User profiles for O. Pybus
Oliver PybusUniversity of Oxford / Royal Veterinary College Verified email at zoo.ox.ac.uk Cited by 76270 |
Unifying the epidemiological and evolutionary dynamics of pathogens
A key priority for infectious disease research is to clarify how pathogen genetic variation,
modulated by host immunity, transmission bottlenecks, and epidemic dynamics, determines the …
modulated by host immunity, transmission bottlenecks, and epidemic dynamics, determines the …
[HTML][HTML] Evolutionary analysis of the dynamics of viral infectious disease
Many organisms that cause infectious diseases, particularly RNA viruses, mutate so rapidly
that their evolutionary and ecological behaviours are inextricably linked. Consequently, …
that their evolutionary and ecological behaviours are inextricably linked. Consequently, …
SARS-CoV-2 evolution in the Omicron era
Since SARS-CoV-2 BA.5 (Omicron) emerged and spread in 2022, Omicron lineages have
markedly diversified. Here we review the evolutionary trajectories and processes that …
markedly diversified. Here we review the evolutionary trajectories and processes that …
[HTML][HTML] A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology
The ongoing pandemic spread of a new human coronavirus, SARS-CoV-2, which is associated
with severe pneumonia/disease (COVID-19), has resulted in the generation of tens of …
with severe pneumonia/disease (COVID-19), has resulted in the generation of tens of …
[HTML][HTML] Rapid epidemic expansion of the SARS-CoV-2 Omicron variant in southern Africa
The SARS-CoV-2 epidemic in southern Africa has been characterized by three distinct waves.
The first was associated with a mix of SARS-CoV-2 lineages, while the second and third …
The first was associated with a mix of SARS-CoV-2 lineages, while the second and third …
[HTML][HTML] Emergence of SARS-CoV-2 omicron lineages BA. 4 and BA. 5 in South Africa
Three lineages (BA.1, BA.2 and BA.3) of the severe acute respiratory syndrome coronavirus
2 (SARS-CoV-2) Omicron variant of concern predominantly drove South Africa’s fourth …
2 (SARS-CoV-2) Omicron variant of concern predominantly drove South Africa’s fourth …
Genomics and epidemiology of the P. 1 SARS-CoV-2 lineage in Manaus, Brazil
… SARS-CoV-2 circulated undetected in Brazil for more than a month as it spread north from
Sã o Paulo. In Manaus, transmission reached unprecedented levels after a momentary respite …
Sã o Paulo. In Manaus, transmission reached unprecedented levels after a momentary respite …
Bayesian coalescent inference of past population dynamics from molecular sequences
We introduce the Bayesian skyline plot, a new method for estimating past population
dynamics through time from a sample of molecular sequences without dependence on a …
dynamics through time from a sample of molecular sequences without dependence on a …
Assignment of epidemiological lineages in an emerging pandemic using the pangolin tool
The response of the global virus genomics community to the severe acute respiratory
syndrome coronavirus 2 (SARS-CoV-2) pandemic has been unprecedented, with significant …
syndrome coronavirus 2 (SARS-CoV-2) pandemic has been unprecedented, with significant …
An investigation of transmission control measures during the first 50 days of the COVID-19 epidemic in China
Responding to an outbreak of a novel coronavirus [agent of coronavirus disease 2019 (COVID-19)]
in December 2019, China banned travel to and from Wuhan city on 23 January 2020 …
in December 2019, China banned travel to and from Wuhan city on 23 January 2020 …