Estimates of early outbreak-specific SARS-CoV-2 epidemiological parameters from genomic data.

We estimate the basic reproductive number and case counts for 15 distinct Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) outbreaks, distributed across 11 populations (10 countries and one cruise ship), based solely on phylodynamic analyses of genomic data. Our results indicate that, prior to significant public health interventions, the reproductive numbers for 10 (out of 15) of these outbreaks are similar, with median posterior estimates ranging between 1.4 and 2.

Swiss public health measures associated with reduced SARS-CoV-2 transmission using genome data.

Genome sequences from evolving infectious pathogens allow quantification of case introductions and local transmission dynamics. We sequenced 11,357 severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genomes from Switzerland in 2020-the sixth largest effort globally. Using a representative subset of these data, we estimated viral introductions to Switzerland and their persistence over the course of 2020.

Quantification of the spread of SARS-CoV-2 variant B.1.1.7 in Switzerland.

Background: In December 2020, the United Kingdom (UK) reported a SARS-CoV-2 Variant of Concern (VoC) which is now named B.1.1.

The origin and early spread of SARS-CoV-2 in Europe.

The investigation of migratory patterns during the SARS-CoV-2 pandemic before spring 2020 border closures in Europe is a crucial first step toward an in-depth evaluation of border closure policies. Here we analyze viral genome sequences using a phylodynamic model with geographic structure to estimate the origin and spread of SARS-CoV-2 in Europe prior to border closures. Based on SARS-CoV-2 genomes, we reconstruct a partial transmission tree of the early pandemic and coinfer the geographic location of ancestral lineages as well as the number of migration events into and between European regions.

Metagenomic analysis reveals distinct patterns of denitrification gene abundance across soil moisture, nitrate gradients.

This study coupled a landscape-scale metagenomic survey of denitrification gene abundance in soils with in situ denitrification measurements to show how environmental factors shape distinct denitrification communities that exhibit varying denitrification activity. Across a hydrologic gradient, the distribution of total denitrification genes (nap/nar + nirK/nirS + cNor/qNor + nosZ) inferred from metagenomic read abundance exhibited no consistent patterns. However, when genes were considered independently, nirS, cNor and nosZ read abundance was positively associated with areas of higher soil moisture, higher nitrate and higher annual denitrification rates, whereas nirK and qNor read abundance was negatively associated with these factors.

Greenhouse Gas Emissions from Septic Systems in New York State.

Onsite septic systems use microbial processes to eliminate organic wastes and nutrients such as nitrogen; these processes can contribute to air pollution through the release of greenhouse gases (GHGs). Current USEPA estimates for septic system GHG emissions are based on one study conducted in north-central California and are limited to methane; therefore, the contribution of these systems to the overall GHG emission budget is unclear. This study quantified and compared septic system GHG emissions from the soil over leach fields and the roof vent, which are the most likely locations for gas emissions during normal septic system operation.