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. Viral variants were defined based on ≥5 hallmark mutations along the whole genome shared by ≥30 genomes. SARS-CoV-2 genotype was determined for 24,181 patients using next-generation genome and gene sequencing (in 47 and 11% of cases, respectively) or variant-specific qPCR (in 42% of cases). Sixteen variants were identified by analyzing viral genomes from 9,788 SARS-CoV-2-diagnosed patients. Our data show that since the first SARS-CoV-2 epidemic episode in Marseille, importation through travel from abroad was documented for seven of the new variants. In addition, for the B.1.160 variant of Pangolin classification (a.k.a. Marseille-4), we suspect transmission from farm minks. In conclusion, we observed that the successive epidemic peaks of SARS-CoV-2 infections are not linked to rebounds of viral genotypes that are already present but to newly introduced variants. We thus suggest that border control is the best mean of combating this type of introduction, and that intensive control of mink farms is also necessary to prevent the emergence of new variants generated in this animal reservoir.

Our results show that louse-borne infectious diseases affected nearly one-third of Napoleon's soldiers buried in Vilnius and indicate that these diseases might have been a major factor in the French retreat from Russia.

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Plague is characterized by geographical foci from which it re-emerges after decades of silence, a fact currently explained by enzootic and epizootic cycles between plague-susceptible and plagueresistant rodents. To assess the potential role of soil in plague epidemiology, we experimentally investigated whether Yersinia pestis could persist alive and virulent in soil. Sterilized soil inoculated with virulent Y. pestis biotype Orientalis was regularly sampled for 40 weeks in duplicate. Each sample was observed by acridine orange staining and immunofluorescence using an anti-Y. pestis polyclonal antibody, and DNA was extracted for PCR amplification and sequencing of the Y. pestis ureD, caf1 and pla genes. All samples were inoculated onto selective agar, and samples from soil that had been incubated for 10, 60, 165, 210 and 280 days were also inoculated into each of two BALB/c female mice. The mouse experiment was performed in triplicate. Non-inoculated, sterilized soil samples were used as negative controls. Microorganisms fluorescing orange and detected by immunofluorescence were identified as Y. pestis in all samples. They were recovered in pure agar cultures for up to 30 weeks but thereafter were contaminated with Pseudomonas spp. Soil that had been inoculated with Y. pestis proved to be fully virulent in mice, which died with Y. pestis septicaemia and multiple organ involvement. Negative control mice showed no signs of disease. These data indicate that Y. pestis biotype Orientalis can remain viable and fully virulent after 40 weeks in soil. This study is a first step on which to base further investigations of a potential telluric reservoir for Y. pestis, which could represent an alternative mechanism for the maintenance of plague foci.

One thousand one hundred and nineteen cases of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron variant cases have been diagnosed at

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Multiple SARS‐CoV‐2 variants have successively, or concomitantly spread worldwide since the summer of 2020. A few co‐infections with different variants were reported and genetic recombinations, common among coronaviruses, were reported or suspected based on co‐detection of signature mutations of different variants in a given genome. Here we report three infections in southern France with a Delta 21J_AY.4‐Omicron 21K/BA.1 “Deltamicron” recombinant. The hybrid genome harbors signature mutations of the two lineages, supported by a mean sequencing depth of 1163–1421 reads and a mean nucleotide diversity of 0.1%–0.6%. It is composed of the near full‐length spike gene (from codons 156–179) of an Omicron 21K/BA.1 variant in a Delta 21J/AY.4 lineage backbone. Importantly, we cultured an isolate of this recombinant and sequenced its genome. It was observed by scanning electron microscopy. As it is misidentified with current variant screening quantitative polymerase chain reaction (qPCR), we designed and implemented for routine diagnosis a specific duplex qPCR. Finally, structural analysis of the recombinant spike suggested its hybrid content could optimize viral binding to the host cell membrane. These findings prompt further studies of the virological, epidemiological, and clinical features of this recombinant.

Yersinia pestis has been found in human body lice during plague outbreaks. To evaluate the role that the human body louse plays as a vector of plague, we allowed lice to feed on rabbits made bacteremic by intravenous inoculation of 10(9) colony-forming units of 3 strains of Y. pestis. High mortality rates were observed in all lice 2 and 3 days after infection. The lice remained infected with the strains for their life span and excreted viable organisms in their feces from day 1, although they were unable to lay eggs. The lice infected with 2 virulent strains of Y. pestis transmitted the organisms during feeding to uninfected rabbits, which became septicemic and died of plague (with 1 exception) 1 day later. Infections were transmitted to naive lice that were fed on these rabbits, showing that lice can be vectors of Y. pestis in an experimental model.