User profiles for O. G. Pybus
Oliver PybusUniversity of Oxford / Royal Veterinary College Verified email at zoo.ox.ac.uk Cited by 75969 |
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 …
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 …
Genomics and epidemiology of the P. 1 SARS-CoV-2 lineage in Manaus, Brazil
Cases of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection in
Manaus, Brazil, resurged in late 2020 despite previously high levels of infection. Genome …
Manaus, Brazil, resurged in late 2020 despite previously high levels of infection. Genome …
The effect of human mobility and control measures on the COVID-19 epidemic in China
The ongoing coronavirus disease 2019 (COVID-19) outbreak expanded rapidly throughout
China. Major behavioral, clinical, and state interventions were undertaken to mitigate the …
China. Major behavioral, clinical, and state interventions were undertaken to mitigate the …
[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 …
[HTML][HTML] Origins and evolutionary genomics of the 2009 swine-origin H1N1 influenza A epidemic
In March and early April 2009, a new swine-origin influenza A (H1N1) virus (S-OIV) emerged
in Mexico and the United States 1 . During the first few weeks of surveillance, the virus …
in Mexico and the United States 1 . During the first few weeks of surveillance, the virus …