K. Koelle

Influenza A genomic diversity during human infections underscores the strength of genetic drift and the existence of tight transmission bottlenecks

This paper analyzes defective viral genomes (DVGs) in influenza A virus infections to show genetic drift drives within-host evolution and transmission bottlenecks limit between-host spread.

Genetic drift and purifying selection shape within-host influenza A virus populations during natural swine infections

This study examines within-host influenza A virus diversity and evolution in swine, finding low genetic diversity and evidence of purifying selection and genetic drift.

Transmission bottleneck size estimation from de novo viral genetic variation

This paper estimates transmission bottleneck sizes using de novo viral genetic variation in recipients, finding tight bottlenecks for influenza A and SARS-CoV-2.

Epidemiological inference for emerging viruses using segregating sites

This paper introduces a tree-free method to infer epidemiological parameters from viral sequence data by analyzing segregating site trajectories, showing it can estimate reproduction numbers and index case timing accurately.

Within-host evolutionary dynamics and tissue compartmentalization during acute SARS-CoV-2 infection

This study uses daily saliva and nasal samples to track SARS-CoV-2 genetic variants in infected individuals, revealing stochastic evolution, mutational hotspots, and compartmentalization between sample sites.

Influenza A virus reassortment in mammals gives rise to genetically distinct within-host sub-populations

This study examines reassortment dynamics of influenza A virus in guinea pigs, ferrets, and swine, finding reassortment is common but more frequent in ferrets and guinea pigs than swine, with spatial compartmentalization observed.

Influenza A virus undergoes compartmentalized replication in vivo dominated by stochastic bottlenecks

This study tracks influenza A virus diversity in ferrets, showing compartmentalized replication and stochastic bottlenecks shaping genetic diversity within lung lobes.

Fitness estimation for viral variants in the context of cellular coinfection

This study develops models to estimate viral variant fitness in the context of cellular coinfection and applies them to H5N1 data, finding previous estimates may have underestimated fitness advantages.

Heterogeneity in viral infections increases the rate of deleterious mutation accumulation

The paper shows that viral coinfection and cellular heterogeneity in viral output increase the rate of deleterious mutation accumulation during replication.

Limited within-host diversity and tight transmission bottlenecks limit SARS-CoV-2 evolution in acutely infected individuals

The paper analyzes SARS-CoV-2 within-host diversity and transmission bottlenecks in acute infections, finding limited diversity and narrow bottlenecks that restrict variant spread.

Reanalysis of deep-sequencing data from Austria points towards a small SARS-COV-2 transmission bottleneck on the order of one to three virions

The paper reanalyzes SARS-CoV-2 deep-sequencing data from Austria and finds the transmission bottleneck is likely very tight, with 1-3 virions.

Avian influenza A viruses reassort and diversify differently in mallards and mammals

This study compares avian influenza A virus reassortment in mallards and guinea pigs, finding higher reassortant frequencies and diversity in mallards.

Transmission of SARS-CoV-2 in domestic cats imposes a narrow bottleneck

This study shows SARS-CoV-2 in cats has limited within-host genetic variation and a narrow transmission bottleneck, with a variant H655Y emerging and spreading across transmission pairs.

Recombinant SARS-CoV-2 genomes are currently circulating at low levels

The paper identifies 1175 putative recombinant SARS-CoV-2 genomes from over 537,000 sequences, estimates they make up at most 5% of circulating viruses in the USA and UK, and highlights substitutions of concern in some recombinants.

The Dynamics of Influenza A H3N2 Defective Viral Genomes from a Human Challenge Study

This study analyzes defective viral genomes (DVGs) in longitudinal human challenge studies of influenza A H3N2, finding genetic drift drives their evolution rather than selection.

CpG-creating Mutations are Costly in Many Human Viruses

The paper examines the cost of CpG-creating mutations in various human viruses using existing genomic data and finds they are generally costly.

Impact of preexisting virus-specific maternal antibodies on cytomegalovirus population genetics in a monkey model of congenital transmission

This study examines how maternal antibodies affect CMV genetic diversity in a monkey model, finding no impact on viral genetic diversity despite reduced viral load and congenital transmission.

Coinfection of semi-infectious particles can contribute substantially to influenza infection dynamics

The paper models the role of semi-infectious particles and coinfection in influenza dynamics, finding SIPs significantly contribute to viral load and co-infection is frequent during early infection.

Genetic signatures of human cytomegalovirus variants acquired by seronegative glycoprotein B vaccinees

This paper analyzes the genetic composition of HCMV variants in gB vaccinees and placebo recipients, finding reduced viral shedding and altered viral population dynamics in vaccinated individuals.

Why Are CD8 T Cell Epitopes of Human Influenza A Virus Conserved?

This paper investigates why CD8 T cell epitopes of influenza A virus are conserved, proposing mechanisms that explain their persistence despite potential escape variants.

Selection on non-antigenic gene segments of seasonal influenza A virus and its impact on adaptive evolution

This study develops a population genetic model to show that selection on non-antigenic gene segments influences the adaptive evolution and lineage turnover of seasonal influenza A/H3N2 virus.

Preexisting antibodies can protect against congenital cytomegalovirus infection in monkeys

This study shows that preexisting antibodies can prevent congenital cytomegalovirus infection in monkeys by blocking placental transmission.

Transmission Bottleneck Size Estimation from Pathogen Deep-Sequencing Data, with an Application to Human Influenza A Virus

This paper introduces a beta-binomial sampling method to estimate transmission bottleneck sizes from pathogen sequencing data, showing it outperforms existing methods and finding a mean bottleneck size of 196 virions for influenza A virus.