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Number of items: 65.

A

Abbas, KM (2020). vaccine-impact/epi_covid. [Data Collection]. Github. https://github.com/vaccine-impact/epi_covid

Abbott, S, Bennett, C, Hickson, J, Allen, J, Sherratt, K and Funk, S (2020). National and Subnational Estimates of the Covid 19 Reproduction Number (R) for the United States of America Based on Test Results. [Data Collection]. Harvard Dataverse. https://doi.org/10.7910/DVN/BZ7FPH

Abbott, S, Bevan, J, Sherratt, K, Gibbs, H, Finger, F, Hellewell, J, Campbell, P, Barks, P, , M, Haze, L and Meakin, S (2020). epiforecasts/covidregionaldata: Preliminary release candidate. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.3957539

Abbott, S and Funk, S (2021). epiforecasts/covid19.sgene.utla.rt. [Data Collection]. Github. https://github.com/epiforecasts/covid19.sgene.utla.rt

Abbott, S, Funk, S, Munday, JD and Hellewell, J (2020). epiforecasts/WuhanSeedingVsTransmission: Resubmission to Wellcome Open Research. [Data Collection]. Zenodo. http://doi.org/10.5281/zenodo.3631830

Abbott, S, Gaythorpe, KA, Imai, N and Liu, Y (2020). seabbs/CovidInterventionReview: CC0 license. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.3728162

Abbott, S, Sherratt, K, Funk, S and Hellewell, J (2020). epiforecasts/covid: Submission release. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.3746396

Aldridge, RW, Lewer, D, Beale, S, Johnson, AM, Zambon, M, Hayward, AC and Fragaszy, E (2020). Dataset: Seasonality and immunity to laboratory-confirmed seasonal coronaviruses (HCoV-NL63, HCoV-OC43, and HCoV-229E): results from the Flu Watch cohort study. [Data Collection]. UCL Institute of Health Informatics, London, United Kingdom. https://doi.org/10.14324/000.ds.10093909

B

Bell, S, Clarke, R, Mounier-Jack, S and Paterson, P (2020). Parents’ and guardians’ views and experiences of accessing routine childhood vaccinations in England during the coronavirus (COVID-19) pandemic: cross-sectional survey and qualitative interview data. [Data Collection]. London School of Hygiene & Tropical Medicine, London, United Kingdom. https://doi.org/10.17037/DATA.00001861.

Bell, S, Clarke, R, Mounier-Jack, S and Paterson, P (2020). Parents’ and guardians’ views on the acceptability of a future COVID-19 vaccine for themselves and their children: cross-sectional survey and qualitative interview data. [Data Collection]. London School of Hygiene & Tropical Medicine, London, United Kingdom. https://doi.org/10.17037/DATA.00001862.

Bhaskaran, K and Inglesby, P (2021). opensafely/covid-vs-noncovid-deaths-research. [Data Collection]. Github. https://github.com/opensafely/covid-vs-noncovid-deaths-research

C

Candido, DS, Claro, IM, de Jesus, JG, Souza, WM, Moreira, FRR, Dellicour, S, Mellan, TA, du Plessis, L, Pereira, RHM, Sales, FCS, Manuli, ER, Thézé, J, Almeida, L, Menezes, MT, Voloch, CM, Fumagalli, MJ, Coletti, TM, da Silva, CAM, Ramundo, MS, Amorim, MR, Hoeltgebaum, HH, Mishra, S, Gill, MS, Carvalho, LM, Buss, LF, Prete, CA, Ashworth, J, Nakaya, HI, Peixoto, PS, Brady, OJ, Nicholls, SM, Tanuri, A, Rossi, Átila D., Braga, CK, Gerber, AL, de C. Guimarães, AP, Gaburo, N, Alencar, CS, Ferreira, AC, Lima, CX, Levi, JE, Granato, C, Ferreira, GM, Francisco, RS, Granja, F, Garcia, MT, Moretti, ML, Perroud, MW, Castiñeiras, Terezinha M. P. P., Lazari, CS, Hill, SC, de Souza Santos, AA, Simeoni, CL, Forato, J, Sposito, AC, Schreiber, AZ, Santos, MNN, de Sá, CZ, Souza, RP, Resende-Moreira, LC, Teixeira, MM, Hubner, J, Leme, PAF, Moreira, RG, Nogueira, ML, Ferguson, NM, Costa, SF, Proenca-Modena, JL, Vasconcelos, ATR, Bhatt, S, Lemey, P, Wu, C, Rambaut, A, Loman, NJ, Aguiar, RS, Pybus, OG, Sabino, EC and Faria, NR (2020). Data from: Evolution and epidemic spread of SARS-CoV-2 in Brazil. [Data Collection]. Dryad. http://doi.org/10.5061/dryad.rxwdbrv5z

Candido, DS, Claro, IM, de Jesus, JG, Souza, WM, Moreira, FRR, Dellicour, S, Mellan, TA, du Plessis, L, Pereira, RHM, Sales, FCS, Manuli, ER, Thézé, J, Almeida, L, Menezes, MT, Voloch, CM, Fumagalli, MJ, Coletti, TM, da Silva, CAM, Ramundo, MS, Amorim, MR, Hoeltgebaum, HH, Mishra, S, Gill, MS, Carvalho, LM, Buss, LF, Prete, CA, Ashworth, J, Nakaya, HI, Peixoto, PS, Brady, OJ, Nicholls, SM, Tanuri, A, Rossi, Átila D., Braga, CK, Gerber, AL, de C. Guimarães, AP, Gaburo, N, Alencar, CS, Ferreira, AC, Lima, CX, Levi, JE, Granato, C, Ferreira, GM, Francisco, RS, Granja, F, Garcia, MT, Moretti, ML, Perroud, MW, Castiñeiras, Terezinha M. P. P., Lazari, CS, Hill, SC, de Souza Santos, AA, Simeoni, CL, Forato, J, Sposito, AC, Schreiber, AZ, Santos, MNN, de Sá, CZ, Souza, RP, Resende-Moreira, LC, Teixeira, MM, Hubner, J, Leme, PAF, Moreira, RG, Nogueira, ML, Ferguson, NM, Costa, SF, Proenca-Modena, JL, Vasconcelos, ATR, Bhatt, S, Lemey, P, Wu, C, Rambaut, A, Loman, NJ, Aguiar, RS, Pybus, OG, Sabino, EC and Faria, NR (2020). Evolution and epidemic spread of SARS-CoV-2 in Brazil. [Data Collection]. Science. https://doi.org/10.1126/science.abd2161

Checchi, F (2020). francescochecchi/aden_covid. [Data Collection]. London School of Hygiene & Tropical Medicine, London, United Kingdom. https://github.com/francescochecchi/aden_covid

Clifford, S and Quilty, B (2020). cmmid/pcr_test_trace. [Data Collection]. Github. https://github.com/cmmid/pcr_test_trace

Clifford, S, Quilty, BJ, Russell, TW, Liu, Y, Chan, YD, Pearson, CAB, Eggo, RM, Endo, A, CMMID COVID-19 Working Group, Flasche, S and Edmunds, WJ (2020). cmmid/travel_screening_strategies. [Data Collection]. Github. https://github.com/cmmid/travel_screening_strategies

Clifford, S, Quilty, B, CMMID nCoV working group, Pearson, C, Flasche, S and Eggo, RM (2020). Effectiveness of airport-based interventions at detecting travellers and delaying an outbreak of COVID-19 (formerly 2019-nCoV). [Data Collection]. Github. https://github.com/cmmid/screening_outbreak_delay

Coletti, P, Wambua, J, Gimma, A, Willem, L, Vercruysse, S, Vanhoutte, B, Jarvis, CI, Van Zandvoort, K, Edmunds, J, Beutels, P and Hens, N (2020). Social contact data from CoMix survey (Belgium). [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.4035001

D

Davies, NG, Abbott, S, Barnard, RC, Jarvis, CI, Kucharski, AJ, Munday, J, Pearson, CAB, Russell, TW, Tully, DC, Washburne, AD, Wenseleers, T, Gimma, A, Waites, W, Wong, KL, van Zandvoort, K, Silverman, JD, Diaz-Ordaz, K, Keogh, R, Eggo, RM, Funk, S, Jit, M, Atkins, KE and Edmunds, WJ (2021). Analysis data and code for "Estimated transmissibility and impact of SARS-CoV-2 Variant of Concern 202012/01 in England". [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.4549674

Davies, NG, Abbott, S, Barnard, RC, Jarvis, CI, Kucharski, AJ, Munday, J, Pearson, CAB, Russell, TW, Tully, DC, Washburne, AD, Wenseleers, T, Gimma, A, Waites, W, Wong, KL, van Zandvoort, K, Silverman, JD, Diaz-Ordaz, K, Keogh, R, Eggo, RM, Funk, S, Jit, M, Atkins, KE and Edmunds, WJ (2021). Analysis data and code for "Estimated transmissibility and impact of SARS-CoV-2 lineage B.1.1.7 in England". [Data Collection]. Zenodo. http://doi.org/10.5281/zenodo.4562961

Davies, NG, Jarvis, CI, CMMID COVID-19 Working Group, Edmunds, WJ, Jewell, NP, Diaz-Ordaz, K and Keogh, RH (2021). Increased mortality in community-tested cases of SARS-CoV-2 lineage B.1.1.7. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.4579856

Davies, NG, Kucharski, AJ, Eggo, RM, Gimma, A, COVID-19 Working Group and Edmunds, WJ (2020). cmmid/covid-uk. [Data Collection]. Github. https://github.com/cmmid/covid-uk

E

Endo, A, Abbott, S, Kucharski, AJ and Funk, S (2020). Extended data: Estimating the overdispersion in COVID-19 transmission using outbreak sizes outside China. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.3740348

Endo, A, Abbott, S, Kucharski, AJ and Funk, S (2020). akira-endo/COVID19_clustersize: Estimating the amount of superspreading using outbreak sizes of COVID-19 outside China. [Data Collection]. Zenodo. http://doi.org/10.5281/zenodo.3741744

Enria, L, Waterlow, N, Rogers, N, Brindle, H, Lal, S, Eggo, RM, Lees, S and Roberts, C (2020). Trust and Transparency in times of Crisis: Results from an Online Survey During the First Wave (April 2020) of the COVID-19 Epidemic in the UK - Qualitative Data. [Data Collection]. London School of Hygiene & Tropical Medicine, London, United Kingdom. https://doi.org/10.17037/DATA.00001859.

Enria, L, Waterlow, N, Rogers, N, Brindle, H, Lal, S, Eggo, RM, Lees, S and Roberts, C (2021). Trust and Transparency in times of Crisis: Results from an Online Survey During the First Wave (April 2020) of the COVID-19 Epidemic in the UK - Quantitative Data. [Data Collection]. London School of Hygiene & Tropical Medicine, London, United Kingdom. https://doi.org/10.17037/DATA.00002015.

G

Gaskell, KM, Johnson, M, Gould, V, Hunt, A, Stone, NR, Waites, W, Kasstan, B, Chantler, T, Lal, S, Roberts, Ch, Goldblatt, D, Eggo, RM and Marks, M (2021). Extremely high SARS-CoV-2 seroprevalence in a strictly-Orthodox Jewish community in the UK. [Data Collection]. London School of Hygiene & Tropical Medicine, London, United Kingdom.

Gibbs, H, CMMID nCov Working Group, Eggo, RM, Grundy, C and Kucharski, AJ (2020). UK Colocation Dashboard. [Data Collection]. Github. https://cmmid.github.io/colocation_dashboard_cmmid/

H

Hellewell, J, Abbott, S, Gimma, A, Bosse, N, Jarvis, C, Russell, T, Munday, J, Kucharski, A, Edmunds, WJ, Funk, S, Eggo, R, Sun, F, Flasche, S, Quilty, B, Davies, N, Liu, Y, Clifford, S, Klepac, P, Jit, M, Diamond, C, Gibbs, H and Van Zandvoort, K (2020). Feasibility of controlling COVID-19 outbreaks by isolation of cases and contacts. [Data Collection]. Github. https://github.com/cmmid/ringbp/

Hellewell, J, Lucas, T, Davis, E, Abbott, S, Gimma, A and Thompson, R (2020). timcdlucas/ringbp: Code as used in the paper "Engagement and adherence trade-offs for SARS-CoV-2 contact tracing". [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.4221774

J

Jarvis, C (2021). jarvisc1/comix_uk_covid_restrictions. [Data Collection]. Github. https://github.com/jarvisc1/comix_uk_covid_restrictions

Jarvis, C, Van zandvoort, K, Gimma, A, Prem, K, CMMID, Cwg, Klepac, P, Rubin, GJ and Edmunds, WJ (2020). Contact survey during COVID-19. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.3741391

Jombart, T, Abbott, S, Gimma, A, Zandvoort, K, Clifford, S, Jarvis, C, Russell, T, Funk, S, Gibbs, H, Eggo, RM, Kucharski, AJ, CMMID COVID-19 Working Group and Edmunds, WJ (2020). Inferring COVID-19 cases from deaths of confirmed cases. [Data Collection]. CMMID Repository. https://cmmid.github.io/visualisations/inferring-covid19-cases-from-deaths

Jombart, T, Clifford, S, Pearson, Carl A. B. Pearson, Rees, E, Nightingale, E, Procter, S and Knight, G (2020). thibautjombart/covid19_bed_occupancy: Second major release. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.3746662

Jung, S, Endo, A, Kinoshita, R and Nishiura, H (2021). SungmokJung/Projection_Japan_COVID19 v1.0.0. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.4576936

K

Kucharski, AJ, Russell, TW, Diamond, C, CMMID nCoV working group, Funk, S and Eggo, RM (2020). Probability of a large 2019-nCoV outbreak following introduction of cases. [Data Collection]. Github. https://cmmid.github.io/visualisations/new-outbreak-probability

L

Leclerc, QJ, Fuller, NM, Knight, LE, Funk, S and Knight, GM (2020). COVID19 settings of transmission - collected reports database. [Data Collection]. Figshare. https://doi.org/10.6084/m9.figshare.12173343.v3

Leclerc, QJ, Nightingale, E and Abbott, S (2020). qleclerc/nhs_pathways_report. [Data Collection]. Github. https://github.com/qleclerc/nhs_pathways_report

Leng, T and Flasche, S (2020). tsleng93/SocialBubble: Social Bubble (including density dependence). [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.3982789

Liu, Y (2020). yangclaraliu/COVID19_NPIs_vs_Rt. [Data Collection]. Github. https://github.com/yangclaraliu/COVID19_NPIs_vs_Rt

Liu, Y, Funk, S and Flasche, S (2020). yangclaraliu/2019nCoV_proportion_asym: WOR Submission. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.3709941

Liu, Y, Gong, W, Clifford, S, Sundaram, ME, CMMID COVID-19 Working Group, Jit, M, Flasche, S and Klepac, P (2020). yangclaraliu/covid_surveillance_strategy: WOR Submission. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.4017353

N

Nightingale, E, Waterlow, N, Clifford, S and Rees, E (2020). COVID-19 length of hospital stay. [Data Collection]. Github. https://github.com/esnightingale/los_review

O

Otieno, GP, Murunga, N, Agoti, CN, Gallagher, KE, Awori, JO and Nokes, DJ (2020). Replication Data for: Surveillance of endemic human coronaviruses (HCoV-NL63, OC43 and 229E) associated with pneumonia in Kilifi, Kenya. [Data Collection]. Harvard Dataverse. https://doi.org/10.7910/DVN/ZQ1DJY

P

Parker, E (2020). Covid 2019 tracker. [Data Collection]. London School of Hygiene & Tropical Medicine, London, United Kingdom. https://vac-lshtm.shinyapps.io/ncov_tracker/

Pavelka, M, van Zandvoort, K, Abbott, S, Sherratt, K, Majdan, M, Jarcuska, P, Krajci, M, Flasche, S and Funk, S (2021). Data and R code accompanying the manuscript "The impact of population-wide rapid antigen testing on SARS-CoV-2 prevalence in Slovakia". [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.4570938

Pearson, CAB, Russell, TW and Kucharski, AJ (2021). cmmid/SA2UK. [Data Collection]. Github. https://github.com/cmmid/SA2UK

Pearson, CAB, Van zandvoort, K, Jarvis, CI, Davies, NG, Thompson, S, Checchi, F, Jit, M, Eggo, RM and LSHTM CMMID COVID-19 Working Group (2020). Projections of COVID-19 epidemics in LMIC countries. [Data Collection]. London School of Hygiene & Tropical Medicine, London, United Kingdom. https://doi.org/10.17037/DATA.00001564.

Phelan, J and Deelder, W (2020). COVID-Profiler. [Data Collection]. London School of Hygiene & Tropical Medicine, London, United Kingdom. https://github.com/jodyphelan/covid-profiler

Prem, K, Liu, Y, Russell, TW, Kucharski, AJ, Eggo, RM, Davies, N, Jit, M, Klepac, P, Flasche, S, Clifford, S, Pearson, CAB, Munday, JD, Abbott, S, Gibbs, H, Rosello, A, Quilty, BJ, Jombart, T, Sun, F, Diamond, C, Gimma, A, Van zandvoort, K, Funk, S, Jarvis, CI, Edmunds, WJ, Bosse, NI and Hellewell, J (2020). Age-structured SEIR model for COVID-19 outbreak in Wuhan, China. [Data Collection]. Github. https://github.com/kieshaprem/covid19-agestructureSEIR-wuhan-social-distancing

Prem, K, Van Zandvoort, K, Klepac, P, Eggo, RM, Davies, N, CMMID nCov working group, Cook, AR and Jit, M (2020). kieshaprem/synthetic-contact-matrices. [Data Collection]. Github. https://github.com/kieshaprem/synthetic-contact-matrices

Q

Quilty, BJ, Hellewell, J, Clifford, S and CMMID COVID-19 working group (2021). R code for: "Confirmatory testing with a second lateral flow test may mitigate false positives at low levels of SARS-CoV-2 prevalence in English schools". [Data Collection]. London School of Hygiene & Tropical Medicine, London, United Kingdom. https://doi.org/10.17037/DATA.00002074.

R

Russell, TW, Golding, N, Hellewell, J, Abbott, S, Pearson, CAB, Van zandvoort, K, Jarvis, CI, Gibbs, H, Liu, Y, Eggo, RM, Edmunds, WJ, Kucharski, AJ and CMMID COVID-19 working group (2020). Reconstructing the global dynamics of unreported COVID-19 cases and infections. [Data Collection]. Github. https://github.com/thimotei/covid_underreporting

Russell, TW, Hellewell, J, Abbott, S, Jarvis, C, Zandvoort, Kv, Ratnayake, R, CMMID nCov working group, Flasche, S, Eggo, RM, Edmunds, WJ and Kucharski, AJ (2020). thimotei/CFR_calculation. [Data Collection]. Github. https://github.com/thimotei/CFR_calculation

Russell, TW, Hellewell, J, Jarvis, CI, Van-Zandvoort, K, Abbott, S, Ratnayake, R, Flasche, S, Eggo, RM and Kucharski, AJ (2020). Estimating the infection and case fatality ratio for COVID-19 using age-adjusted data from the outbreak on the Diamond Princess cruise ship. [Data Collection]. Github. https://github.com/thimotei/cCFRDiamondPrincess

Russell, TW, Wu, JT, Clifford, S, CMMID COVID-19 working group, Edmunds, WJ, Kucharski, AJ and Jit, M (2020). thimotei/covid_travel_restrictions. [Data Collection]. Github. https://github.com/thimotei/covid_travel_restrictions

S

Sherratt, K (2020). epiforecasts/rt-comparison-uk-public: v1.0.0. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.4029074

Sherratt, K, Bevan, J, Gibbs, H, Finger, F, Hellewell, J, Campbell, P, Funk, S, Boyes, R, Barks, P, , M, Lee, H, Hickson, J and Meakin, S (2021). epiforecasts/covidregionaldata: Beta release. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.3957539

T

Tazare, J (2020). johntaz/COVID-Collateral. [Data Collection]. Github. https://github.com/johntaz/COVID-Collateral

Thomas, S (2020). COVID-19 risk group - Neurological disease codelist. [Data Collection]. London School of Hygiene & Tropical Medicine, London, United Kingdom. https://doi.org/10.17037/DATA.00001704.

Tomlinson, LA, Iwagami, M, Bidulka, P and Wong, AY (2020). Supplementary data for “Comparisons of Staphylococcus aureus infection and other outcomes between users of angiotensin-converting-enzyme inhibitors and angiotensin II receptor blockers: lessons for COVID-19 from a nationwide cohort study”. [Data Collection]. London School of Hygiene & Tropical Medicine, London, United Kingdom. https://doi.org/10.17037/PUBS.04656578.

V

Vaccine Centre (2020). COVID-19 vaccine development pipeline. [Data Collection]. London School of Hygiene & Tropical Medicine, London, United Kingdom. https://vac-lshtm.shinyapps.io/ncov_vaccine_landscape/

W

Walker, J, Grint, D, Strongman, H, Eggo, RM, Peppa, M, Minassian, C, Mansfield, KE, Rentsch, C, Douglas, IJ, Mathur, R, Wong, A, Quint, JK, Andrews, N, Lopez-bernal, J, Scott, A, Ramsay, M, Smeeth, L and McDonald, H (2020). UK prevalence of risk factors for severe COVID-19 disease, by age and region: point prevalence estimates in 2019 and 2014, using electronic health records. [Data Collection]. London School of Hygiene & Tropical Medicine, London, United Kingdom. https://doi.org/10.17037/DATA.00001833.

Williamson, E, Walker, AJ, Bhaskaran, KJ, Bacon, S, Bates, C, Morton, CE, Curtis, HJ, Mehrkar, A, Evans, D, Inglesby, P, Cockburn, J, Mcdonald, HI, MacKenna, B, Tomlinson, L, Douglas, IJ, Rentsch, CT, Mathur, R, Wong, A, Grieve, R, Harrison, D, Forbes, H, Schultze, A, Croker, RT, Parry, J, Hester, F, Harper, S, Perera, R, Evans, S, Smeeth, L and Goldacre, B (2020). opensafely/risk-factors-research. [Data Collection]. Github. https://github.com/ebmdatalab/opensafely-risk-factors-research

Y

Yakob, L and Nightingale, E (2020). lwyakob/COVIDsaturates. [Data Collection]. Github. https://github.com/lwyakob/COVIDsaturates

This list was generated on Sat Apr 17 02:27:06 2021 BST.