Detection of SARS-CoV-2 variants in hospital wastewater in Peru, 2022. / Detección de variantes del SARS-CoV-2 en aguas residuales de hospitales en Perú, 2022.

OBJECTIVE.: To identify the presence of the SARS-CoV-2 virus in wastewater from hospitals in Peru. MATERIALS AND METHODS.: Water samples were collected from the effluents of nine hospitals in Peru during March and September 2022. SARS-CoV-2 was identified by using Illumina sequencing. Variant, lineage and clade assignments were carried out using the Illumina and Nextclado tools. We verified whether the SARS-CoV-2 variants obtained from wastewater were similar to those reported by the National Institute of Health of Peru from patients during the same period and region. RESULTS.: Eighteen of the 20 hospital wastewater samples (90%) provided sequences of sufficient quality to be classified as the Omicron variant according to the WHO classification. Among them, six (30%) were assigned by Nextclade to clades 21K lineage BA.1.1 (n=1), 21L lineage BA.2 (n=2), and 22B lineages BA.5.1 (n=2) and BA .5.5 (n=1). CONCLUSIONS.: SARS-CoV-2 variants were found in hospital wastewater samples and were similar to those reported by the surveillance system in patients during the same weeks and geographic areas. Wastewater monitoring could provide information on the environmental and temporal variation of viruses such as SARS-CoV-2.Motivation for the study. To contribute to the surveillance of environmental samples from hospital effluents in order to achieve early warning of possible infectious disease outbreaks. Main findings. The Omicron variant of the COVID-19 virus was detected in wastewater from hospitals in Puno, Cuzco and Cajamarca; these results are similar to the reports by the Peruvian National Institute of Health based on nasopharyngeal swab samples. Implications. The presence of the Omicron variant in hospital wastewater during the third wave of the pandemic should raise awareness of the treatment system before wastewater is discharged into the public sewer system.

Identification of Xenologs and Their Characteristic Low Expression Levels in the Cyanobacterium Synechococcus elongatus.

Horizontal gene transfer (HGT) is a central process in prokaryotic evolution. Once a gene is introduced into a genome by HGT, its contribution to the fitness of the recipient cell depends in part on its expression level. Here we show that in Synechococcus elongatus PCC 7942, xenologs derived from non-cyanobacterial sources exhibited lower expression levels than native genes in the genome. In accord with our observation, xenolog codon adaptation indexes also displayed relatively low expression values. These results are in agreement with previous reports that suggested the relative neutrality of most xenologs. However, we also demonstrated that some of the xenologs detected participated in cellular functions, including iron starvation acclimation and nitrate reduction, which corroborate the role of HGT in bacterial adaptation. For example, the expression levels of some of the xenologs detected are known to increase under iron-limiting conditions. We interpreted the overall pattern as an indication that there is a selection pressure against high expression levels of xenologs. However, when a xenolog protein product confers a selective advantage, natural selection can further modulate its expression level to meet the requirements of the recipient cell. In addition, we show that ORFans did not exhibit significantly lower expression levels than native genes in the genome, which suggested an origin other than xenology.

Halomonas nitroreducens sp. nov., a novel nitrate- and nitrite-reducing species.

We have carried out a polyphasic taxonomic study of strain 11ST, a halophilic, Gram-negative bacterium that is able to respire on nitrate and nitrite in anaerobiosis. Strain 11ST was isolated from a solar saltern in Cahuil, a region next to Pichilemu (Chile). It grows at NaCl concentrations within the range of 3-20 % w/v (optimum 5-7.5 %), temperatures from 4 to 45 degrees C (optimum 20-32 degrees C) and within a pH range of 5-10 (optimum pH 7-9). Its 16S rRNA gene sequence indicates that it belongs to the genus Halomonas in the class Gammaproteobacteria. Its closest relatives are Halomonas alimentaria, H. denitrificans, H. organivorans and H. ventosae, with the type strains of which our strain showed maximum 16S rRNA gene sequence similarity values of 97.1-98.1 %. Its G+C content is 65.3 mol%. DNA-DNA hybridization studies showed 54.2 % relatedness between strain 11ST and H. alimentaria DSM 15356T and 47.2 % relatedness between strain 11ST and H. organivorans CECT 5995T. Lower DNA-DNA hybridization percentages were obtained against the type strains of other related Halomonas species. Its major fatty acids are C12 : 0 3-OH (5.56 %), iso-C15 : 0 2-OH/C16 : 1 omega 7c (22.30 %), C16 : 0 (27.80 %) and C18 : 1 omega 7c (29.92 %). The proposed name for the novel species is Halomonas nitroreducens sp. nov., with strain 11ST (=CECT 7281T =LMG 24185T) being the type strain.