Human coronaviruses (HCoVs), including SARS-CoV and MERS-CoV, are zoonotic
pathogens that originated in wild animals. HCoVs have large genomes that encode a fixed …

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 …

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 …

Wildlife reservoirs of broad-host-range viruses have the potential to enable evolution of viral
variants that can emerge to infect humans. In North America, there is phylogenomic …

There are outstanding evolutionary questions on the recent emergence of human
coronavirus SARS-CoV-2 including the role of reservoir species, the role of recombination …

Abstract HYpothesis testing using PHYlogenies (HyPhy) is a scriptable, open-source
package for fitting a broad range of evolutionary models to multiple sequence alignments …

Two different sarbecoviruses have caused major human outbreaks in the past two decades,.
Both of these sarbecoviruses, SARS-CoV-1 and SARS-CoV-2, engage ACE2 through the …

Inference of how evolutionary forces have shaped extant genetic diversity is a cornerstone of
modern comparative sequence analysis. Advances in sequence generation and increased …

Lymphoid tissue is a key reservoir established by HIV-1 during acute infection. It is a site
associated with viral production, storage of viral particles in immune complexes, and viral …

Exploring theoretically plausible alternative models for explaining the phenomenon under
study is a crucial step in advancing scientific knowledge. This paper advocates model …