D. L. Robertson

Lysogeny destabilizes computationally simulated microbiomes

This study shows that temperate and virulent phages affect microbiome diversity and stability differently in simulated ecosystems.

The recency and geographical origins of the bat viruses ancestral to SARS-CoV and SARS-CoV-2

The paper identifies the recent origin and geographical distribution of bat viruses ancestral to SARS-CoV and SARS-CoV-2, showing they circulated in Asia before spilling over into humans.

The origins and molecular evolution of SARS-CoV-2 lineage B.1.1.7 in the UK

This study investigates the origins and molecular evolution of SARS-CoV-2 lineage B.1.1.7 (Alpha) in the UK, finding that a chronically-infected immunocompetent individual likely drove its rapid mutation and spread.

Selection analysis identifies unusual clustered mutational changes in Omicron lineage BA.1 that likely impact Spike function

The paper identifies 13 rare mutations in the Omicron S-gene that cluster in functionally important regions and likely impact Spike function, suggesting cooperative interactions that mitigate fitness costs.

The Interferon Resistance of Transmitted HIV-1 is a Consequence of Enhanced Replicative Fitness

The paper identifies that transmitted HIV-1's interferon resistance stems from enhanced replicative fitness rather than specific IFN resistance.

Defining the Characteristics of Type I Interferon Stimulated Genes: Insight from Expression Data and Machine Learning

This paper identifies characteristics of type I interferon stimulated genes (ISGs) using expression data and machine learning, finding they are less conserved, have lower GC-content, and differ in network properties compared to non-ISGs.

Unique protein features of SARS-CoV-2 relative to other Sarbecoviruses

The paper identifies unique protein features of SARS-CoV-2 compared to other Sarbecoviruses, highlighting regions that may support human infection and transmission.

Exploring the natural origins of SARS-CoV-2 in the light of recombination

This paper traces the origins of SARS-CoV-2 to horseshoe bats in China and Southeast Asia, identifies recombination events in Sarbecoviruses, and highlights the need for more wildlife sampling to understand zoonotic spillover risks.

Recurrent emergence and transmission of a SARS-CoV-2 Spike deletion H69/V70

This paper identifies a recurrent SARS-CoV-2 Spike deletion (H69/V70) that increases infectivity and compensates for RBD mutations, suggesting it may facilitate immune escape and variant emergence.

Respiratory disease in cats associated with human-to-cat transmission of SARS-CoV-2 in the UK

This study reports two cases of SARS-CoV-2 infection in UK cats linked to human-to-cat transmission, showing mild to severe respiratory disease and genetic variation in the viral genome.

Bacteriophage deficiency characterizes respiratory virome dysbiosis in childhood asthma

The paper examines the respiratory virome in preschool children with and without asthma during asymptomatic periods, finding bacteriophage deficiency and increased eukaryotic viral presence in asthmatic children.

Natural selection in the evolution of SARS-CoV-2 in bats, not humans, created a highly capable human pathogen

The paper shows SARS-CoV-2's ability to infect humans stems from its evolutionary history in bats, not human adaptation, with evidence of positive selection in bat viruses and weak purifying selection in SARS-CoV-2.

Evolutionary origins of the SARS-CoV-2 sarbecovirus lineage responsible for the COVID-19 pandemic

This paper estimates the divergence date of SARS-CoV-2 from its bat reservoir to be between 1948 and 1982, identifies non-recombinant regions for phylogenetic analysis, and highlights the role of horseshoe bats in viral emergence.