R. A. Goldstein

Within-host diversity improves phylogenetic and transmission reconstruction of SARS-CoV-2 outbreaks

This study shows that incorporating within-host genetic diversity improves phylogenetic and transmission reconstruction of SARS-CoV-2 outbreaks.

SARS-CoV-2 convergent evolution cannot be reliably inferred from phylogenetic analyses

This paper develops a method to detect homoplasy in SARS-CoV-2 phylogenetic trees and finds that phylogenetics provides limited support for convergent evolution.

Whole genome sequencing of Herpes Simplex Virus 1 directly from human cerebrospinal fluid reveals selective constraints in neurotropic viruses.

This study uses whole genome sequencing of HSV-1 from CSF and skin lesions to identify selective constraints and recombination patterns in neurotropic viruses.

In Vivo Emergence of a Novel Protease Inhibitor Resistance Signature in HIV-1 Matrix

The paper identifies a novel protease inhibitor resistance signature in HIV-1 matrix through genotypic and phenotypic analysis of patients failing PI therapy.

Preadaptation of pandemic GII.4 noroviruses in hidden virus reservoirs years before emergence

This paper shows that GII.4 noroviruses preadapt and circulate undetected for years before causing a new pandemic, with changes in host immunity enabling spread rather than genetic changes alone.