Independent capture events have been identified in primates, rodents, lagomorphs, and carnivores, where they are involved in the formation of a syncytium layer at the fetomaternal interface via trophoblast cell-cell fusion. We searched for similar genes within the suborder Ruminantia where the placenta lacks an extended syncytium layer but displays a heterologous cell-fusion process unique among eutherian mammals.

Ancestral capture of syncytin-Car1, a fusogenic endogenous retroviral envelope gene involved in placentation and conserved in Carnivora.

Syncytins are envelope protein genes of retroviral origin that have been captured for a function in placentation. Two such genes have already been identified in simians, two distinct, unrelated genes have been identified in Muridae, and a fifth gene has been identified in the rabbit. Here, we searched for similar genes in the Laurasiatheria clade, which diverged from Euarchontoglires--primates, rodents, and lagomorphs--shortly after mammalian radiation (100 Mya).