The number of SARS-CoV-2 recombinants identified during the pandemic has increased since the era of Omicron variants, but XBB.1.5 (or Omicron 23A) is the first lineage comprised of hybrid genomes to predominate at the country and global scales. Very interestingly, the XBB.1.5 recombinant, like the Marseille-4B subvariant (B.1.160/20A.EU2) and the pandemic variant B.1.1.7 (20I/Alpha) previously, has its ORF8 gene inactivated by a stop codon. XBB.1.5 was generated through two successive main events: a recombination between SARS-CoV-2 of lineages BA.2.10.1.1 (BJ.1) and BA.2 75.3.1.1.1 (BM.1.1.1) that generated the XBB (22F) lineage; then ORF8 gene inactivation by a stop codon. We further identified that a stop codon was present at 89 (74%) codons of the ORF8 gene in ≥1 of 15,222,404 genomes available in GISAID, and at 15 codons (12%) in ≥1,000 genomes. Thus, it is very likely that stop codons in ORF8 gene contributed on at least 3 occasions and independently during the SARS-CoV-2 pandemic to the evolutionary success of a lineage that became transiently predominant, most recently XBB.1.5. Such association of gene loss with evolutionary success, which suits the recently described Mistigri rule, is an important biological phenomenon very unknown in virology while largely described in cellular organisms.

The role of hydroxychloroquine (HCQ) in lowering the viral load of patients with COVID-19 is controversial. In our Institute, we treated more than 30,000 people with COVID-19 in 2020 and 2021, using the same diagnostic tools and the same treatment dosages. In this retrospective comparative study of data collected over this period, we aimed to compare the viral clearance in the nasopharynx as determined by qPCR in patients who were treated with HCQ and those who were not. As a new feature, we adjusted the data according to the most significant confounding factors (age, initial viral load, and timescale between the onset of symptoms and treatment). Of the 1 276 patients selected from our database, 776 were treated with HCQ and 500 were not. Viral clearance in the treatment group was reached significantly earlier than in the non-treatment group, at days 5, 10 and 30. These differences remain significant after adjustments for confounding factors. In conclusion, although age, initial viral load, and time to treatment do influence the viral load in patients with COVID-19, hydroxychloroquine associated with azithromycin still independently significantly lowered viral load more rapidly than other treatments, including azithromycin alone.

The human head louse (Pediculus humanus capitis) is an obligate ectoparasite of humans and has the potential to uncover aspects of human history that cannot be directly inferred from genetic data derived from humans. Previous studies have shown that global louse populations exhibit restricted patterns of genetic variation. However, these studies were restricted both genetically and lacked a global sampling. With the aim of capturing the genetic diversity of head louse populations from around the world, we generated whole genome sequences of human head lice from 43 countries, spanning five continents and Oceania, to determine if louse nuclear diversity mirrors its mitochondrial haplotypes or if population genetic structure, genetic diversity, and population connectivity are associated with geographical regions or host behavior. Here we show that there are five nuclear genetic clusters that are associated with large geographical regions, either at continental or intercontinental levels. High genetic variation was found between African and non-African individuals and the highest genetic diversity was found in samples from sub-Saharan Africa, similar to that of humans. Unlike the mitochondrial clades examined in previous studies, nuclear genetic clusters of lice examined here are highly structured based on geography (continentally and major regions within continents). Results from our genome analyses revealed that host-mediated global dispersal as the likely primary process in shaping diversity and maintaining genetic population boundaries within the nuclear genome of the human head louse.

The increasingly wide knowledge of the microbiota, as well as its continuous relation with several pathologies, favours the interest, discovery and classification of all the bacteria that are part of it. The isolation of strain P3519T is possible thanks to the application of new strategies such as culturomics and taxono-genomics. Strain Marseille-P3519T isolated from the fecal flora of a 25-year-old healthy French woman was a Gram-positive anaerobic bacterium, non-motile and non-spore-forming. The 16S rRNA gene sequence of Marseille-P3519 showed 98.57% of sequence similarity with Lactobacillus caviae MOZM2, the closest species, phylogenetically. Its genome had 2,237,367 bp with 45.42 mol% of G+C content. These findings support that strain Marseille-P3519 is a new member of the genus Lactobacillus for which the name Lactobacillus caccae sp. nov., is proposed.