Culture and identification of a "Deltamicron" SARS-CoV-2 in a three cases cluster in southern France.

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.

Performance and pre-analytical stability of self-collected samples versus clinician cervical samples for the detection of HPV16, HPV18 and a pool of 12 other HPV types on the Roche Cobas 8800 System.

This study aimed to validate the agreement between human papillomavirus (HPV) tests self-collected samples versus clinician cervical specimens, and the pre-analytical stability of self-sampling. One hundred and fifty-seven women aged between 25 and 65 years who presented to the gynaecological department of the "CLEMENTVILLE" clinic in Montpellier voluntarily participated in HPV screening by self-sampling. Polymerase chain reaction was used to detect the presence of HPV16, HPV18 and a pool of 12 other HPV types on the Roche Cobas 8800 System. Median age was 40 years (range 20-73 and IQR 31-49 years). The overall HPV prevalence on the population studied was 27%. The agreement between clinician cervical samples and self-collected vaginal presented good agreement (Kappa =0.90) and high sensitivity (0.91) and specificity (0.98). For swabs stored for 7 days at room temperature, the HPV results presented substantial agreement (Kappa =0.89) and high sensitivity (0.97) and specificity (0.93). Our data showed that the HPV assay performed in the self-collected vaginal samples have high consistency of results with the clinician cervical samples. The use of self-collected cervical sample could be a simple and inexpensive approach in cervical cancer screening programs due to their high pre-analytical stability.

Rapid and Accurate Diagnosis of Dermatophyte Infections Using the DendrisCHIP® Technology.

Dermatophytosis is a superficial fungal infection with an ever-increasing number of patients. Culture-based mycology remains the most commonly used diagnosis, but it takes around four weeks to identify the causative agent. Therefore, routine clinical laboratories need rapid, high throughput, and accurate species-specific analytical methods for diagnosis and therapeutic management. Based on these requirements, we investigated the feasibility of DendrisCHIP® technology as an innovative molecular diagnostic method for the identification of a subset of 13 pathogens potentially responsible for dermatophytosis infections in clinical samples. This technology is based on DNA microarray, which potentially enables the detection and discrimination of several germs in a single sample. A major originality of DendrisCHIP® technology is the use of a decision algorithm for probability presence or absence of pathogens based on machine learning methods. In this study, the diagnosis of dermatophyte infection was carried out on more than 284 isolates by conventional microbial culture and DendrisCHIP®DP, which correspond to the DendrisCHIP® carrying oligoprobes of the targeted pathogens implicated in dermatophytosis. While convergence ranging from 75 to 86% depending on the sampling procedure was obtained with both methods, the DendrisCHIP®DP proved to identify more isolates with pathogens that escaped the culture method. These results were confirmed at 86% by a third method, which was either a specific RT-PCR or genome sequencing. In addition, diagnostic results with DendrisCHIP®DP can be obtained within a day. This faster and more accurate identification of fungal pathogens with DendrisCHIP®DP enables the clinician to quickly and successfully implement appropriate antifungal treatment to prevent the spread and elimination of dermatophyte infection. Taken together, these results demonstrate that this technology is a very promising method for routine diagnosis of dermatophytosis.