Objectives HCoV-HKU1 diversity and evolution was scarcely studied. We performed next-generation sequencing (NGS) and analysis of HCoV-HKU1 genomes over five years. Methods NGS used Illumina technology on NovaSeq 6000 following whole genome PCR amplification by a in-house set of primers designed using Gemi and PrimalScheme. Genome assembly and analyses used CLC Genomics, Mafft, BioEdit, Nextstrain, Nextclade, MEGA and iTol bioinformatic tools. Spike molecular modelling and dynamics simulations used Molegro Molecular Viewer/Hyperchem. Results Twenty-eight PCR systems allowed obtaining 158 HCoV-HKU1 genomes including 69 and 89 of genotype A and B, respectively. Both genotypes co-circulated during the study period but one predominated each year. 1,683 amino acid substitutions including 80 in ≥10 genomes were detected in genotype A relatively to a 2004 reference. H512R in spike, first detected in 2009 and reported as involved in antibody neutralization, was found in all genotype A, almost always with V387I and K478N, and was predicted here to significantly improve cellular TMPRSS2 protein binding. 1,802 amino acid substitutions including 64 in ≥10 genomes were detected in genotype B relatively to a 2005 reference. Conclusion This study substantially expands the global set of HCoV-HKU1 genomes. Genomics with protein structural analyses contributed to our understanding of HCoV-HKU1 evolution.

The diversity and evolution of the genomes of Human Bocavirus (HBoV), which causes respiratory diseases, have been scarcely studied. Here, we aimed to obtain and characterize HBoV genomes from patients’s nasopharyngeal samples collected between 2017-2022 period (five years). Next-generation sequencing (NGS) used Illumina technology after having implemented using GEMI an in-house multiplex PCR amplification strategy. Genomes were assembled and analyzed with CLC Genomics, Mafft, BioEdit, MeV, Nextclade, MEGA, and iTol. A total of 213 genomes were obtained. Phylogeny classified them all as of Bocavirus 1 (HBoV1) species. Five HBoV1 genotypes determined by hierarchical clustering analysis of 27 variable genome positions were scattered over the study period although with differences in yearly prevalence. A total of 167 amino acid substitutions were detected. Besides, coinfection was observed for 52% of the samples, rhinoviruses then adenoviruses (HAdVs) being the most common viruses. Principal component analysis showed that HBoV1 genotype α tended to be significantly correlated with HAdV co-infection. Subsequent HAdV typing for HBoV1-positive samples and negative controls demonstrated that HAdVC species predominated but HAdVB was that significantly HBoV1-associated. Overall, we described here the first HBoV1 genomes sequenced for France. HBoV1 and HAdVB association deserves further investigation.

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.