Field epidemiology · Genomic surveillance · Arboviruses

Rhys Inward

I’m a field epidemiology fellow with the UK Health Security Agency (UKHSA) and a final-year DPhil candidate at the University of Oxford. I use pathogen genomes, surveillance data, and climate and mobility data to understand how infections such as dengue, chikungunya and SARS-CoV-2 are introduced and spread, and to turn that into evidence for surveillance and outbreak response.

Research Tutorials Timeline & CV

Map of England covered in thousands of orange points joined by curved lines, showing how the largest Omicron BA.1 transmission lineage spread across the country

The largest Omicron BA.1 transmission lineage in England (11,351 genomes), reconstructed by continuous phylogeography and coloured by date. Adapted (cropped from Fig. 3C) from Tsui, McCrone, Lambert, Bajaj, Inward, Bosetti et al., Science 2023 (author manuscript, CC BY 4.0).

From research to public health

Field epidemiology →

Surveillance

Seeing outbreaks clearly

How sampling and reporting shape what genomic and case data can tell us (Nature Communications, Epidemics), and how surveillance and modelling can work globally (Nature Medicine).

Spread

Tracing introductions

Reconstructing how pathogens arrive and spread: Omicron and Delta in England (Science, Nature), dengue in Vietnam (EID) and cholera in Malawi (EID).

UKFETP

On the front line

Since September 2026, applying these skills with UKHSA’s North West Field Service: surveillance, outbreak response and applied projects.

Tools

Analyses others can rerun

Reproducible pipelines that researchers and public health teams can run locally, including GRAPEVNE and a data pipeline for climate-sensitive diseases.

Selected publications

All publications →

Nature Communications · 2022

Using multiple sampling strategies to estimate SARS-CoV-2 epidemiological parameters from genomic sequencing data

First author

Which genomes you analyse matters. With SARS-CoV-2 data from Hong Kong and Amazonas, Brazil, we showed that estimates of Rt and growth rate shift with sampling choices, while R0 and the date of origin are relatively robust.

Read the paper: Using multiple sampling strategies to estimate SARS-CoV-2 epidemiological parameters from genomic sequencing data Code for Using multiple sampling strategies to estimate SARS-CoV-2 epidemiological parameters from genomic sequencing data

Science · 2023

Genomic assessment of invasion dynamics of SARS-CoV-2 Omicron BA.1

Joint first author

From 115,622 genomes, we identified more than 6,000 separate introductions of Omicron BA.1 into England. Six of the eight largest lineages were already spreading when Omicron was first reported in southern Africa, and importation continued despite restrictions on travel from southern Africa.

Read the paper: Genomic assessment of invasion dynamics of SARS-CoV-2 Omicron BA.1 Code for Genomic assessment of invasion dynamics of SARS-CoV-2 Omicron BA.1

Emerging Infectious Diseases · 2023

Reemergence of Cosmopolitan genotype dengue virus serotype 2, southern Vietnam

Joint first author

We traced how the Cosmopolitan genotype of DENV-2 re-emerged in Ho Chi Minh City, its probable routes of introduction and the timeline of events. The findings highlight the need for continuous, systematic genomic surveillance.

Read the paper: Reemergence of Cosmopolitan genotype dengue virus serotype 2, southern Vietnam Code for Reemergence of Cosmopolitan genotype dengue virus serotype 2, southern Vietnam

What I work on

Research →

DENV

Dengue genotype dynamics

Where new dengue genotypes come from, how they spread, and why some replace the ones already circulating.

CHIKV

Chikungunya transmission

Renewal-equation models of chikungunya outbreaks in France and Brazil, and how climate shapes them.

UKFETP

Field epidemiology

Surveillance, outbreak response and applied projects with UKHSA’s North West Field Service.

PPIE

Patient & public involvement

Working with patients, families and the public on research questions and tools.

Latest tutorials

All tutorials →

Genotype replacement in R

Dengue

Tutorial

Estimate how fast a new dengue genotype takes over, with a logistic model fitted to sequence counts.

Estimating Rt with a renewal equation

Methods

Tutorial

Simulate an outbreak from the renewal equation, then recover the time-varying reproduction number.

Dengue: a primer

Dengue

Primer

The virus, its serotypes and genotypes, how it spreads, and where to find data.

Get in touch

I’m happy to talk about collaborations, field epidemiology and patient involvement, or, away from work, hiking, squash and choral music. Email rhys.inward@biology.ox.ac.uk.

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Rhys smiling on a carved wooden bench, between a wooden Yoda and a carved scallop shell