Within-host SARS-CoV-2 viral kinetics informed by complex life course exposures reveals different intrinsic properties of Omicron and Delta variants

Russell TW, Townsley H, Abbott S, Hellewell J, Carr EJ, Chapman L, Pung R, Quilty BJ, Hodgson D, Fowler AS, Adams L, Bailey C, Mears HV, Harvey R, Clayton B, O’Reilly N, Ngai Y, Nicod J, Gamblin S, Williams B, Gandhi S, Swanton C, Beale R, Bauer DL, Wall EC, Kucharski A.

2023

doi:10.1101/2023.05.17.23290105.

Publisher Correction: Genomic reconstruction of the SARS CoV-2 epidemic in England.

Vöhringer HS, Sanderson T, Sinnott M, De Maio N, Nguyen T, Goater R, Schwach F, Harrison I, Hellewell J, Ariani CV, Gonçalves S, Jackson DK, Johnston I, Jung AW, Saint C, Sillitoe J, Suciu M, Goldman N, Panovska-Griffiths J, Wellcome Sanger Institute COVID-19 Surveillance Team, COVID-19 Genomics UK (COG-UK) Consortium*, Birney E, Volz E, Funk S, Kwiatkowski D, Chand M, Martincorena I, Barrett JC, Gerstung M.

Nature, 2022

doi:10.1038/s41586-022-04887-8.

Genomic reconstruction of the SARS-CoV-2 epidemic in England.

Vöhringer HS, Sanderson T, Sinnott M, De Maio N, Nguyen T, Goater R, Schwach F, Harrison I, Hellewell J, Ariani CV, Gonçalves S, Jackson DK, Johnston I, Jung AW, Saint C, Sillitoe J, Suciu M, Goldman N, Panovska-Griffiths J, Wellcome Sanger Institute COVID-19 Surveillance Team, COVID-19 Genomics UK (COG-UK) Consortium*, Birney E, Volz E, Funk S, Kwiatkowski D, Chand M, Martincorena I, Barrett JC, Gerstung M.

Nature, 2021

doi:10.1038/s41586-021-04069-y.

When intuition falters: repeated testing accuracy during an epidemic.

Hay JA, Hellewell J, Qiu X.

Eur J Epidemiol, 2021

doi:10.1007/s10654-021-00786-w.

Exploring surveillance data biases when estimating the reproduction number: with insights into subpopulation transmission of COVID-19 in England.

Sherratt K, Abbott S, Meakin SR, Hellewell J, Munday JD, Bosse N, CMMID COVID-19 Working Group, Jit M, Funk S.

Philos Trans R Soc Lond B Biol Sci, 2021

doi:10.1098/rstb.2020.0283.

Genomic reconstruction of the SARS-CoV-2 epidemic in England

Vöhringer HS, Sanderson T, Sinnott M, Maio ND, Nguyen T, Goater R, Schwach F, Harrison I, Hellewell J, Ariani C, Gonçalves S, Jackson D, Johnston I, Jung AW, Saint C, Sillitoe J, Suciu M, Goldman N, Panovska-Griffiths J, Birney E, Volz E, Funk S, Kwiatkowski D, Chand M, Martincorena I, Barrett JC, Gerstung M, The Wellcome Sanger Institute Covid-19 Surveillance Team, The COVID-19 Genomics UK (COG-UK) Consortium.

2021

doi:10.1101/2021.05.22.21257633.

Estimating the effectiveness of routine asymptomatic PCR testing at different frequencies for the detection of SARS-CoV-2 infections.

Hellewell J, Russell TW, SAFER Investigators and Field Study Team, Crick COVID-19 Consortium, CMMID COVID-19 working group, Beale R, Kelly G, Houlihan C, Nastouli E, Kucharski AJ.

BMC Med, 2021

doi:10.1186/s12916-021-01982-x.

Assessing the impact of low-technology emanators alongside long-lasting insecticidal nets to control malaria.

Hellewell J, Sherrard-Smith E, Ogoma S, Churcher TS.

Philos Trans R Soc Lond B Biol Sci, 2021

doi:10.1098/rstb.2019.0817.

Practical considerations for measuring the effective reproductive number, Rt.

Gostic KM, McGough L, Baskerville EB, Abbott S, Joshi K, Tedijanto C, Kahn R, Niehus R, Hay JA, De Salazar PM, Hellewell J, Meakin S, Munday JD, Bosse NI, Sherrat K, Thompson RN, White LF, Huisman JS, Scire J, Bonhoeffer S, Stadler T, Wallinga J, Funk S, Lipsitch M, Cobey S.

PLoS Comput Biol, 2020

doi:10.1371/journal.pcbi.1008409.

Estimating the time-varying reproduction number of SARS-CoV-2 using national and subnational case counts

Abbott S, Hellewell J, Thompson RN, Sherratt K, Gibbs HP, Bosse NI, Munday JD, Meakin S, Doughty EL, Chun JY, Chan YD, Finger F, Campbell P, Endo A, Pearson CAB, Gimma A, Russell T, Flasche S, Kucharski AJ, Eggo RM, Funk S, CMMID COVID modelling group.

2020

doi:10.12688/wellcomeopenres.16006.2.

Estimating the effectiveness of routine asymptomatic PCR testing at different frequencies for the detection of SARS-CoV-2 infections

Hellewell J, Russell TW, Beale R, Kelly G, Houlihan C, Nastouli E, Kucharski AJ, The SAFER Investigators and Field Study Team, The Crick COVID-19 Consortium, CMMID COVID-19 working group.

2020

doi:10.1101/2020.11.24.20229948.

Reconstructing the early global dynamics of under-ascertained COVID-19 cases and infections.

Russell TW, Golding N, Hellewell J, Abbott S, Wright L, Pearson CAB, van Zandvoort K, Jarvis CI, Gibbs H, Liu Y, Eggo RM, Edmunds WJ, Kucharski AJ, CMMID COVID-19 working group.

BMC Med, 2020

doi:10.1186/s12916-020-01790-9.

Exploring surveillance data biases when estimating the reproduction number: with insights into subpopulation transmission of Covid-19 in England

Sherratt K, Abbott S, Meakin SR, Hellewell J, Munday JD, Bosse N, Jit M, Funk S, CMMID Covid-19 working group.

2020

doi:10.1101/2020.10.18.20214585.

Implications of the school-household network structure on SARS-CoV-2 transmission under different school reopening strategies in England

Munday JD, Sherratt K, Meakin S, Endo A, Pearson CAB, Hellewell J, Abbott S, Bosse NI, Atkins KE, Wallinga J, Edmunds WJ, van Hoek AJ, Funk S, CMMID COVID 1-9 Working Group.

2020

doi:10.1101/2020.08.21.20167965.

Using a real-world network to model localized COVID-19 control strategies.

Firth JA, Hellewell J, Klepac P, Kissler S, CMMID COVID-19 Working Group, Kucharski AJ, Spurgin LG.

Nat Med, 2020

doi:10.1038/s41591-020-1036-8.

Reconstructing the early global dynamics of under-ascertained COVID-19 cases and infections

Russell TW, Russell TW, Golding N, Hellewell J, Abbott S, Wright L, Pearson CAB, Pearson CAB, Zandvoort Kv, Jarvis CI, Gibbs H, Liu Y, Eggo RM, Edmunds WJ, Kucharski AJ.

2020

doi:10.1101/2020.07.07.20148460.

An imperfect tool: contact tracing could provide valuable reductions in COVID-19 transmission if good adherence can be achieved and maintained.

Davis EL, Lucas TCD, Borlase A, Pollington TM, Abbott S, Ayabina D, Crellen T, Hellewell J, Pi L, Medley GF, Hollingsworth TD, Klepac P.

2020

doi:10.1101/2020.06.09.20124008.

Combining fine-scale social contact data with epidemic modelling reveals interactions between contact tracing, quarantine, testing and physical distancing for controlling COVID-19

Firth JA, Hellewell J, Klepac P, Kissler S, Kucharski AJ, Spurgin LG, CMMID COVID-19 working group.

2020

doi:10.1101/2020.05.26.20113720.

The transmissibility of novel Coronavirus in the early stages of the 2019-20 outbreak in Wuhan: Exploring initial point-source exposure sizes and durations using scenario analysis.

Abbott S, Hellewell J, Munday J, CMMID nCoV working group, Funk S.

Wellcome Open Res, 2020

doi:10.12688/wellcomeopenres.15718.1.

Estimating the infection and case fatality ratio for COVID-19 using age-adjusted data from the outbreak on the Diamond Princess cruise ship

Russell TW, Hellewell J, Jarvis CI, Van Zandvoort K, Abbott S, Ratnayake R, Flasche S, Eggo RM, Edmunds WJ, Kucharski AJ, CMMID COVID-19 working group.

2020

doi:10.1101/2020.03.05.20031773.

Feasibility of controlling 2019-nCoV outbreaks by isolation of cases and contacts

Hellewell J, Abbott S, Gimma A, Bosse NI, Jarvis CI, Russell TW, Munday JD, Kucharski AJ, Edmunds WJ, Funk S, Eggo RM, CMMID nCoV working group.

2020

doi:10.1101/2020.02.08.20021162.

The transmissibility of novel Coronavirus in the early stages of the 2019-20 outbreak in Wuhan: Exploring initial point-source exposure sizes and durations using scenario analysis

Abbott S, Hellewell J, Munday J, Funk S, CMMID nCoV working group.

2020

doi:10.12688/wellcomeopenres.15718.1.

Ivermectin as a novel complementary malaria control tool to reduce incidence and prevalence: a modelling study.

Slater HC, Foy BD, Kobylinski K, Chaccour C, Watson OJ, Hellewell J, Aljayyoussi G, Bousema T, Burrows J, D'Alessandro U, Alout H, Ter Kuile FO, Walker PGT, Ghani AC, Smit MR.

Lancet Infect Dis, 2020

doi:10.1016/s1473-3099(19)30633-4.

Evaluating the performance of malaria genomics for inferring changes in transmission intensity using transmission modelling

Watson OJ, Okell LC, Hellewell J, Slater HC, Unwin HJT, Omedo I, Bejon P, Snow RW, Noor AM, Rockett K, Hubbart C, Nankabirwa JI, Greenhouse B, Chang H, Ghani AC, Verity R.

2019

doi:10.1101/793554.

The impact of reactive mass vaccination campaigns on measles outbreaks in the Katanga region, Democratic Republic of Congo

Funk S, Takahashi S, Hellewell J, Gadroen K, Carrion-Martin I, van Lenthe M, Rivette K, Dietrich S, Edmunds WJ, Siddiqui R, Rao VB.

2019

doi:10.1101/19003434.

Using ante-natal clinic prevalence data to monitor temporal changes in malaria incidence in a humanitarian setting in the Democratic Republic of Congo.

Hellewell J, Walker P, Ghani A, Rao B, Churcher TS.

Malar J, 2018

doi:10.1186/s12936-018-2460-9.

Variation in natural exposure to anopheles mosquitoes and its effects on malaria transmission.

Guelbéogo WM, Gonçalves BP, Grignard L, Bradley J, Serme SS, Hellewell J, Lanke K, Zongo S, Sepúlveda N, Soulama I, Wangrawa DW, Yakob L, Sagnon N, Bousema T, Drakeley C.

Elife, 2018

doi:10.7554/elife.32625.

Examining the human infectious reservoir for Plasmodium falciparum malaria in areas of differing transmission intensity.

Gonçalves BP, Kapulu MC, Sawa P, Guelbéogo WM, Tiono AB, Grignard L, Stone W, Hellewell J, Lanke K, Bastiaens GJH, Bradley J, Nébié I, Ngoi JM, Oriango R, Mkabili D, Nyaurah M, Midega J, Wirth DF, Marsh K, Churcher TS, Bejon P, Sirima SB, Drakeley C, Bousema T.

Nat Commun, 2017

doi:10.1038/s41467-017-01270-4.