IntroductionMolecular surveillance is an important tool for detecting chains of transmission and controlling the HIV epidemic. This can also improve our knowledge of molecular and epidemiological factors for the optimization of prevention. Our objective was to illustrate this by studying the molecular and epidemiological evolution of the cluster including the new circulating recombinant form (CRF) 94_cpx of HIV-1, detected in 2017 and targeted by preventive actions in 2018.MethodsIn June 2022, 32 HIV-1 sequence databases from French laboratories were screened to identify all individuals who had acquired CRF94_cpx or a similar strain, whatever the date of diagnosis. Phylogenetic analyses were performed with the sequences identified, and biological parameters were collected at the time of diagnosis and after the start of treatment to analyse the evolution of the cluster. Full genomes were sequenced to characterize the new strains.ResultsWe analysed 98 HIV-1 isolates: 63 were CRF94, three were unclassifiable, and the other 32 formed a new cluster containing a new recombinant, CRF132_94B, derived from CRF94 and a subtype B strain. At least 95% of the individuals in both the CRF94 and CRF132 clusters were men who have sex with men (MSM), most of whom had acquired HIV less than 12 months before diagnosis. The number of CRF94 diagnoses declined drastically after 2018, but CRF132 strains spread widely between 2020 and 2022, into a different area of Ile-de-France region and within a younger population nevertheless aware of pre-exposure prophylaxis. Higher viraemia, lower CD4 cell counts and delayed treatment efficacy suggested that CRF94 was more virulent than CRF132, possibly due to the F subtype fragment of the vif gene.ConclusionsThese findings highlight the role of the MSM transmission cluster in spreading HIV and new variants. They show also the benefits of cluster surveillance for improving the targeting of preventive interventions, detecting the emergence of new strains and enriching our knowledge on virulence mechanisms. However, these investigations require support with sufficient resources dedicated to a regional or national programme to be responsive and effective.

We analyzed 324,734 SARS-CoV-2 variant screening tests from France enriched with 16,973 whole-genome sequences sampled during September 1, 2021-February 28, 2022. Results showed the estimated growth advantage of the Omicron variant over the Delta variant to be 105% (95% CI 96%-114%) and that of the BA.2 lineage over the BA.1 lineage to be 49% (95% CI 44%-52%). Quantitative PCR cycle threshold values were consistent with an increased ability of Omicron to generate breakthrough infections. Epidemiologic modeling shows that, in spite of its decreased virulence, the Omicron variant can generate important critical COVID-19 activity in hospitals in France. The magnitude of the BA.2 wave in hospitals depends on the level of relaxing of control measures but remains lower than that of BA.1 in median scenarios.

The newly identified coronavirus SARS-CoV-2 is responsible for the worldwide pandemic COVID-19. Considerable efforts have been devoted for the development of effective vaccine strategies against COVID-19. The SARS-CoV-2 spike protein has been identified as the major antigen candidate for the development of COVID-19 vaccines. The Pfizer-BioNTech COVID-19 vaccine comirnaty is a lipid nanoparticle-encapsulated mRNA encoding a full-length and prefusion-stabilized SARS-CoV-2 spike protein. In the present study, synthetic peptide-based ELISA assays were performed to identify linear B-cell epitopes into the spike protein that contribute to elicitation of antibody response in comirnaty- vaccinated individuals. The synthetic S2P6 peptide containing the spike residues 1138/1169 and to a lesser extent, the synthetic S1P4 peptide containing the spike residues 616/644 were recognized by the immune sera from comirnaty vaccine recipients but not COVID-19 recovered patients. We assume that the synthetic S2P6 peptide and to a lesser extent the synthetic S1P4 peptide, could be of interest to measure the dynamic of antibody response to COVID-19 mRNA vaccines. The S2P6 peptide has been identified as immunogenic in adult BALB/c mice that received protein-peptide conjugates in a prime-boost schedule. This raises the question on the role of the B-cell epitope peptide containing the SARS-CoV-2 spike residues 1138/1169 in protective efficacy of the Pfizer-BioNTech COVID-19 vaccine comirnaty.

Since early 2021, SARS-CoV-2 variants of concern (VOCs) have been causing epidemic rebounds in many countries. Their properties are well characterized at the epidemiological level but the potential underlying within-host determinants remain poorly understood. We analyze a longitudinal cohort of 6944 individuals with 14 304 cycle threshold (Ct) values of reverse-transcription quantitative polymerase chain reaction (RT-qPCR) VOC screening tests performed in the general population and hospitals in France between February 6 and August 21, 2021. To convert Ct values into numbers of virus copies, we performed an additional analysis using droplet digital PCR (ddPCR). We find that the number of viral genome copies reaches a higher peak value and has a slower decay rate in infections caused by Alpha variant compared to that caused by historical lineages. Following the evidence that viral genome copies in upper respiratory tract swabs are informative on contagiousness, we show that the kinetics of the Alpha variant translate into significantly higher transmission potentials, especially in older populations. Finally, comparing infections caused by the Alpha and Delta variants, we find no significant difference in the peak viral copy number. These results highlight that some of the differences between variants may be detected in virus load variations.

We analysed 131,478 SARS-CoV-2 variant screening tests performed in France from September 1st to December 18, 2021. Tests consistent with the presence of the Omicron variant exhibit significantly higher cycle threshold Ct values, which could indicate lower amounts of virus genetic material. We estimate that the transmission advantage of the Omicron variant over the Delta variant is +105% (95% confidence interval: 96-114%). Based on these data, we use mechanistic mathematical modelling to explore scenarios for early 2022.

To assess SARS-CoV-2 variants spread, we analysed 36,590 variant-specific reverse-transcription-PCR tests performed on samples from 12 April–7 May 2021 in France. In this period, contrarily to January–March 2021, variants of concern (VOC) β (B.1.351 lineage) and/or γ (P.1 lineage) had a significant transmission advantage over VOC α (B.1.1.7 lineage) in Île-de-France (15.8%; 95% confidence interval (CI): 15.5–16.2) and Hauts-de-France (17.3%; 95% CI: 15.9–18.7) regions. This is consistent with VOC β’s immune evasion abilities and high proportions of prior-SARS-CoV-2-infected persons in these regions.

Analysing 92,598 variant screening tests performed on SARS-CoV-2 positive samples collected in France between 1 July and 31 August 2021 shows an increase of Kappa-like infections. Full genome sequencing reveals that these correspond to Delta variants bearing the S:E484Q mutation. Most of these sequences belong to a phylogenetic cluster and also bear the S:T95I mutation. Further monitoring is needed to determine if this trend is driven by undocumented superspreading events or an early signal of future viral evolutionary dynamics

SARS-CoV-2 variants raise major concerns regarding the control of COVID-19 epidemics. We analyse 40,000 specific RT-PCR tests performed on SARS-CoV-2-positive samples collected between Jan 26 and Feb 16, 2021. We find a high transmission advantage of variants and show that their spread in the country is more advanced than anticipated.

SARS-CoV-2 variants raise concern regarding the mortality caused by COVID-19 epidemics. We analyse 88,375 cycle amplification (Ct) values from variant-specific RT-PCR tests performed between January 26 and March 13, 2021. We estimate that on March 12, nearly 85% of the infections were caused by the Alpha variant and that its transmission advantage over wild type strains was between 38 and 44%. We also find that tests positive for Alpha and Beta/Gamma variants exhibit significantly lower cycle threshold (Ct) values.

Variants of severe acute respiratory syndrome coronavirus 2 raise concerns regarding the control of coronavirus disease epidemics. We analyzed 40,000 specific reverse transcription PCR tests performed on positive samples during January 26-February 16, 2021, in France. We found high transmission advantage of variants and more advanced spread than anticipated.

SARS-CoV-2 variants threaten our ability to control COVID-19 epidemics. We analyzed 36,590 variant-specific RT-PCR tests performed on samples collected between April 12 and May 7, 2021 in France to compare variant spread. Contrarily to January to March 2021, we found that the V2 variant had a significant transmission advantage over V1 in some regions (15.1 to 16.1% in Ile-de-France and 16.1 to 18.8% in Hauts-de-France). This shift in transmission advantage is consistent with the immune evasion abilities of V2 and the high levels of immunization in these regions.

We analysed 9,030 variant-specific RT-PCR tests performed on SARS-CoV-2-positive samples collected in France between 31 May and 21 June 2021. This analysis revealed rapid growth of the Delta variant in three of the 13 metropolitan French regions and estimated a +79% (95% confidence interval: 52–110%) transmission advantage compared with the Alpha variant. The next weeks will prove decisive and the magnitude of the estimated transmission advantages of the Delta variant could represent a major challenge for public health authorities.

Background The spread of carbapenemase-producing Enterobacteriaceae (CPE) in the Southwest Indian Ocean area (SIOA) is poorly documented. Reunion Island is a French overseas territory located close to Madagascar and connected with Southern Africa, Indian sub-continent and Europe, with several weekly flights. Here we report the results of the CPE surveillance program in Reunion Island over a six-year period. Methods All CPE were collected between January 2011 and December 2016. Demographics and clinical data of the carrier patients were collected. We determined their susceptibility to antimicrobials, identified the carbapenemases and ESBL by PCR and sequencing, and explored their genetic relationship using pulsed-field gel electrophoresis and multi-locus sequence typing. Results A total of 61 CPEs isolated from 53 patients were retrieved in 6 public or private laboratories of the island. We found that 69.8% of CPE patients were linked to a foreign country of SIOA and that almost half of CPE cases (47.2%) reached the island through a medical evacuation. The annual number of CPE cases strongly increased over the studied period (one case in 2011 vs. 21 cases in 2016). A proportion of 17.5% of CPE isolates were non-susceptible to colistin. bla(NDM) was the most frequent carbapenemase (79.4%), followed by bla(IMI) (11.1%), and bla(IMP-10) (4.8%). Autochtonous CPE cases (30.2%) harboured CPE isolates belonging to a polyclonal population. Conclusions Because the hospital of Reunion Island is the only reference healthcare setting of the SIOA, we can reasonably estimate that its CPE epidemiology reflects that of this area. Mauritius was the main provider of foreign CPE cases (35.5%). We also showed that autochthonous isolates of CPEs are mostly polyclonal, thus unrelated to cross-transmission. This demonstrates the local spread of carbapenemase-encoding genes (i.e. bla(NDM)) in a polyclonal bacterial population and raises fears that Reunion Island could contribute to the influx of NDM-carbapenemase producers into the French mainland territory.

Epidemiological surveillance of Neisseria gonorrhoeae has become a major issue, due to the increasing number of cases and the emergence of multidrug-resistant clinical isolates.1 However, little is known about the epidemiology of N. gonorrhoeae in the Indian Ocean. We conducted a retrospective study between 20 October 2016 and 10 April 2017 to characterise the main circulating genotypes of N. gonorrhoeae and their resistance profiles on two islands in the Indian Ocean, Reunion and Mayotte. These islands are part of French overseas territories, and are populated by approximately 860 000 and 250 000 inhabitants, respectively. In total, 206 N. gonorrhoeae isolates were obtained within a network of 40 private and hospital laboratories, and 88 viable isolates (72 from Reunion and 16 from Mayotte) were selected at random for further microbiological and molecular investigations. Minimum inhibitory concentrations (MICs) were determined for six antibiotics using E-tests (Biomerieux, Marcy l’Etoile, France) and interpreted according to European Committee …

BackgroundWith more than 300 million infections estimated annually worldwide, dengue is the most prevalent arboviral infection. On Reunion Island, after a large outbreak in 1977-78, only limited episodes of viral circulation or sporadic cases were reported till 2015.AimOur objective was to document and report on the circulation of dengue virus after the occurrence of a small outbreak during austral summer 2015/16 and until the large outbreak of 2018.MethodsBeside the mandatory notification of biologically confirmed dengue cases, additional systems of surveillance were set up: estimation of dengue-like syndrome in people seeking care by their family doctor, surveillance of emergency department visits related to dengue, surveillance of hospitalised dengue patients and deaths classifications.ResultsAfter a moderate outbreak during summer 2015/16 with 231 cases, 2017 was characterised by limited viral circulation (97 cases) which, however, persisted during the austral winter. By February 2018, the number of cases had increased and led to a peak at the beginning of May 2018. More than 6,000 cases were reported this year (dengue virus type 2 only). In addition, six deaths of dengue patients were notified.ConclusionIn 2017, the persistence of transmission during winter created favourable conditions for the emergence of an epidemic during summer 2018. After this moderate epidemic wave, the viral circulation persisted during winter 2018 for the second year, opening the door for the second wave in 2019 and for potential endemisation of the disease on Reunion Island in the near future.

The spread of carbapenemase-producing Enterobacteriaceae in the Southwest Indian Ocean islands is poorly known. Here we describe an outbreak of colistin-resistant Enterobacter cloacae harbouring blaIMI-1 in the French overseas department of Mayotte. Between October 2015 and January 2017, all isolates of imipenem-non-susceptible E. cloacae at Mayotte Medical Center and University Hospital of Reunion Island were screened for carbapenemase production. Positive isolates were typed by pulsed-field gel electrophoresis and whole-genome sequencing (WGS)-based multilocus sequence typing (MLST), and all β-lactamase genes were identified by PCR and sequencing. Resistance profiles were determined by agar diffusion and Etest. Genetic support of the blaIMI-1 gene was determined by WGS. A total of 18 E. cloacae isolates harbouring blaIMI-1 were detected in 17 patients from Mayotte. Pulsed-field gel electrophoresis (PFGE) analysis showed 16 of the 18 strains to be clonally related and belonging to ST820. Based on clinical data, this outbreak most likely had a community origin. The blaIMI-1 gene in the 18 isolates was carried by a new variant of an integrative mobile element involving the Xer recombinases, called EcloIMEX-8. The mcr-1–mcr-5 genes were absent from the collection. The isolates belonged to E. cloacae cluster XI, known to be colistin heteroresistant. Here we report the first outbreak of IMI-1-producing Enterobacteriaceae. IMI-1-producers may be underdetected in microbiology laboratories because of their unusual antimicrobial resistance profile (resistant to imipenem but with intermediate resistance to ertapenem and susceptible to extended-spectrum cephalosporins) and the absence of blaIMI-1 in the panel of genes targeted by molecular diagnostic kits.

Alphaviruses are arthropod borne RNA viruses of medical importance. Geographical expansion of mosquitoes of the Aedes genus in the past decades has been associated with major Alphavirus-associated outbreaks. Climate changes and intensification of air travels have favored vector expansion and virus dissemination in new territories leading to virus emergence not only in tropical areas but also in temperate regions. The detection of emergence is based upon surveillance networks with epidemiological and laboratory investigation.

In 2005–2006 a major epidemics of Chikungunya disease occurred in South-West Indian Ocean islands. In Reunion Island, the magnitude of Chikungunya infection related symptoms was high and with over 38% of serological prevalence in the population. This epidemics illustrated the potential threat of emerging arboviral diseases for inhabitants of Reunion Island and elsewhere since vectors are worldwide distributed. A sentinel surveillance network was set-up to detect emerging pathogens associated with fever over 38 °C and in the absence of known etiologic causes. Leptospirosis is caused by a pathogenic spirochete of the Leptospira genus and is an endemic and recurrent seasonal disease of great concern in Reunion Island. To accurately diagnose potentially infected patients and to advise Health authorities on the presence of emerging pathogens, a rapid diagnostic test was needed that could differentiate between these 3 pathogens.

We report two cases of severe influenza infection imported by tourist patients from their country of origin and developed during travel. While studies have reported cases of influenza infections acquired during travel, here we examine two cases of severe influenza infection contracted in the country of origin that led to diagnosis and therapeutic problems in the destination country. No international recommendation exists concerning influenza vaccination before travel, and few countries recommend it for all travelers. Our study suggests that travel should be canceled when infectious signs are observed before departure. Influenza is a very common infection that is often benign, but sometimes very severe. The most severe cases include shock, acute respiratory distress syndrome (ARDS), myocarditis, rhabdomyolysis, and multiple organ failure. Management can require exceptional therapies, such as extracorporeal membrane oxygenation. A number of studies have focused on influenza infection in travelers. Cases of influenza acquired during travel have been reported in this literature, but no study has examined cases of influenza imported from the country of origin and developed while abroad. The latter situation may lead to 1) diagnostic problems during the nonepidemic season or in places where diagnostic techniques are lacking and 2) therapeutic difficulties resulting from the unavailability of techniques for the management of severe influenza infection in tourist areas. Here, we report two cases of extremely severe influenza infection imported by tourists from their country of origin and developed during travel.