Coinfections and iterative detection of respiratory viruses among 17,689 patients between March 2021 and December 2022 in Southern France.

Objectives: We aimed to describe coinfections and iterative infections with respiratory viruses diagnosed over a 22-month period in 2021-2022 in public university hospitals of the second largest French city.

Material And Methods: Respiratory virus infections were diagnosed by qPCR with the Fast Track Diagnostics Respiratory Pathogens 21 on nasopharyngeal swabs collected between 01/03/2021-31/10/2022 and sent for routine diagnosis purpose to our clinical microbiology-virology laboratory at public university hospitals of Marseille, Southern France.

Results: Nasopharyngeal swabs from 17,689 patients were tested, of which 8,133 (46 %) were positive for ≥1 respiratory virus and 1,255 (15%) were co-infected with ≥2 viruses including 213 (2.

Strategic Aeromedical Evacuations of the French Armed Forces in French Guiana From 2018 to 2020.

Introduction: The French Armed Forces are deployed in French Guiana (FG) to protect national territory and ensure the security of strategically important sites. Military health support (MHS) provides medical support for missions in this tropical environment, which is hazardous and where confrontations are possible. MHS must organize tactical and strategic evacuations (Strat-AEs), so that an optimal level of care can be delivered.

Role of SARS-CoV-2 mutations in the evolution of the COVID-19 pandemic.

Objectives: The SARS-CoV-2 pandemic and large-scale genomic surveillance provided an exceptional opportunity to analyze mutations that appeared over three years in viral genomes. Here we studied mutations and their epidemic consequences for SARS-CoV-2 genomes from our center.

Methods: We analyzed 61,397 SARS-CoV-2 genomes we sequenced from respiratory samples for genomic surveillance.

Long-Read Sequencing and Genome Assembly Pipeline of Two Clones (3D7, W2) Using Only the PromethION Sequencer from Oxford Nanopore Technologies without Whole-Genome Amplification.

Antimalarial drug resistance has become a real public health problem despite WHO measures. New sequencing technologies make it possible to investigate genomic variations associated with resistant phenotypes at the genome-wide scale. Based on the use of hemisynthetic nanopores, the PromethION technology from Oxford Nanopore Technologies can produce long-read sequences, in contrast to previous short-read technologies used as the gold standard to sequence Plasmodium.

Updated estimation of cutaneous leishmaniasis incubation period in French Guiana.

Background: The cutaneous leishmaniasis (CL) incubation period (IP) is defined as the time between parasite inoculation by sandfly bite and the onset of the first CL lesion. IP distribution is difficult to assess for CL because the date of exposure to an infectious bite cannot be accurately determined in endemic areas. IP current estimates for CL range from 14 days to several months with a median around 30-60 days, as established by a few previous studies in both New and Old Worlds.

Monkeypox clinical disease: Literature review and a tool proposal for the monitoring of cases and contacts.

The human monkeypox disease has mainly been described in Western and Central Africa. Since May 2022, the monkeypox virus has been spreading worldwide in a new epidemiological pattern, where cases result from person-to-person transmission, and develop clinically milder or less typical illness than during previous outbreaks in endemic areas. The newly-emerging monkeypox disease needs to be described over the long term, to improve cases definitions, to implement prompt control measures against epidemics, and to provide supportive care.

Role and Limits of COVID-19 Vaccines in the Delicate Transition from Pandemic Mitigation to Endemic Control.

The recent surge of COVID-19 related to the Omicron variant emergence has thrown a harsh light upon epidemic control in the near future. This should lead the scientific and medical community to question the long-term vaccine strategy for SARS-CoV-2 control. We provide here a critical point of view regarding the virological evolution, epidemiological aspects, and immunological drivers for COVID-19 control, including a vaccination strategy.

The emergence, spread and vanishing of a French SARS-CoV-2 variant exemplifies the fate of RNA virus epidemics and obeys the Mistigri rule.

The nature and dynamics of mutations associated with the emergence, spread, and vanishing of SARS-CoV-2 variants causing successive waves are complex. We determined the kinetics of the most common French variant ("Marseille-4") for 10 months since its onset in July 2020. Here, we analyzed and classified into subvariants and lineages 7453 genomes obtained by next-generation sequencing.

Who Were Hospitalized Deceased Patients from COVID-19 During the First Year of Pandemic? Retrospective Analysis of 1104 Deceased Patients in South of France.

Introduction: Following the first year of the COVID-19 pandemic, a complete analysis of the characteristics of the deceased hospitalized patients was performed, to identify factors related to premature mortality and to compare patient profiles according to the epidemic periods.

Methods: Retrospective analysis of 1104 deceased patients in two University Hospitals in South-eastern France, between March 1, 2020 and March 12, 2021 from Hospital's electronic medical records was performed.

Results: Mean age was 80 years (± 11.

Control of common viral epidemics but not of SARS-CoV-2 through the application of hygiene and distancing measures.

Background: We systematically survey respiratory and gastrointestinal infections of viral origin in samples sent to our university hospital institute in Marseille, southern France. Here, we evaluated whether the measures implemented to fight COVID-19 had an effect on the dynamics of viral respiratory or gastrointestinal infections.

Methods: We analysed PCR performed and positive for the diagnoses of viral respiratory and gastrointestinal infections over five years (January 2017-February 2021).

Blister Beetle Dermatitis Outbreaks in Mali.

Introduction: Meloidae are distributed in temperate and arid regions but are also common in subtropical and tropical savannahs. These insects contain cantharidin, a vesicant substance that can cause poisoning by ingestion and dermatitis by direct contact.

Material And Methods: We describe recurrent Meloidae-related dermatitis outbreaks and their health impact by analyzing medical consultation records and meteorological data.

Analysis of SARS-CoV-2 Variants From 24,181 Patients Exemplifies the Role of Globalization and Zoonosis in Pandemics.

After the end of the first epidemic episode of SARS-CoV-2 infections, as cases began to rise again during the summer of 2020, we at IHU Méditerranée Infection in Marseille, France, intensified the genomic surveillance of SARS-CoV-2, and described the first viral variants. In this study, we compared the incidence curves of SARS-CoV-2-associated deaths in different countries and reported the classification of SARS-CoV-2 variants detected in our institute, as well as the kinetics and sources of the infections. We used mortality collected from a COVID-19 data repository for 221 countries.

Early chains of transmission of COVID-19 in France, January to March 2020.

IntroductionSARS-CoV-2, the virus that causes COVID-19, has spread rapidly worldwide. In January 2020, a surveillance system was implemented in France for early detection of cases and their contacts to help limit secondary transmissions.AimTo use contact-tracing data collected during the initial phase of the COVID-19 pandemic to better characterise SARS-CoV-2 transmission.

SARS-CoV-2 Vaccination and Protection Against Clinical Disease: A Retrospective Study, Bouches-du-Rhône District, Southern France, 2021.

From January 18th to August 13th, 2021, 13,804 unvaccinated and 1,156 patients who had received at least one COVID-19 vaccine dose were tested qPCR-positive for SARS-CoV-2 in our center. Among vaccinated patients, 949, 205 and 2 had received a single, two or three vaccine doses, respectively. Most patients (80.

The Effect of Topical Oxygen Therapy in Horses Affected with Mycosis of the Guttural Pouch: An Experimental Pilot Study and a Case Series.

The management of bleeding originating from the guttural pouch (GP) has a high success rate, but the resolution of the macroscopic inflammatory lesions in the case of mycosis (GPM) is highly variable; the resolution of neurological disorders is inconstant and challenging. Our aim was to test the feasibility and safety of topical oxygen therapy (TOT) in horses after induction of GPM and in cases with naturally occurring disease. This study was an in vivo experimental and retrospective two-phase study.

Consequences of the COVID-19 Outbreak Lockdown on Non-Viral Infectious Agents as Reported by a Laboratory-Based Surveillance System at the IHU Méditerranée Infection, Marseille, France.

The objective of this paper is to describe the surveillance system MIDaS and to show how this system has been used for evaluating the consequences of the French COVID-19 lockdown on the bacterial mix of AP-HM and the antibiotic resistance. MIDas is a kind of surveillance activity hub, allowing the automatic construction of surveillance control boards. We investigated the diversity and resistance of bacterial agents from respiratory, blood, and urine samples during the lockdown period (from week 12 to 35 of 2020), using the same period of years from 2017 to 2019 as control.

Increased risk of severe malaria in travellers during the COVID-19 pandemic.

We observed an increase in severe cases of falciparum malaria among French service members (who are travellers in endemic areas) in 2020, associated with an increase in the time between onset of symptoms and diagnosis/treatment. The COVID-19 epidemic may have lengthened the malaria diagnosis process, mainly due to clinical similarities.

Evaluation of Strategies to Fight COVID-19: The French Paradigm.

(1) Background: We collected COVID-19 mortality data and the age distribution of the deceased in France and other European countries, as well as specifically in the cities of Paris and Marseille, and compared them. (2) Methods: Data on mortality related to COVID-19 and the associated age distribution were collected from government institutions in various European countries. In France, data were obtained from INSEE and Santé Publique France.

Lessons learned from the investigation of a COVID-19 cluster in Creil, France: effectiveness of targeting symptomatic cases and conducting contact tracing around them.

Background: This study presents the methods and results of the investigation into a SARS-CoV-2 outbreak in a professional community. Due to the limited testing capacity available in France at the time, we elaborated a testing strategy according to pre-test probability.

Methods: The investigation design combined active case finding and contact tracing around each confirmed case with testing of at-risk contact persons who had any evocative symptoms (n = 88).

Fecal glucocorticoid metabolites reflect hypothalamic-pituitary-adrenal axis activity in muskoxen (Ovibos moschatus).

Muskoxen (Ovibos moschatus), a taxonomically unique Arctic species, are increasingly exposed to climate and other anthropogenic changes. It is critical to develop and validate reliable tools to monitor their physiological stress response in order to assess the impacts of these changes. Here, we measured fecal glucocorticoid metabolite (FGM) levels in response to the administration of adrenocorticotropic hormone (ACTH) in the winter (1 IU/kg) and summer (2 IU/kg) using two enzyme immunoassays, one targeting primarily cortisol and the other targeting primarily corticosterone.