Erik Volz
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View article: Quantifying the predictability of evolution by analysis of coalescent rate variation
Quantifying the predictability of evolution by analysis of coalescent rate variation Open
We investigate the question of how to predict evolution from phylogenetic patterns, and we frame the problem in terms of predicting phylogenetic placement of new or circulating lineages. This leads us to develop a class of coalescent model…
View article: Diagnostics of dated phylogenies in microbial population genetics
Diagnostics of dated phylogenies in microbial population genetics Open
Microbial population genetic studies often involve the use of a dated phylogeny to show how the genomes are related over a relevant timescale. Many tools have recently been developed to date the nodes of a standard phylogeny, but all make …
View article: HIV-1 Transmission Clustering and Phylodynamics Highlight the Important Role of Young Men Who Have Sex with Men
HIV-1 Transmission Clustering and Phylodynamics Highlight the Important Role of Young Men Who Have Sex with Men Open
More persons living with HIV reside in the Southern United States than in any other region, yet little is known about HIV molecular epidemiology in the South. We used cluster and phylodynamic analyses to evaluate HIV transmission patterns …
View article: Robust phylodynamic inference and model specification for HIV transmission dynamics
Robust phylodynamic inference and model specification for HIV transmission dynamics Open
The robustness and statistical efficiency of phylodynamic models have been tested by many investigators. However, little attention has been given to model specification and inductive bias that can occur if the model is misspecified or prov…
View article: Sequencing HIV Diagnostic Samples to Detect Genetic Clusters and Assess Sequence Coverage Gaps
Sequencing HIV Diagnostic Samples to Detect Genetic Clusters and Assess Sequence Coverage Gaps Open
Background HIV molecular cluster detection in the United States relies on HIV sequences obtained from drug resistance testing during clinical care (“routine care sequences”). This approach misses people who are not linked to care or who re…
View article: Untangling the effects of within-host and between-host natural selection in viruses with applications to evolution of HIV-1 co-receptor usage
Untangling the effects of within-host and between-host natural selection in viruses with applications to evolution of HIV-1 co-receptor usage Open
The fitness of a pathogen can be characterised at multiple levels corresponding to different stages of its life cycle, including replication within target cells (replicative capacity), immune evasion, and the capacity to infect new hosts (…
View article: Evidence for circulation of high-virulence HIV-1 subtype B variants in the United Kingdom
Evidence for circulation of high-virulence HIV-1 subtype B variants in the United Kingdom Open
The evolution of HIV-1 virulence has significant implications for epidemic control. Recent phylogenomic analyses identified low-prevalence HIV-1 variants exhibiting significant differences in disease progression. We analysed 40 888 partial…
View article: Phylogenetic signatures reveal multilevel selection and fitness costs in SARS-CoV-2
Phylogenetic signatures reveal multilevel selection and fitness costs in SARS-CoV-2 Open
Background Large-scale sequencing of SARS-CoV-2 has enabled the study of viral evolution during the COVID-19 pandemic. Some viral mutations may be advantageous to viral replication within hosts but detrimental to transmission, thus carryin…
View article: Lineage frequency time series reveal elevated levels of genetic drift in SARS-CoV-2 transmission in England
Lineage frequency time series reveal elevated levels of genetic drift in SARS-CoV-2 transmission in England Open
Genetic drift in infectious disease transmission results from randomness of transmission and host recovery or death. The strength of genetic drift for SARS-CoV-2 transmission is expected to be high due to high levels of superspreading, and…
View article: Strategy to develop broadly effective multivalent COVID-19 vaccines against emerging variants based on Ad5/35 platform
Strategy to develop broadly effective multivalent COVID-19 vaccines against emerging variants based on Ad5/35 platform Open
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron strain has evolved into highly divergent variants with several sub-lineages. These newly emerging variants threaten the efficacy of available COVID-19 vaccines. To mi…
View article: Phylogenetic signatures reveal multilevel selection and fitness costs in SARS-CoV-2
Phylogenetic signatures reveal multilevel selection and fitness costs in SARS-CoV-2 Open
Background Large-scale sequencing of SARS-CoV-2 has enabled the study of viral evolution during the COVID-19 pandemic. Some viral mutations may be advantageous to viral replication within hosts but detrimental to transmission, thus carryin…
View article: Assessing transmission attribution risk from simulated sequencing data in HIV molecular epidemiology
Assessing transmission attribution risk from simulated sequencing data in HIV molecular epidemiology Open
Background: HIV molecular epidemiology (ME) is the analysis of sequence data together with individual-level clinical, demographic, and behavioral data to understand HIV epidemiology. The use of ME has raised concerns regarding identificati…
View article: Author Correction: Epidemiological drivers of transmissibility and severity of SARS-CoV-2 in England
Author Correction: Epidemiological drivers of transmissibility and severity of SARS-CoV-2 in England Open
1. Page 1, Abstract: "basic reproduction number 8.3 (95% credible interval (CrI) 7.7-8.8)"has been corrected to "basic reproduction number 8.4 (95% credible interval (CrI) 7.8-9.1)"2. Page 1, Abstract: "basic infection fatality ratio (2.9%…
View article: HIV-1 Transmission linkages among persons with incident infection to inform public health surveillance
HIV-1 Transmission linkages among persons with incident infection to inform public health surveillance Open
Background: We evaluated features of HIV transmission networks involving persons diagnosed during incident HIV infection (IHI) to assess network-based opportunities to curtail onward transmission. Methods: Transmission networks were constr…
View article: Genomic assessment of invasion dynamics of SARS-CoV-2 Omicron BA.1
Genomic assessment of invasion dynamics of SARS-CoV-2 Omicron BA.1 Open
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern (VOCs) now arise in the context of heterogeneous human connectivity and population immunity. Through a large-scale phylodynamic analysis of 115,622 Omicron BA…
View article: Epidemiological drivers of transmissibility and severity of SARS-CoV-2 in England
Epidemiological drivers of transmissibility and severity of SARS-CoV-2 in England Open
As the SARS-CoV-2 pandemic progressed, distinct variants emerged and dominated in England. These variants, Wildtype, Alpha, Delta, and Omicron were characterized by variations in transmissibility and severity. We used a robust mathematical…
View article: Investigation of hospital discharge cases and SARS-CoV-2 introduction into Lothian care homes
Investigation of hospital discharge cases and SARS-CoV-2 introduction into Lothian care homes Open
The majority of patients discharged from hospitals were ruled out for introduction of SARS-CoV-2 into care homes, highlighting the importance of screening all new admissions when faced with a novel emerging virus and no available vaccine.
View article: The use of representative community samples to assess SARS-CoV-2 lineage competition: Alpha outcompetes Beta and wild-type in England from January to March 2021
The use of representative community samples to assess SARS-CoV-2 lineage competition: Alpha outcompetes Beta and wild-type in England from January to March 2021 Open
Genomic surveillance for SARS-CoV-2 lineages informs our understanding of possible future changes in transmissibility and vaccine efficacy and will be a high priority for public health for the foreseeable future. However, small changes in …
View article: Epidemiological drivers of transmissibility and severity of SARS-CoV-2 in England
Epidemiological drivers of transmissibility and severity of SARS-CoV-2 in England Open
As the SARS-CoV-2 pandemic progressed, distinct variants emerged and dominated in England. These variants, Wildtype, Alpha, Delta, and Omicron were characterized by variations in transmissibility and severity. We used a robust mathematical…
View article: Genomic assessment of invasion dynamics of SARS-CoV-2 Omicron BA.1
Genomic assessment of invasion dynamics of SARS-CoV-2 Omicron BA.1 Open
Summary SARS-CoV-2 variants of concern (VOCs) arise against the backdrop of increasingly heterogeneous human connectivity and population immunity. Through a large-scale phylodynamic analysis of 115,622 Omicron genomes, we identified >6,000…
View article: Model design for nonparametric phylodynamic inference and applications to pathogen surveillance
Model design for nonparametric phylodynamic inference and applications to pathogen surveillance Open
Inference of effective population size from genomic data can provide unique information about demographic history and, when applied to pathogen genetic data, can also provide insights into epidemiological dynamics. The combination of nonpa…
View article: Lineage frequency time series reveal elevated levels of genetic drift in SARS-CoV-2 transmission in England
Lineage frequency time series reveal elevated levels of genetic drift in SARS-CoV-2 transmission in England Open
Genetic drift in infectious disease transmission results from randomness of transmission and host recovery or death. The strength of genetic drift for SARS-CoV-2 transmission is expected to be high due to high levels of superspreading, and…