Wastewater surveillance locally and globally is important for the investigation of the molecular epidemiological features of SARS-CoV-2 in the environment. The current study investigated the genomic diversity and mutation profile of SARS-CoV-2 variants in wastewater for the period spanning COVID-19 pandemic up to December, 2022. A total of 3618 complete SARS-CoV-2 genome sequences from waste water samples submitted to the GISAID database were retrieved. The SARS-CoV-2 sequences were subjected to pairwise alignment against reference, followed by clade and lineage assignment (based on Nextstrain, GISAID and Pango), distance metric phylogenetic analysis, and detection of substitution mutations. Following GISAID, Nextstrain, and Pango nomenclatures, an overall agreement in clade and lineage determination in wastewater samples was observed. There was successive appearance, dissemination, and disappearance of SARS-CoV-2 lineages along time in wastewater. The SARS-CoV-2 genomes from wastewater were clustered into the variants of concern (VOC) as Alpha GRY (B.1.1.7 + Q.7), Delta GK (B.1.617.2 + AY.*), and Omicron GRA (BA.1*, BA.2* + B.1.1.529, BA.5*). The evolutionary rate was 9.63e-04 substitutions/site/year for SARS-CoV-2 in wastewater. B.1.1.7 was less prevalent than B.1.617.2 in 2021, appeared in succession, and BA.1, BA.2, BA.5 were serially detected in 2022, the latter strain continued to persist in wastewater. The N501Y, E484K/Q, K417N/T, L452R, T478K spike substitutions remained dominant attribute of SARS-CoV-2 VOCs. The study underlines the importance of wastewater surveillance for enumerating spatiotemporal diversity of SARS-CoV-2 variants and mutations, which might pave the way for novel antiviral and vaccine designing towards management and prevention of SARS-CoV-2 infection.

Lacticaseibacillus rhamnosus (L. rhamnosus) is widely recognized as a probiotic species, and it exists in a variety of environments including host gut and dairy products. This work aimed at conducting a large-scale comparative genomics analysis of 384 L. rhamnosus genomes (257 whole-sequence or metagenomic-assembled genomes from gut-associated isolates [122 and 135 retrieved from the UHGG and NCBI databases, respectively] and 127 genomes from dairy isolates [34 from the NCBI database; 93 isolated from a cheese sample and sequenced here]). Our results showed that L. rhamnosus had a large and open pan-genome (15,253 pan-genes identified from all 384 genomes; 15,028 pan-genes if the 93 cheese-originated isolates were excluded). The core-gene phylogenetic tree constructed from the 384 L. rhamnosus genomes comprised five phylogenetic branches, with a random distribution of dairy and gut-associated isolates/genomes across the tree. No significant difference was identified in the overall profile of metabolism-related genes between dairy and gut-associated genomes; however, notably, the gut-associated strains/isolates contained more genes coding for specific metabolic pathways and carbohydrate-active enzymes, e.g., lacto-N-biosidase (EC 3.2.1.140; GT20) and lacto-N-biose phosphorylase/galacto-N-biose phosphorylase (EC 2.4.1.211; GH112). Further, we found that there was obvious intra-species diversification of the 93 cheese-originated L. rhamnosus isolates, forming three clades (Clades A, B, and C) in the reconstructed core-gene phylogenetic tree. There were numerous single nucleotide variations (over 10,000) across the three clades. Moreover, significant differences were observed in the content of metabolism-related genes across clades (p < 0.05, Adonis test), characterized by the enrichment in glycoside hydrolases in Clade C and the possession of unique metabolic pathways in each clade. These results implicated genomics/functional diversification of L. rhamnosus in a single food matrix and niche-driven adaptive evolution of isolates from dairy and host gut-associated origins. Our study shed insights into the selection of candidate strains for food industry applications.

Torque teno virus (TTV) is considered to be an ubiquitous member of the commensal human blood virome commonly reported in mixed genotype co-infections. This study investigates the genomic diversity of TTV in blood samples from 816 febrile Tanzanian children. Metagenomic next-generation sequencing was used to screen for TTV in individual blood samples from a cohort of 816 febrile Tanzanian paediatric outpatients. For positive samples, the number of TTV species and genotypes present were evaluated. We investigate the linear relationship between individual TTV diversity and the patient age by linear regression. TTV was detected in 97.2% of sera. ORF1 analysis revealed the presence of 149 genotypes from 38 species, suggesting the presence of 13 new species. These genotypes were mostly present as co-infections with a median of 11 genotypes/subject (range: 1−71). In terms of species, we found a median of nine species/subject (range: 1−29). We further show a significant association between the diversity of co-detected TTV and the age of the subjects (p value < 0.0001). This study shows that significant TTV genomic diversity is acquired by the age of five and that this diversity tends to increase with age, which indicates a repetitive TTV acquisition during the first months/years of life.

As genomic-scale data sets become economically feasible for most organisms, a key question for conservation biology is whether the increased resolution offered by new genomic approaches justifies repeating earlier studies based on traditional markers, rather than investing those same time and monetary resources in less-known species. Genomic studies offer clear advantages when the objective is to identify adaptive loci that may be critical to conservation policy-makers. However, the answer is far less certain for the population and landscape studies based on neutral loci that dominate the conservation genetics research agenda. We used RADseq to revisit earlier molecular studies of the IUCN Critically Endangered Magdalena River turtle (Podocnemis lewyana), documenting the conservation insights gained by increasing the number of neutral markers by several orders of magnitude. Earlier research indicated that P. lewyana has the lowest genetic diversity known for any chelonian, and little or no population differentiation among independent rivers. In contrast, the RADseq data revealed discrete population structure with isolation-by-distance within river segments and identified precise population breaks clearly delineating management units. It also confirmed that the species does not have extremely low heterozygosity and that effective population sizes are probably sufficient to maintain long-term evolutionary potential. Contrary to earlier inferences from more limited population genetic markers, our genomic data suggest that management strategies should shift from active genetic rescue to more passive protection without extreme interventions. We conclude with a list of examples of conservation studies in other vertebrates indicating that for many systems a genomic update is worth the investment.