Samoilov, A. E. | bioRxiv Science

bioRxiv2022

Identification and genetic characterization of MERS-related coronavirus isolated from Nathusius' pipistrelle (Pipistrellus nathusii) near Zvenigorod (Moscow region, Russia)

The majority of emerging infectious diseases are caused by pathogens with zoonotic origin, and most of these emerged from wildlife reservoirs. Bats are diverse, and widely distributed globally, and are the known or hypothesized reservoir of a series of emerging zoonotic viruses. Analyses of bat viromes have been used to identify novel viruses with potential to cause human infection. We characterized the fecal virome of 26 samples collected from six bat species captured during 2015 in Moscow Region. Of these 13/26 (50%) samples were found to be coronavirus positive. We sequenced and assembled the complete genome of a novel MERS-related Betacoronavirus from Pipistrellus nathusii, named MOW-BatCoV strain 15-22. Of P. nathusii 3/6 samples were found to carriers of MOW-BatCoVs. The genome organization of MOW-BatCoV/15-22 was identical to other known MERS-related coronaviruses. Phylogenetic analysis of whole genomes suggests that MOW-BatCoV/15-22 falls into a distinct subclade closely related to human and camel MERS-CoV, and MERS-related CoVs from the bat species Hypsugo savii and Pipistrellus kuhlii (from Italy) and Neoromicia capensis (from South Africa). Unexpectedly, phylogenetic analysis of the novel MOW-BatCoV 15-22 spike genes showed the closest similarity to a bat CoV Neoromicia/5038 and CoVs from Erinaceus europaeus (the European hedgehog), thus MOW-BatCoV could arise as result of recombination between ancestral viruses of bats and hedgehogs. Computer molecular docking analysis of MOW-BatCoV 15-22 Spike glycoprotein binding to DPP4 receptors of different mammal species predicted highest binding interaction with DPP4 of the bat M. brandtii (docking score -320.15) and the European hedgehog, E. europaeus (docking score -294.51). Hedgehogs are widely kept as pets, and are commonly found in areas of human habitation. Our finding of a novel bat-CoV likely able to infect hedgehogs suggests the potential for hedgehogs to act as intermediate hosts for bat-CoVs between bats and humans.

genomics↗

bioRxiv2018

Shifts in the gut microbiota structure caused by Helicobacter pylori eradication therapy

The human gut microbiome plays an important role both in health and disease. The use of antibiotics can alter gut microbiota composition, which can cause complications of various kinds. Here we report a whole genome sequencing metagenomic study of the intestinal microbiota changes caused by Helicobacter pylori eradication therapy. We have found the decrease in taxonomic alpha-diversity due to the therapy. The changes observed were more extensive for patients with duodenal ulcer and female ones. As well across the patients under the therapy we have detected the shifts in the metabolic potential and resistome. Seven KEGG pathways associated with quorum sensing, genetic Information processing and environmental Information processing were increased, while metabolic pathways related with metabolism of cofactors and vitamins and glycan biosynthesis and metabolism decreased. Changes in the resistome profile have also been identified. We observed perturbations in intraspecies structures, which were higher in group of patients under the therapy than in control group of people without treatment. The Eubacterium rectale pangenome extracted from metagenomic data were changed. We also isolated and sequenced Enterococcus faecium strains from two patients before and after eradication therapy. After the therapy this bacterium increased as the antibiotic resistance in vitro, as well the number of ARGs to macrolides and tetracyclines and metagenomic relative abundance in comparison with strains before therapy. In summary, microbial community demonstrated shift to reduce metabolic potential and to increased mechanisms, which mediate more survival condition through intraspecies perturbations.\n\nImportanceThe human gut microbiome plays an important role both in health and disease. The use of antibiotics can alter gut microbiota composition, which can cause complications of various kinds. H. pylori eradication therapy causes multiple shifts and alterations (including intraspecies changes) of the intestinal microbiota structure and leads to the accumulation of genes which determine resistance to macrolides. Since these changes are not the same for patients with various diseases, patients with duodenal ulcer may be further paid special attention for reducing side effects, such as antibiotic-induced dysbiosis. Also, study of antibiotic treatment in terms of its impact upon the human gut microbiota allows shedding light on of the complex processes that cause accumulation and spread of antibiotic resistance. An identification and understanding of these complicated processes may help to constrain antibiotic resistance spread, which is of great importance for human health care.

microbiology↗