A

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

Abbott, S, Bosse, N, DeWitt, M, Rau, A, Chateigner, A, Mareschal, S and Hellewell, J (2020). epiforecasts/EpiSoon. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.3746394

Abbott, S and Funk, S (2021). epiforecasts/covid19.sgene.utla.rt. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.5236661

Abbott, S and Fyles, M (2021). martyn1fyles/HouseholdContactTracing. [Data Collection]. Github. https://github.com/martyn1fyles/HouseholdContactTracing

Abbott, S, Russell, TW, Hellewell, J and Kucharski, AJ (2023). thimotei/legacy_ct_modelling: Final version. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.10223417

Abbott, S, Sherratt, K, Gibbs, H, Finger, F, Campbell, P, Hellewell, J, Barks, P, Meakin, S and Lee, H (2020). epiforecasts/NCoVUtils. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.3635417

Adetifa, IMO, Uyoga, S, Gitonga, JN, Mugo, D, Otiende, M, Nyagwange, J, Karanja, HK, Tuju, J, Wanjiku, P, Aman, R, Mwangangi, M, Amoth, P, Kasera, K, Ng’ang’a, W, Rombo, C, Yegon, C, Kithi, K, Odhiambo, E, Rotich, T, Orgut, I, Kihara, S, Bottomley, C, Kagucia, EW, Gallagher, KE, Etyang, A, Voller, S, Lambe, T, Wright, D, Barasa, E, Tsofa, B, Bejon, P, Ochola-Oyier, LI, Agweyu, A, Scott, JAG and Warimwe, GM (2021). Replication Data for: Temporal trends of SARS-CoV-2 seroprevalence in transfusion blood donors during the first wave of the COVID-19 epidemic in Kenya. [Data Collection]. Harvard Dataverse. https://doi.org/10.7910/DVN/FQUNVD

Adeyemi, OO, Ndodo, ND, Sulaiman, MK, Ayansola, OT, Buhari, OIN, Akanbi, OA, Bolarinwa, OA, Chukwu, C, Joel, IY, Omoare, AA, Wahab, KW, Obiekea, C, Buhari, MO, Ahumibe, A, Kolawole, CF, Okoi, C, Omotesho, OB, Mba, N, Adeniyi, O, Babatunde, O, Akintunde, N, Ayinla, G, Akande, OW, Odunola, RA, Saka, MJ, Musa, OI, Durotoye, IA, Ihekweazu, C, Adetifa, IM and Fadeyi, A (2023). SARS-CoV-2 variants-associated outbreaks of COVID-19 in a tertiary institution, North-Central Nigeria: Implications for epidemic control. S1 Data. [Data Collection]. PLOS ONE. https://doi.org/10.1371/journal.pone.0280756.s003

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

Alexander, N, Dye, C, Busch, MP, Buss, L, Prete Jr, CA, Brady, OJ, Mee, P, Abrahim, CMM, Crispim, MAE, da Costa, AG, Salomon, T, Mayaud, P, Oikawa, MK, Faria, N and Sabino, EC (2024). Dynamics of SARS-CoV-2 infection over two epidemic waves in Manaus, Brazil: a serological study of seven thousand blood donors. [Data Collection]. Open Science Framework. https://doi.org/10.17605/OSF.IO/ZVUCJ

Assefa, N, Demissie, L, Teklemarriam, Z, Oundo, JO, Madrid, L, Dessie, Y and Scott, JAG (2021). Replication Data for: Seroprevalence of anti–SARS-CoV-2 antibodies in women attending antenatal care in eastern Ethiopia. [Data Collection]. Harvard Dataverse. https://doi.org/10.7910/DVN/XIWCXN

actions-user, Sherratt, K, Gruson, H, Funk, S, Bracher, J, BIOCOM-SC, Walraven, R, miraanto, h-veronika, Rodiah, I, gr3gr3, Kraus, D, hgurung-iem, epiforecasts-bot, Xu, FT, Heyder, S, aniruddhadiga, Abbott, S, Sun, T, Mingio, M, Deuschel, J, pmontman, janezz25, neele-itwm, Gibson, G, EpiGraph, Tarantino, B, Karlen, D, Bhatia, S and borjarv (2022). covid19-forecast-hub-europe/covid19-forecast-hub-europe. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.6401421

B

Barnard, RC (2022). rosannaclairebarnard/covidm-mtd-Omi. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.6806636

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

Bottomley, C (2021). christian-bottomley/mixture_model_sarscov2. [Data Collection]. Github. https://github.com/christian-bottomley/mixture_model_sarscov2

Bracher, J, Wolffram, D, Deuschel, J, Görgen, K, Ketterer, J, Ullrich, A, Abbott, S, Barbarossa, M, Bertsimas, D, Bhatia, S, Bodych, M, Bosse, NI, Burgard, J, Castro, L, Fairchild, G, Fuhrmann, J, Funk, S, Gogolewski, K, Gu, Q, Heyder, S, Hotz, T, Kheifetz, Y, Kirsten, H, Krueger, T, Krymova, E, Li, M, Meinke, J, Michaud, I, Niedzielewski, K, Ożański, T, Rakowski, F, Scholz, M, Soni, S, Srivastava, A, Zieliński, J, Zou, D, Gneiting, T and Schienle, M (2021). KITmetricslab/covid19-forecast-hub-de. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.4439666

Brand, S and Ojal, J (2021). ojal/KenyaSerology. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.4705243

Bresser, M, Erhardt, R, Shanaube, K, Simwinga, M, Mahlatsi, P, Belus, J, Schaap, A, Amstutz, A, Gachie, T, Glass, T, Kangolo, B, Mota, M, Floyd, S, Katende, B, Klinkenberg, E, Ayles, H, Reither, K and Ruperez, M (2023). Evaluation of COVID-19 antigen rapid diagnostic tests for self-testing in Lesotho and Zambia - Lesotho data. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.8429840

Bresser, M, Erhardt,, R, Shanaube, K, Simwinga, M, Mahlatsi, P, Belus, J, Schaap, A, Amstutz, A, Gachie, T, Glass, T, Kangolo, B, Mota, M, Floyd, S, Katende, B, Klinkenberg, E, Ayles, H, Reither, K and Ruperez, M (2023). Evaluation of COVID-19 antigen rapid diagnostic tests for self-testing in Lesotho and Zambia - Zambia data. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.8426699

Burke, R (2021). rachaelmburke/tbcovidblantyre. [Data Collection]. Github. https://github.com/rachaelmburke/tbcovidblantyre

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, ÁD, 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, ÁD, 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

Cerqueira-Silva, T, de Araujo Oliveira, V, Paixão, ES, Júnior, JB, Penna, GO, Werneck, GL, Pearce, N, Barreto, ML, Boaventura, VS and Barral-Netto, M (2022). Duration of protection of CoronaVac plus heterologous BNT162b2 booster in the Omicron period in Brazil. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.6657862

Chapman, LAC (2021). LloydChapman/COVID_homeless_modelling. [Data Collection]. Github. https://github.com/LloydChapman/COVID_homeless_modelling

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

Checchi, F (2022). francescochecchi/mortality_capture_recapture_analysis. [Data Collection]. Github. https://github.com/francescochecchi/mortality_capture_recapture_analysis

Clifford, S and Hackman, J (2023). Effectiveness of BNT162b2 and ChAdOx1 against SARS-CoV-2 household transmission. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.7618847

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

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 (2021). CSV-format data for: Increased mortality in community-tested cases of SARS-CoV-2 lineage B.1.1.7. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.5105920

Davies, NG (2020). cmmid/covid-age. [Data Collection]. Github. https://github.com/cmmid/covid-age

Davies, NG (2020). nicholasdavies/covidm-alpha. [Data Collection]. Github. https://github.com/nicholasdavies/covidm-alpha

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

De Figueiredo, A (2021). Global intent to accept COVID-19 vaccines. [Data Collection]. OSF. https://osf.io/8vezs

De figueiredo, A (2021). Impact of vaccine passports on inclination to accept COVID-19 vaccinations in the UK. [Data Collection]. OSF. https://osf.io/xh9p7/

Dobreva, Z, Gimma, A, Rohan, H, Djoudalbaye, B, Tshangela, A, Jarvis, CI, Van Zandvoort, K and Quaife, M (2022). Additional file 1 of Characterising social contacts under COVID-19 control measures in Africa. [Data Collection]. Figshare. https://doi.org/10.6084/m9.figshare.21316250.v1

E

Els, F, Maree, G, Naidoo, Y, Naidoo, L, Mahamuza, P, Macheke, M, Ndlovu, N, Iwu-Jaja, C, Taukobong, S, Maposa, S, O'reilly, KM, Yousif, M, McCarthy, K and Rachida, S (2025). Wastewater surveillance overcomes socio-economic limitations of laboratory-based surveillance when monitoring disease transmission: the South African experience during the COVID-19 pandemic. [Data Collection]. Figshare. https://doi.org/10.6084/m9.figshare.28227206.v1

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 and Kucharski, AJ (2020). akira-endo/COVID19_backwardtracing. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.4050267

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.

F

Funk, S (2022). epiforecasts/ons_severity_estimates. [Data Collection]. Github. https://github.com/epiforecasts/ons_severity_estimates

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. https://doi.org/10.17037/DATA.00002084.

Gibbs, H (2021). cmmid/uk_movement_communities_covid. [Data Collection]. Github. https://github.com/cmmid/uk_movement_communities_covid

Gibbs, H, Waterlow, NR, Cheshire, J, Danon, L, Liu, Y, Grundy, C, Kucharski, AJ and Eggo, RM (2021). Population disruption: estimating changes in population distribution in the UK during the COVID-19 pandemic - Estimates for Local Authority Districts. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.5013619

Glazik, R (2021). Data supporting "A Snapshot of the Practicality of, and Barriers to, Implementation of COVID-19 Interventions: Public Health and Healthcare Workers' Perceptions". [Data Collection]. London School of Hygiene and Tropical Medicine, London, United Kingdom. https://doi.org/10.17037/DATA.00002321.

Graham, S (2023). grahams99/Enhanced_surveillance_questionnaire. [Data Collection]. Github. https://github.com/grahams99/Enhanced_surveillance_questionnaire

H

Ha, BTT, Ngoc Quang, L, Quoc Thanh, P, Duc, DM, Mirzoev, T and Bui, TMA (2021). Community engagement in the prevention and control of COVID-19: Insights from Vietnam. Qualitative transcripts. [Data Collection]. PLOS One. https://doi.org/10.1371/journal.pone.0254432.s002

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

Hellewell, J, Russell, TW, The SAFER Investigators and Field Study Team, The Crick COVID-19 Consortium, CMMID COVID-19 working group, Beale, R, Kelly, G, Houlihan, C, Nastouli, E and Kucharski, AJ (2020). cmmid/pcr-profile. [Data Collection]. Github. https://github.com/cmmid/pcr-profile

Hodgson, D and Abbott, S (2022). dchodge/hero-study: Version submitted with WOR reviewers comments. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.5215671

J

Jarju, S, Senghore, E, Brotherton, H, Saidykhan, A, Jallow, S, Krubally, E, Sinjanka, E, Ndene, MN, Bajo, F, Sanyang, MM, Saidy, B, Bah, A, Mohammed, NI, Forrest, K, Clarke, E, Dalessandro, U, Sesay, AK, Usuf, E, Cerami, C, Roca, A, Kampmann, B and De silva, T (2022). Circulation of respiratory viruses during the COVID-19 pandemic in the Gambia. [Data Collection]. Open Science Framework. https://doi.org/10.17605/OSF.IO/TSF78

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

Jombart, T, Abbott, S, Gimma, A, Van zandvoort, K and Jarvis, C (2020). Inferring COVID-19 cases from recent death. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.3733046

K

Kitonsa, J, Kamacooko, O, Bahemuka, UM, Kibengo, F, Kakande, A, Wajja, A, Basajja, V, Lumala, A, Ssemwanga, E, Asaba, R, Mugisha, J, Pierce, BF, Shattock, R, Kaleebu, P and Ruzagira, E (2021). Survey data on willingness to participate in COVID-19 vaccine trials among healthcare workers in three Ugandan hospitals. [Data Collection]. London School of Hygiene & Tropical Medicine, London, United Kingdom. https://doi.org/10.17037/DATA.00002168.

Knight, G (2021). gwenknight/hai_first_wave. [Data Collection]. Github. https://github.com/gwenknight/hai_first_wave

Koech, A, Omuse, G, Mugo, A, Mwaniki, I, Mutunga, J, Mukhanya, M, Wanje, O, Mwashigadi, G, Katana, G, Craik, R, Von Dadelszen, P, Le Doare, K, Temmermen, M and The PRECISE Network (2024). SARS-CoV-2 Seroprevalence in Kenya dataset. [Data Collection]. London School of Hygiene & Tropical Medicine, London, United Kingdom. https://doi.org/10.17037/DATA.00003755.

Koltai, M (2021). Source data for "Date of introduction and epidemiologic patterns of SARS-CoV-2 in Mogadishu, Somalia: estimates from transmission modelling of satellite-based excess mortality data in 2020". [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.5534768

Koltai, M (2021). mbkoltai/covid_lmic_model: Model fitting excess mortality data in Mogadishu v1.0. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.5534762

Kucharski, AJ (2021). adamkucharski/covid-import-model. [Data Collection]. Github. https://github.com/adamkucharski/covid-import-model

Kutima, B, Kagucia, W, Mwai, K, Kimani, M, Sigilai, A, Mugo, D, Karani, K, Akech, D, Toroitich, M, Karia, B, Tuju, J, Ziraba, AK, Bigogo, G, Ochieng, C, Onyango, C, Lidechi, S, Munywoki, PK, Uyoga, S, Adetifa, IMO, Ochola-Oyier, LI, Bejon, P, Scott, JAG, Agweyu, A, Warimwe, GM and Nyagwange, J (2023). Replication Data for: Comparative performance of the InBios SCoV-2 DetectTM IgG ELISA and the in-house KWTRP ELISA in detecting SARS-CoV-2 spike IgG antibodies in Kenyan populations. [Data Collection]. Harvard Dataverse. https://doi.org/10.7910/DVN/FOYVMT

L

Laban, N (2021). Comparable exposure to SARS-CoV-2 in young children and healthcare workers in Zambia. [Data Collection]. Figshare. https://doi.org/10.6084/m9.figshare.14237285.v2

Lazarus, JV, Ratzan, S, Palayew, A, Billari, FC, Binagwaho, A, Kimball, S, Larson, HJ, Melegaro, A, Rabin, K, White, TM and El-Mohandes, A (2020). COVID-SCORE: A global survey to assess public perceptions of government responses to COVID-19 (COVID-SCORE-10). [Data Collection]. PLoS One. https://doi.org/10.1371/journal.pone.0240011

Leclerc, QJ (2021). qleclerc/COVID_bed_occupancy. [Data Collection]. Github. https://github.com/qleclerc/COVID_bed_occupancy

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.v5

Lindsey, BB, Villabona-Arenas, CJ, Atkins, KE and Campbell, F (2021). Chjulian/sheffield_HT: Characterising within-hospital SARS-CoV-2 transmission events. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.5769865

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

Liu, Y (2022). yangclaraliu/COVID_Vac_Delay. [Data Collection]. Github. https://github.com/yangclaraliu/COVID_Vac_Delay

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

Liu, Y, Procter, SR, Pearson, CAB, Madriz Montero, A, Torres-Rueda, S, Asfaw, E, Uzochukwu, B, Drake, T, Bergren, E, Eggo, RM, Ruiz, F, Ndembi, N, Nonvignon, J, Jit, M and Vassall, A (2023). yangclaraliu/covid_vac_africa: BMCMed_R3. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.7618748

Liu, Y, Sandmann, FG, Barnard, RC, Pearson, CA, CMMID Working-19 Working Group, Pastore, R, Pebody, R, Flasche, S and Jit, M (2021). Optimising health and economic impacts of COVID-19 vaccine rollout strategies in the WHO European Region. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.4964148

Lovell-Read, FA, Funk, S, Obolski, U, Donnelly, CA and Thompson, RN (2021). Supplementary material from "Interventions targeting non-symptomatic cases can be important to prevent local outbreaks: SARS-CoV-2 as a case study". [Data Collection]. The Royal Society. https://doi.org/10.6084/m9.figshare.c.5416023.v1

M

Mee, P, Alexander, N and Colón-González, FJ (2021). Paul-Mee/clic_brazil. [Data Collection]. Github. https://github.com/Paul-Mee/clic_brazil

Munday, JD (2021). jdmunday/SchoolHouseholdNetworksCOVID: Initial release. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.4552421

Munday, JD and Jarvis, CI (2021). jdmunday/CoMix_schools_reopening. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.5172069

Munday, JD, Jarvis, CI, Gimma, A, Wong, KL, van Zandvoort, K, Funk, S and Edmunds, WJ (2021). CoMix - Age structured contact matrices for 9 key periods of the COVID-19 epidemic in England. [Data Collection]. Zenodo. http://doi.org/10.5281/zenodo.4677018

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

Nilles, EJ and Kucharski, AJ (2024). enilles1/immunoepidemiology. [Data Collection]. Github. https://github.com/enilles1/immunoepidemiology

O

O'Reilly, KM (2022). kath-o-reilly/wbe_prevalence_england_python. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.6674384

Osterrieder, A, Poomchaichote, T, Cuman, G, Pan-ngum, W, Cheah, P, Waithira, N, Mukaka, M, Naemiratch, B, Kulpijit, N, Chanviriyavuth, R, Asarath, S, Ruangkajorn, S, Silan, M, Stoppa, S, Zuanna, GD, Cheah, PK, Ongkili, D, Schneiders, M, Mackworth-Young, CR and Cheah, PY (2020). Online survey questions: Social, ethical and behavioural aspects of COVID-19. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.3764912

P

Palmer, J, Sherratt, K, Martin-Nielsen, R, Bevan, J, Gibbs, H, CMMID COVID-19 Working Group, Funk, S and Abbott, S (2021). covidregionaldata: Subnational data for COVID-19 epidemiology. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.3957539

Parker, E (2021). vac-lshtm/VaC_tracker. [Data Collection]. Github. https://github.com/vac-lshtm/VaC_tracker

Parker, E and Horne, E (2022). opensafely/ckd-coverage-ve. [Data Collection]. Github. https://github.com/opensafely/ckd-coverage-ve

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

Pearce, N (2021). PROTECT initiative extended Covid-19 occupational questionnaire. [Data Collection]. OSF. https://doi.org/10.17605/OSF.IO/HDC8S

Pearson, CAB, Bozzani, F, Procter, SR, Davies, NG, Huda, M, Jensen, HT, Keogh-Brown, M, Khalid, M, Sweeney, S, Torres-Rueda, S, Eggo, RM, Vassall, A and Jit, M (2021). Simulation results for "COVID-19 vaccination in Sindh Province, Pakistan: a modelling study of health impact and cost-effectiveness". [Data Collection]. Zenodo. http://doi.org/10.5281/zenodo.5070957

Pearson, CAB (2021). cmmid/covidTestVac. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.4725814

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

Pillai, AN, Hladish, T, Pearson, CAB, Toh, B, Noah4944 and Stoltzfus, A (2023). tjhladish/covid-abm: Active Vaccination Experiment 2023-02-02. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.7601663

Prem, K (2021). kieshaprem/synthetic-contact-matrices. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.4889499

Prem, K, Liu, Y, Russell, TW, Kucharski, AJ, Eggo, RM, Davies, NG, 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

Pung, R (2023). rachaelpung/covid_missed_infections. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.7538046

Pung, R (2022). rachaelpung/cruise_networks. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.6009026

Pung, R (2021). rachaelpung/serial_interval_covid_b.1.617.2. [Data Collection]. Github. https://github.com/rachaelpung/serial_interval_covid_b.1.617.2

Q

Quaife, M (2020). mquaife/kenya_mixing. [Data Collection]. Github. https://github.com/mquaife/kenya_mixing

Quilty, B (2021). cmmid/covid_quar_test_import_risk. [Data Collection]. Github. https://github.com/cmmid/covid_quar_test_import_risk

Quilty, B (2021). cmmid/quar_test_contact_tracing. [Data Collection]. Github. https://github.com/cmmid/quar_test_contact_tracing

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

Rees, EM, Nightingale, ES, Jafari, Y, Waterlow, NR, Clifford, S, B. Pearson, CA, CMMID Working Group, Jombart, T, Procter, SR and Knight, GM (2020). Additional file 2 of COVID-19 length of hospital stay: a systematic review and data synthesis. [Data Collection]. Figshare. https://doi.org/10.6084/m9.figshare.12910557.v1

Roberts, C, Brindle, H, Rogers, N, Eggo, RM, Enria, L and Lees, S (2021). Data for: "Vaccine Confidence and Hesitancy at the start of COVID-19 vaccine deployment in the UK: An embedded mixed-methods study". [Data Collection]. London School of Hygiene & Tropical Medicine, London, United Kingdom. https://doi.org/10.17037/DATA.00002337.

Rosello, A, Abbott, S and Barnard, RC (2021). rmjlros/COVID19_care_home_NPIs. [Data Collection]. Github. https://github.com/rmjlros/COVID19_care_home_NPIs

Russell, TW (2023). Fits and plot data for the paper: "Combined analyses of within-host SARS-CoV-2 viral kinetics and information on past exposures to the virus in a human cohort identifies intrinsic differences of Omicron and Delta variants". [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.10223385

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 and Kucharski, AJ (2024). thimotei/legacy_nAb_kinetics. [Data Collection]. Github. https://github.com/thimotei/legacy_nAb_kinetics/

S

Sanderson, T (2023). Processed INSDC dataset for MOV analysis. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.8252387

Sanderson, T and Ruis, C (2023). theosanderson/molnupiravir. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.8101002

Scortichini, M, Schneider dos santos, R, De' Donato, De Sario, M, Michelozzi, P, Davoli, M, Masselot, P, Sera, F and Gasparrini, A (2020). gasparrini/ItalyCOVIDdeath. [Data Collection]. Github. https://github.com/gasparrini/ItalyCOVIDdeath

Sera, F, Abbott, S and Roye, D (2021). fsera/COVIDWeather. [Data Collection]. London School of Hygiene & Tropical Medicine, London, United Kingdom. https://doi.org/10.5281/zenodo.5215841

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

Sherratt, K and Funk, S (2022). covid19-forecast-hub-europe/euro-hub-ensemble: Zenodo release. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.6895699

Simons, D (2021). DidDrog11/smoking_covid_bayes. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.4002046

Simons, D, Shahab, L, Brown, J and Perski, O (2021). The association of smoking status with SARS-CoV-2 infection, hospitalisation and mortality from COVID-19: A living rapid evidence review and Bayesian meta-analyses (version 11) - Data. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.4002046

Simons, D, Shahab, L, Brown, J and Perski, O (2020). The association of smoking status with SARS-CoV-2 infection, hospitalisation and mortality from COVID-19: A living rapid evidence review and Bayesian meta-analyses (version 9) - Data. [Data Collection]. Figshare. https://doi.org/10.6084/m9.figshare.12756020.v4

Strongman, H and Carreira, H (2021). STATA Do files for "Factors associated with excess mortality in the first wave of COVID-19 pandemic in the UK: a cohort analysis using the Clinical Practice Research Databank". [Data Collection]. London School of Hygiene & Tropical Medicine, London, United Kingdom. https://doi.org/10.17037/DATA.00002560.

U

Uyoga, S, Adetifa, IM, Otiende, M, Gitonga, JN, Mugo, D, Nyagwange, J, Karanja, HK, Tuju, J, Makale, J, Aman, R, Mwangangi, M, Amoth, P, Kasera, K, Ng’ang’a, W, Chege, E, Yegon, C, Kithi, K, Odhiambo, E, Rotich, T, Orgut, I, Kihara, S, Bottomley, C, Kagucia, EW, Gallagher, KE, Etyang, A, Voller, S, Lambe, T, Wright, D, Barasa, E, Tsofa, B, Mwangangi, J, Bejon, P, Ochola-Oyier, LI, Warimwe, GM, Agweyu, A and Scott, JAG (2021). Replication Data for: Prevalence of SARS-CoV-2 Antibodies from a one-year National Serosurveillance of Kenyan Blood Transfusion Donors. [Data Collection]. Harvard Dataverse. https://doi.org/10.7910/DVN/3E1YSQ

W

Wang, SY, Stark, A, Evan Ray, Bosse, N, Reich, NG, Sherratt, K, Shah, A, Wattanachit, N, Khoale1096, Huang, YD, Gerding, A, Gruson, H, Cramer, E, Shandross, L, Abbott, S and Funk, S (2021). reichlab/covidHubUtils. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.5207939

Waterlow, NR, Van Leeuwen, E, Davies, N, Flasche, S and Eggo, RM (2021). cmmid/coronavirus_immunity. [Data Collection]. Github. https://github.com/cmmid/coronavirus_immunity

Willem, L, Hoang, VT, Funk, S, Coletti, P, Beutels, P and Hens, N (2020). Social Contact Rates (SOCRATES) Data Tool. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.3706787

Woodhouse, M, Aspinall, W, Sparks, R, Brooks-Pollock, E and Relton, CL (2022). Alternative Covid-19 mitigation measures in school classrooms: Analysis using an agent-based model of SARS-CoV-2 transmission. [Data Collection]. Dryad. https://doi.org/10.5061/dryad.pk0p2ngr3

Wu, JT, Mei, S, Luo, S, Leung, K, Liu, D, Lv, Q, Liu, J, Li, Y, Prem, K, Jit, M, Weng, J, Feng, T, Zheng, X and Leung, GM (2021). Table S4 from A global assessment of the impact of school closure in reducing COVID-19 spread. [Data Collection]. Figshare. https://doi.org/10.6084/m9.figshare.16851696.v1

Y

Yakob, L (2021). lwyakob/COVIDquarantine. [Data Collection]. Github. https://github.com/lwyakob/COVIDquarantine

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

Z

Zheng, B (2023). Anaphylaxis events following COVID-19 antiviral and neutralising monoclonal antibody treatment for non-hospitalised patients. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.8144334

Zirimenya, L, Natukunda, A, Nassuna, J, Nkurunungi, G, Elliott, AM and Webb, E (2025). Data supporting "Temporal trends of SARS-CoV-2 exposure in adolescents: a longitudinal pilot study nested in a Uganda birth cohort". [Data Collection]. London School of Hygiene & Tropical Medicine, London, United Kingdom. https://doi.org/10.17037/DATA.00004678.