Recombination is a pervasive process generating diversity in most viruses. It joins variants
that arise independently within the same molecule, creating new opportunities for viruses to …

High-throughput genomic sequencing is rapidly changing the field of phylogenetics by
decreasing the cost and increasing the quantity and rate of data collection by several orders …

The animal reservoir of SARS-CoV-2 is unknown despite reports of SARS-CoV-2-related
viruses in Asian Rhinolophus bats,,–, including the closest virus from R. affinis, RaTG13 …

Understanding the circumstances that lead to pandemics is important for their prevention.
We analyzed the genomic diversity of severe acute respiratory syndrome coronavirus 2 …

The SARS-CoV-2 epidemic in southern Africa has been characterized by three distinct
waves. The first was associated with a mix of SARS-CoV-2 lineages, while the second and …

Virus host shifts are generally associated with novel adaptations to exploit the cells of the
new host species optimally. Surprisingly, Severe Acute Respiratory Syndrome Coronavirus …

There is intense interest in antibody immunity to coronaviruses. However, it is unknown if
coronaviruses evolve to escape such immunity, and if so, how rapidly. Here we address this …

The lack of an identifiable intermediate host species for the proximal animal ancestor of
SARS-CoV-2, and the large geographical distance between Wuhan and where the closest …

The emergence of new sequencing technologies has facilitated the use of bacterial whole
genome alignments for evolutionary studies and outbreak analyses. These datasets, of …

Abstract Background The 16S rRNA gene is used extensively in bacterial phylogenetics, in
species delineation, and now widely in microbiome studies. However, the gene suffers from …