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13. Association of SARS-CoV-2 clades with clinical, inflammatory and virologic outcomes: An observational study

Author

Young, Barnaby E, Wei, Wycliffe E, Fong, Siew-Wai, Mak, Tze-Minn, Anderson, Danielle E, Chan, Yi-Hao, Pung, Rachael, Heng, Cheryl SY, Ang, Li Wei, Zheng, Adrian Kang Eng, Lee, Bernett, Kalimuddin, Shirin, Pada, Surinder, Tambyah, Paul A, Parthasarathy, Purnima, Tan, Seow Yen, Sun, Louisa, Smith, Gavin JD, Lin, Raymond Tzer Pin, Leo, Yee-Sin, Renia, Laurent, Wang, Lin-Fa, Ng, Lisa FP, Maurer-Stroh, Sebastian, Lye, David Chien, and Lee, Vernon J

Published
2021
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15. Connecting clusters of COVID-19: an epidemiological and serological investigation

Author

Yong, Sarah Ee Fang, Anderson, Danielle Elizabeth, Wei, Wycliffe E, Pang, Junxiong, Chia, Wan Ni, Tan, Chee Wah, Teoh, Yee Leong, Rajendram, Priyanka, Toh, Matthias Paul Han Sim, Poh, Cuiqin, Koh, Valerie T J, Lum, Joshua, Suhaimi, Nur-Afidah Md, Chia, Po Ying, Chen, Mark I-Cheng, Vasoo, Shawn, Ong, Benjamin, Leo, Yee Sin, Wang, Linfa, and Lee, Vernon J M

Published
2020
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20. Virological and serological kinetics of SARS-CoV-2 Delta variant vaccine breakthrough infections: a multicentre cohort study

Author

Chia, Po Ying, Ong, Sean Wei Xiang, Chiew, Calvin J., Ang, Li Wei, Chavatte, Jean-Marc, Mak, Tze-Minn, Cui, Lin, Kalimuddin, Shirin, Chia, Wan Ni, Tan, Chee Wah, Chai, Louis Yi Ann, Tan, Seow Yen, Zheng, Shuwei, Lin, Raymond Tzer Pin, Wang, Linfa, Leo, Yee-Sin, Lee, Vernon J., Lye, David Chien, and Young, Barnaby Edward

Published
2022
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27. Additional file 1 of Relative role of border restrictions, case finding and contact tracing in controlling SARS-CoV-2 in the presence of undetected transmission: a mathematical modelling study

Author

Pung, Rachael, Clapham, Hannah E., Russell, Timothy W., Lee, Vernon J., and Kucharski, Adam J.

Abstract

Additional file 1: Table S1. Mathematical notations. Table S2. Notified and modelled missed imported wild-type SARS-CoV-2 infections in 2020. Table S3. Summary of observed data and modelled outputs for wild-type SARS-CoV-2 transmission. Fig. S1. Contour plots to show the correlation between model parameters. Fig. S2. Posterior estimates for model fitted to time series of linked and unlinked SARS-CoV-2 wild type cases in 2020 using informative and non-informative priors. Fig. S3. Posterior density of the parameters for model fitted to time series of linked and unlinked SARS-CoV-2 wild type cases in 2020 using informative and non-informative priors. Fig. S4. Reproduction number, R of a SARS-CoV-2 wild-type in 2020 and Delta variant case in 2021. Fig. S5. Reproduction number, R of a SARS-CoV-2 Delta variant case in 2021 after adjusting for vaccine coverage and vaccine effectiveness and using notified cases with no information of the case linkage for model fitting. Fig. S6. Posterior estimates for model fitted to time series of SARS-CoV-2 Delta variant cases (without accounting for case linkage) in 2021 using informative and non-informative priors. Fig. S7. Posterior density of the parameters for model fitted to time series of linked and unlinked SARS-CoV-2 Delta variant cases (without accounting for case linkage) in 2021 using informative and non-informative priors. Fig. S8. Daily incidence of COVID-19 cases in Singapore arising from SARS-CoV-2 wild-type transmission in 2020. Fig. S9. Markov chain Monte Carlo trace plots for parameters modelling wild-type SARS-CoV-2 transmission in 2020. Fig. S10. Markov chain Monte Carlo trace plots for parameters modelling SARS-CoV-2 Delta variant transmission in 2021.

Published
2023
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30. Analysis of COVID-19 Incidence and Severity Among Adults Vaccinated With 2-Dose mRNA COVID-19 or Inactivated SARS-CoV-2 Vaccines With and Without Boosters in Singapore

Author

Ng, Oon Tek, primary, Marimuthu, Kalisvar, additional, Lim, Nigel, additional, Lim, Ze Qin, additional, Thevasagayam, Natascha May, additional, Koh, Vanessa, additional, Chiew, Calvin J., additional, Ma, Stefan, additional, Koh, Mingshi, additional, Low, Pin Yan, additional, Tan, Say Beng, additional, Ho, Joses, additional, Maurer-Stroh, Sebastian, additional, Lee, Vernon J. M., additional, Leo, Yee-Sin, additional, Tan, Kelvin Bryan, additional, Cook, Alex R., additional, and Tan, Chorh Chuan, additional

Published
2022
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32. Preparedness for emerging epidemic threats: a Lancet Infectious Diseases Commission

Author

Lee, Vernon J., Aguilera, Ximena, Heymann, David L., Wilder-Smith, Annelies, Bausch, Daniel G., Briand, Sylvie, Bruschke, Christianne, Carmo, Eduardo H., Cleghorn, Sean, Dandona, Lalit, Donnelly, Christl, Fall, Ibrahima Socé, Halton, Jane, Hatchett, Richard, Hong, Felicia, Horby, Peter, Ihekweazu, Chikwe, Jacobs, Michael, Khan, Kamran, Lin, Yijun, Leung, Gabriel, Low, Constance, McDonald, Bethan F., Memish, Ziad A., Morhard, Ryan, Ng, Deborah HL, Nkengasong, John, Pang, Junxiong, Redd, Stephen C., Tan, Karen, Yeo, Wen Qing, Lee, Vernon J, and Heymann, David

Published
2020
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33. Using a HIV registry to develop accurate estimates for the HIV care cascade – the Singapore experience

Author

Ho, Zheng Jie Marc, Huang, Flora, Wong, Chen Seong, Chua, Lily, Stefan, Chen, Mark I?Cheng, and Lee, Vernon J.

Subjects
Registries (in medicine) -- Management, Prevalence studies (Epidemiology) -- Methods, AIDS (Disease) -- Research, AIDS research, HIV infection -- Distribution, Company business management, Company distribution practices, Health
Abstract

: Introduction: Achieving UNAIDS 90‐90‐90 targets is a crucial step towards ending the AIDS epidemic. Many countries have published estimates of care cascades, although often with methodological limitations. We describe an approach that used the national HIV registry as a starting‐point to determine the HIV care cascade and resulting UNAIDS 90‐90‐90 estimates for Singapore in 2014. Methods: HIV is a legally notifiable disease in Singapore. The anonymized HIV registry data provided for a back‐calculation model from the European Centre for Disease Prevention and Control to obtain 2014 estimates for the total number of persons living with HIV (PLHIV), and the count in the registry for proportions diagnosed with HIV and linked to care. Using additional data collected for a simple random sample from the registry, outcomes in 2015 and 2016 were ascertained retrospectively to derive proportions for those retained in care, on antiretroviral therapy, and achieved viral suppression. Findings were extrapolated to derive national estimates and UN90‐90‐90 estimates. Bootstrapped samples from the model and sample were used to derive 95% confidence intervals. Results: An estimated 6900 (95% CI 6650, 7050) persons were living with HIV and AIDS in 2014. Of these, 4948 were diagnosed with HIV, and 4820 had been linked to care. The random sample of 500 persons was further analysed, and of these, 87.2% were retained in care, 84.6% on antiretroviral therapy, and 79.6% had suppressed viral loads. The proportions of HIV‐infected individuals on antiretroviral therapy and achieving viral suppression were 60.7% (95% CI 58.4, 63.6) and 57.1% (95% CI 55.0, 60.5) respectively. The corresponding UNAIDS 90‐90‐90 estimates were 71.7% (95% CI 70.0, 74.2) of all persons diagnosed; 84.6% (95% CI 81.6, 87.4) of diagnosed persons being on antiretroviral therapy, and 94.1% (95% CI 91.6, 96.2) of persons on therapy having achieved viral suppression. Conclusions: A national HIV registry, alongside back‐calculation and additional data from a sample, can be used to estimate attainment of UNAIDS 90‐90‐90 targets and identify system gaps. The registry had advantages of providing a well‐established, comprehensive capture of diagnosed persons and easily accessible data. The same approach can be used elsewhere if similar data are available., Introduction Combination antiretroviral therapy (ART) has greatly reduced HIV‐associated mortality, morbidity and transmissibility. However, new infections, diagnoses of AIDS and deaths attributable to HIV/AIDS remain high. In 2014, the Joint [...]

Published
2019
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35. Impact of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Vaccination and Pediatric Age on Delta Variant Household Transmission

Author

Ng, Oon Tek, primary, Koh, Vanessa, additional, Chiew, Calvin J, additional, Marimuthu, Kalisvar, additional, Thevasagayam, Natascha May, additional, Mak, Tze Minn, additional, Chua, Joon Kiat, additional, Ong, Shannen Si Hui, additional, Lim, Yong Kai, additional, Ferdous, Zannatul, additional, Johari, Alifa Khairunnisa bte, additional, Cui, Lin, additional, Lin, Raymond Tzer Pin, additional, Tan, Kelvin Bryan, additional, Cook, Alex R, additional, Leo, Yee Sin, additional, and Lee, Vernon J M, additional

Published
2022
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36. Epidemiological and Clinical Predictors of COVID-19

Author

Sun, Yinxiaohe, Koh, Vanessa, Marimuthu, Kalisvar, Ng, Oon Tek, Young, Barnaby, Vasoo, Shawn, Chan, Monica, Lee, Vernon J M, De, Partha P, Barkham, Timothy, Lin, Raymond T P, Cook, Alex R, Leo, Yee Sin, Lian Lim, Poh, Ang, Brenda, Chuan Lee, Cheng, Lye, David Chien Boon, Ling, Li Min, Lee, Lawrence Soon-U, Sadarangani, Sapna, Seong Wong, Chen, Lee, Tau Hong, Junhao Lin, Ray, Chia, Po Ying, Sadasiv, Mucheli Sharavan, Ng, Deborah Hee Ling, Choy, Chiaw Yee, Yeo, Tsin Wen, Tan, Glorijoy Shi En, Chan, Yu Kit, Tay, Jun Yang, Lee, Pei Hua, Ong, Sean Wei Xiang, Sutjipto, Stephanie, Wee, Ian Liang En, Frederico, Dimatatac, Go, Chi Jong, and Isais, Florante Santo

Subjects
Male, 0301 basic medicine, Severe Acute Respiratory Syndrome, Logistic regression, Polymerase Chain Reaction, COVID-19 Testing, 0302 clinical medicine, Epidemiology, risk factors, Mass Screening, Medicine, 030212 general & internal medicine, Child, Aged, 80 and over, Singapore, Middle Aged, prediction model, AcademicSubjects/MED00290, Infectious Diseases, Population study, Female, medicine.symptom, Coronavirus Infections, Adult, Microbiology (medical), medicine.medical_specialty, Adolescent, Pneumonia, Viral, Betacoronavirus, Young Adult, 03 medical and health sciences, Correspondence, Major Article, Humans, Pandemics, Mass screening, Aged, Retrospective Studies, Receiver operating characteristic, Clinical Laboratory Techniques, Diagnostic Tests, Routine, SARS-CoV-2, business.industry, Sputum, COVID-19, Retrospective cohort study, Immunoglobulin A, 030104 developmental biology, Immunoglobulin G, Case-Control Studies, Emergency medicine, Akaike information criterion, business
Abstract

Background Rapid identification of COVID-19 cases, which is crucial to outbreak containment efforts, is challenging due to the lack of pathognomonic symptoms and in settings with limited capacity for specialized nucleic acid–based reverse transcription polymerase chain reaction (PCR) testing. Methods This retrospective case-control study involves subjects (7–98 years) presenting at the designated national outbreak screening center and tertiary care hospital in Singapore for SARS-CoV-2 testing from 26 January to 16 February 2020. COVID-19 status was confirmed by PCR testing of sputum, nasopharyngeal swabs, or throat swabs. Demographic, clinical, laboratory, and exposure-risk variables ascertainable at presentation were analyzed to develop an algorithm for estimating the risk of COVID-19. Model development used Akaike’s information criterion in a stepwise fashion to build logistic regression models, which were then translated into prediction scores. Performance was measured using receiver operating characteristic curves, adjusting for overconfidence using leave-one-out cross-validation. Results The study population included 788 subjects, of whom 54 (6.9%) were SARS-CoV-2 positive and 734 (93.1%) were SARS-CoV-2 negative. The median age was 34 years, and 407 (51.7%) were female. Using leave-one-out cross-validation, all the models incorporating clinical tests (models 1, 2, and 3) performed well with areas under the receiver operating characteristic curve (AUCs) of 0.91, 0.88, and 0.88, respectively. In comparison, model 4 had an AUC of 0.65. Conclusions Rapidly ascertainable clinical and laboratory data could identify individuals at high risk of COVID-19 and enable prioritization of PCR testing and containment efforts. Basic laboratory test results were crucial to prediction models., A risk score incorporating easily ascertainable demographic, clinical evaluation, and clinical testing covariates to identify patients at high risk of COVID-19 can help prioritize subjects for testing and public health measures to prevent onward transmission, especially in resource-limited settings.

Published
2020

39. Epidemiological, Clinical, and Phylogenetic Characteristics of the First SARS-CoV-2 Transmission in a Nursing Home of Singapore: A Prospective Observational Investigation

Author

Pang, Junxiong, primary, Tan, Huei Nuo, additional, Mak, Tze Minn, additional, Octavia, Sophie, additional, Maurer-Stroh, Sebastian, additional, Sirota, Fernanda L., additional, Chan, Mark Peng Chew, additional, Leong, Ian Yi Onn, additional, Koh, Valerie T. J., additional, Ooi, Peng Lim, additional, Vasoo, Shawn, additional, Fisher, Dale, additional, Cui, Lin, additional, Rafman, Heidi, additional, Cutter, Jeffery, additional, and Lee, Vernon J., additional

Published
2022
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42. Clinical and virological features of SARS-CoV-2 variants of concern: a retrospective cohort study comparing B.1.1.7 (Alpha), B.1.315 (Beta), and B.1.617.2 (Delta)

Author

Ong, Sean Wei Xiang, Chiew, Calvin J, Ang, Li Wei, Mak, Tze-Minn, Cui, Lin, Toh, Matthias Paul H S, Lim, Yi Ding, Lee, Pei Hua, Lee, Tau Hong, Chia, Po Ying, Maurer-Stroh, Sebastian, Lin, Raymond T P, Leo, Yee-Sin, Lee, Vernon J, Lye, David Chien, and Young, Barnaby Edward

Subjects
B.1.617.2, Cohort Studies, AcademicSubjects/MED00290, SARS-CoV-2, Major Article, COVID-19, severity, Humans, variants of concern, Retrospective Studies
Abstract

Background he impact of SARS-CoV-2 variants of concern (VOCs) on disease severity is unclear. In this retrospective study, we compared outcomes of patients infected with B.1.1.7, B.1.351, and B.1.617.2 with those with wild-type strains from early 2020. Methods National surveillance data from 1-January-2021 to 22-May-2021 were obtained from the Ministry of Health, and outcomes in relation to VOC were explored. Detailed patient level data from all patients with VOC infection admitted to our center between 20-December-2020 and 12-May-2021 were analyzed. Clinical outcomes were compared with a cohort of 846 patients admitted from January-April 2020. Results 829 patients in Singapore in the study period were infected with these 3 VOCs. After adjusting for age and sex, B.1.617.2 was associated with higher odds of oxygen requirement, ICU admission, or death (adjusted odds ratio (aOR) 4.90, [95% CI 1.43-30.78]). 157 of these patients were admitted to our center. After adjusting for age, sex, comorbidities, and vaccination, aOR for pneumonia with B.1.617.2 was 1.88 [95% CI 0.95-3.76]) compared with wild-type. These differences were not seen with B.1.1.7 and B.1.351. Vaccination status was associated with decreased severity. B.1.617.2 was associated with significantly lower PCR Ct values and longer duration of Ct value ≤30 (median duration 18 days for B.1.617.2, 13 days for wild-type). Conclusions There was a signal toward increased severity associated with B.1.617.2. The association of B.1.617.2 with lower Ct value and longer viral shedding provides a potential mechanism for increased transmissibility. These findings provide an impetus for the rapid implementation of vaccination programs.

Published
2021

44. Epidemiological and virological characteristics of influenza B: results of the Global Influenza B Study

Author

Caini, Saverio, Huang, Sue Q., Ciblak, Meral A., Kusznierz, Gabriela, Owen, Rhonda, Wangchuk, Sonam, Henriques, Cláudio M. P., Njouom, Richard, Fasce, Rodrigo A., Yu, Hongjie, Feng, Luzhao, Zambon, Maria, Clara, Alexey W., Kosasih, Herman, Puzelli, Simona, Kadjo, Herve A., Emukule, Gideon, Heraud, Jean-Michel, Ang, Li Wei, Venter, Marietjie, Mironenko, Alla, Brammer, Lynnette, Mai, Le Thi Quynh, Schellevis, François, Plotkin, Stanley, Paget, John, Rudi, Juan Manuel, Dorji, Kunzang, Marins, José Ricardo Pio, de Almeida, Walquiria Aparecida Ferreira, Vernet, Marie-Astrid, Vernet, Guy, Andrade, Winston, Yang, Juan, Li, Ming, Lara, Jenny, de Lozano, Celina, Pebody, Richard, Ellis, Joanna, Green, Helen, Castillo, Leticia, Matute, Maria Luisa, Nurhayati, Donatelli, Isabella, Daouda, Coulibaly, Mott, Joshua A., Razanajatovo, Norosoa Harline, Randrianasolo, Laurence, Lopez, Liza, Balmaseda, Angel, Moreno, Brechla, Cutter, Jeffrey, Lee, Vernon J., Cohen, Cheryl, Badur, Selim, Radchenko, Larysa, and Bresee, Joseph

Published
2015
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46. Age-related risk of household transmission of COVID-19 in Singapore

Author

Pung, Rachael, Park, Minah, Cook, Alex R, and Lee, Vernon J

Abstract

Prior to the implementation of social distancing measures, we monitored the close family contacts of the first 400 cases of COVID-19 in Singapore for SARS-CoV-2 infection to determine the risk of infection with age. Adjusting for gender and household size, the risk of COVID-19 infection in household contacts was found to increase with age.

Published
2021

47. Seroepidemiologic effects of influenza A(H1N1)pdm09 in Australia, New Zealand, and Singapore

Author

Trauer, James M., Bandaranayake, Don, Booy, Robert, Chen, Mark I., Cretikos, Michelle, Drowse, Gary K., Dwyer, Dominic E., Greenberg, Michael E., Huang, Q. Sue, Khandaker, Gulam, Kok, Jen, Laurie, Karen L., Lee, Vernon J., McVerion, Jodie, Walter, Scott, and Markey, Peter G.

Subjects
Swine influenza -- Analysis, Agglutination tests -- Health aspects, Epidemiology -- Analysis, Health
Abstract

Australia, New Zealand (NZ), and Singapore all experience regular influenza seasons that coincide with winter in the Southern Hemisphere. After pandemic influenza A(H1N1) 2009 (A[H1N1]pdm09) emerged during spring in North [...]

Published
2013
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48. Clinical and Virological Features of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Variants of Concern: A Retrospective Cohort Study Comparing B.1.1.7 (Alpha), B.1.351 (Beta), and B.1.617.2 (Delta)

Author

Ong, Sean Wei Xiang, primary, Chiew, Calvin J, additional, Ang, Li Wei, additional, Mak, Tze Minn, additional, Cui, Lin, additional, Toh, Matthias Paul H S, additional, Lim, Yi Ding, additional, Lee, Pei Hua, additional, Lee, Tau Hong, additional, Chia, Po Ying, additional, Maurer-Stroh, Sebastian, additional, Lin, Raymond T P, additional, Leo, Yee Sin, additional, Lee, Vernon J, additional, Lye, David Chien, additional, and Young, Barnaby Edward, additional

Published
2021
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49. Virological and serological kinetics of SARS-CoV-2 Delta variant vaccine-breakthrough infections: a multi-center cohort study

Author

Chia, Po Ying, primary, Xiang Ong, Sean Wei, additional, Chiew, Calvin J, additional, Ang, Li Wei, additional, Chavatte, Jean-Marc, additional, Mak, Tze-Minn, additional, Cui, Lin, additional, Kalimuddin, Shirin, additional, Chia, Wan Ni, additional, Tan, Chee Wah, additional, Ann Chai, Louis Yi, additional, Tan, Seow Yen, additional, Zheng, Shuwei, additional, Pin Lin, Raymond Tzer, additional, Wang, Linfa, additional, Leo, Yee-Sin, additional, Lee, Vernon J, additional, Lye, David Chien, additional, and Young, Barnaby Edward, additional

Published
2021
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50. Risk scorecard to minimize impact of COVID-19 when reopening

Author

Lim, Shin B, primary, Pung, Rachael, additional, Tan, Kellie, additional, Lang, Jocelyn H S, additional, Yong, Dominique Z X, additional, Teh, Shi-Hua, additional, Quah, Elizabeth, additional, Sun, Yinxiaohe, additional, Ma, Stefan, additional, and Lee, Vernon J M, additional

Published
2021
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