Correction to: Microbial function and genital inflammation in young South African women at high risk of HIV infection

Correction to: Microbiome 8, 165 (2020) https://doi.org/10.1186/s40168-020-00932-

Coronavirus3D: 3D structural visualization of COVID-19 genomic divergence.

MotivationAs the COVID-19 pandemic is spreading around the world, the SARS-CoV-2 virus is evolving with mutations that potentially change and fine-tune functions of the proteins coded in its genome.ResultsCoronavirus3D website integrates data on the SARS-CoV-2 virus mutations with information about 3D structures of its proteins, allowing users to visually analyze the mutations in their 3D context.Availability and implementationCoronavirus3D server is freely available at https://coronavirus3d.org

Coronavirus3D: 3D structural visualization of COVID-19 genomic divergence.

MotivationAs the COVID-19 pandemic is spreading around the world, the SARS-CoV-2 virus is evolving with mutations that potentially change and fine-tune functions of the proteins coded in its genome.ResultsCoronavirus3D website integrates data on the SARS-CoV-2 virus mutations with information about 3D structures of its proteins, allowing users to visually analyze the mutations in their 3D context.Availability and implementationCoronavirus3D server is freely available at https://coronavirus3d.org

The interplay of SARS-CoV-2 evolution and constraints imposed by the structure and functionality of its proteins.

The unprecedented pace of the sequencing of the SARS-CoV-2 virus genomes provides us with unique information about the genetic changes in a single pathogen during ongoing pandemic. By the analysis of close to 200,000 genomes we show that the patterns of the SARS-CoV-2 virus mutations along its genome are closely correlated with the structural and functional features of the encoded proteins. Requirements of foldability of proteins' 3D structures and the conservation of their key functional regions, such as protein-protein interaction interfaces, are the dominant factors driving evolutionary selection in protein-coding genes. At the same time, avoidance of the host immunity leads to the abundance of mutations in other regions, resulting in high variability of the missense mutation rate along the genome. "Unexplained" peaks and valleys in the mutation rate provide hints on function for yet uncharacterized genomic regions and specific protein structural and functional features they code for. Some of these observations have immediate practical implications for the selection of target regions for PCR-based COVID-19 tests and for evaluating the risk of mutations in epitopes targeted by specific antibodies and vaccine design strategies

The interplay of SARS-CoV-2 evolution and constraints imposed by the structure and functionality of its proteins

Fast evolution of the SARS-CoV-2 virus provides us with unique information about the patterns of genetic changes in a single pathogen in the timescale of months. This data is used extensively to track the phylodynamic of the pandemic’s spread and its split into distinct clades. Here we show that the patterns of SARS-CoV-2 virus mutations along its genome are closely correlated with the structural features of the coded proteins. We show that the foldability of proteins’ 3D structures and conservation of their functions are the universal factors driving evolutionary selection in protein-coding genes. Insights from the analysis of mutation distribution in the context of the SARS-CoV-2 proteins’ structures and functions have practical implications including evaluating potential antigen epitopes or selection of primers for PCR-based COVID-19 tests

Microbial life beyond the grave: 16S rRNA gene-based metagenomic analysis of bacteria diversity and their functional profiles in cemetery environments

Recent studies have identified cemeteries as potential environmental reservoirs of multi-drug resistant pathogenic bacteria that could contaminate groundwater sources posing public health threats. However, these findings were based on the identification of culturable bacteria and at times not below burial grounds. Investigation on the bacterial diversity and functional profiles of bacterial communities above and below burial grounds in human cemeteries are few. The current study used high-throughput sequencing techniques to determine the bacterial composition and their associated functional profiles in cemetery soil samples collected at the surface and below burial ground in two South African cemeteries (Maitland Cemetery in Cape Town and Fontein Street Cemetery in Middelburg) to evaluate the potential health threat to surrounding populations through contamination of groundwater. Significant differences were observed between sample depths with the clustering of the surface (0 m) and the 2 m samples into separate groups. Pseudomonas and Corynebacterium were the most abundant genera across all samples. Pseudomonas and Rhodococcus were the dominant genera in the 2 m samples while Prauserella and Staphylococcus were dominant in the surface samples. The 2 m samples showed a lower alpha diversity but recorded higher proportions of human diseases functional classes compared to the surface samples. Human disease functional profiles revealed involvement, in infectious (cholera), neurodegenerative (Alzheimer's disease) cardiovascular (hypertrophic cardiomyopathy) immune system (Systemic lupus erythematosus) metabolic (Type I & II diabetes) diseases and cancer. Antibiotic resistance and antibiotics synthesis signatures were also identified. Thus, cemeteries could be potential sources of microbial and antibiotic pollution in groundwater, especially in areas with shallow water tables such as Maitland. Selection of sites for use as cemeteries should, therefore, require a proper understanding of the hydrogeological characteristics of the selected site. However, further studies are required to trace the actual movement of these pollutants into groundwater resources.Table S1. Total OTUs across all cemetery soil samples based on Greengene database.Table S2. Similarities and differences of OTUs between soil samples obtained from different cemeteries.Table S3. Comparison of samples based on Fisher exact test (P value<0.05) at genus level using R companion package.Table S4. Predicted functional classes of the bacterial populations extracted from soils of different cemeteries located in South Africa. The functional classes were explored using Pi-based on the KEGG database (Level 3).Table S5. Predicted functional classes of the bacterial populations extracted from soils of different cemeteries located in South Africa. The functional classes were predicted using Piphillin based on the KEGG database.Table S6. Predicted pathways based on Piphillin results using the KEGG pathway database.The South African Water Research Commission ( www.wrc.org.za ), Grant number K5/2449 ), on the hydrological, geotechnical and health impacts of cemeteries.http://www.elsevier.com/locate/scitotenv2020-03-10hj2018Geolog

The interplay of SARS-CoV-2 evolution and constraints imposed by the structure and functionality of its proteins

Fast evolution of the SARS-CoV-2 virus provides us with unique information about the patterns of genetic changes in a single pathogen in the timescale of months. This data is used extensively to track the phylodynamic of the pandemic’s spread and its split into distinct clades. Here we show that the patterns of SARS-CoV-2 virus mutations along its genome are closely correlated with the structural features of the coded proteins. We show that the foldability of proteins’ 3D structures and conservation of their functions are the universal factors driving evolutionary selection in protein-coding genes. Insights from the analysis of mutation distribution in the context of the SARS-CoV-2 proteins’ structures and functions have practical implications including evaluating potential antigen epitopes or selection of primers for PCR-based COVID-19 tests