Revealing fine-scale spatiotemporal differences in SARS-CoV-2 introduction and spread.
Moreno, Braun, Riemersma et al. Nat Comms. 2020
In spring 2020, Milwaukee County had over 20-fold higher rates of SARS-CoV-2 infection per capita than did nearby Dane County, where Madison is located. We use genomic epidemiology to reveal dramatic differences in the patterns of SARS-CoV-2 introduction and spread. Our data also suggest that Wisconsin’s Safer at Home order reduced SARS-CoV-2 transmission. We speculate that demographic, socioeconomic, and other human factors account for much of the difference in virus spread in Milwaukee vs. Dane Counties.
Using virus sequencing to determine source of SARS-CoV-2 transmission for healthcare worker.
Safdar et al. Emerg Infect Dis. 2020
We have been applying molecular epidemiology to determine whether healthcare workers who become infected with SARS-CoV-2 were likely infected in a professional setting or in the community outside the hospital. This case report shows that a healthcare worker appeared to acquire SARS-CoV-2 in the community and not through treatment of known positive patients.
Molecularly barcoded Zika virus libraries to probe in vivo evolutionary dynamics.
Aliota et al. PLoS Pathog. 2018
A collaborative study in which we constructed libraries of Zika viruses bearing randomized silent mutations (molecular barcodes) to define how viral diversity changes with time during infection.
Infection via mosquito bite alters Zika virus tissue tropism and replication kinetics in rhesus macaques.
Dudley et al. Nat Commun. 2017
Here we show that infected mosquitoes can deliver Zika virus to macaque monkeys. Mosquito infection delayed the time to peak virus load and was associated with dramatic changes in Zika virus genetic diversity in infected monkeys. Mosquito infection is tractable in the laboratory and may slow the pace of Zika evolution.
Oropharyngeal mucosal transmission of Zika virus in rhesus macaques.
Newman et al. Nat Commun. 2017
Human case reports suggest that Zika virus could, in certain circumstances, be transmitted by kissing or other contact. We used a nonhuman primate model to show that transmission via oral exposure is theoretically possible, but likely requires a high dose of virus that is not found in body fluids of most Zika-infected individuals.
Deep Sequencing Reveals Potential Antigenic Variants at Low Frequencies in Influenza A Virus-Infected Humans.
Dinis, Florek et al. J Virol. 2016
Using Illumina deep sequencing, we examined the genetic diversity of influenza viruses infecting individual humans. We found some mutants with the potential to escape from antibody responses, but these were always present at low frequency and there was no evidence that natural selection was acting to increase their frequency. This study suggests that beneficial influenza virus variants are not efficiently selected over the course of a single human infection.
Transmission of SARS-CoV-2 in cats imposes a narrow genetic bottleneck.
Braun, Moreno, et al. biorxiv. 2020
Transmission between hosts imposes a genetic bottleneck on respiratory viruses. The number of genetically distinct viruses that are transferred between hosts in a typical bottleneck (the “bottleneck size”) may differ for different viruses and transmission routes. In a domestic cat model, we show that SARS-CoV-2 transmission between hosts appears to involve stringent bottlenecks, in which only a few viruses are transmitted. Narrow bottlenecks may constrain the pace of SARS-CoV-2 evolution.
Quantifying within-host diversity of H5N1 influenza viruses in humans and poultry in Cambodia.
Moncla et al. PLoS Pathog. 2020
Avian influenza viruses pose a pandemic threat, and it is critical to understand their evolutionary potential in humans. Here we characterize H5N1 avian influenza viruses infecting humans and poultry in Cambodia. Our data show that H5N1 viruses generate putative human-adapting mutations during natural spillover infection, many of which are detected at >5% frequency within-host. However, short infection times, genetic drift, and purifying selection likely restrict their ability to evolve extensively during a single infection.
Diversity of Influenza A(H5N1) Viruses in Infected Humans, Northern Vietnam, 2004-2010.
Imai et al. Emerg Infect Dis. 2018
We define genetic and phenotypic diversity of H5N1 avian influenza viruses infecting humans. Surprisingly, although we detect within-host diversity, there is little evidence for adaptation to humans during a single spillover infection.
An updated influenza A(H3N2) vaccine generates limited antibody responses to previously encountered antigens in children.
Florek et al. Vaccine. 2018
It has been proposed that vaccines containing antigenically novel influenza strains can also boost responses to previously circulating strains. Here we show that this “back boost” effect is weak in children, who have limited influenza exposure histories.
Selective Bottlenecks Shape Evolutionary Pathways Taken during Mammalian Adaptation of a 1918-like Avian Influenza Virus.
Moncla et al. Cell Host Microbe. 2016
This study shows that transmission bottlenecks might become more selective and less random as avian influenza viruses adapt to airborne transmission in mammals. This suggests that natural selection could drive a kind of “phase transition” in avian flu host jumping, accelerating adaptation once beneficial variants randomly arise.
This paper is the cornerstone of one of our major current projects and was a featured article in Cell Host & Microbe.
Selection on haemagglutinin imposes a bottleneck during mammalian transmission of reassortant H5N1 influenza viruses.
Wilker, Dinis et al. Nat Commun. 2013
Here we show that natural selection on the hemagglutinin attachment protein drives genetic bottlenecks as H5N1 influenza viruses adapt to become transmissible between mammals. We further show that viral variants present frequencies as low as 6% in one host can be transmitted by respiratory droplet.
These findings established our interest in transmission bottlenecks and suggest that natural selection could effectively winnow low-frequency transmissible variants from within a viral population.