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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)

24 Pages Posted: 7 Jun 2021

See all articles by Sean Wei Xiang Ong

Sean Wei Xiang Ong

National Centre for Infectious Diseases, Singapore

Calvin J. Chiew

National Centre for Infectious Diseases, Singapore

Li Wei Ang

National Centre for Infectious Diseases, Singapore

Tze-Minn Mak

National Centre for Infectious Diseases, Singapore

Lin Cui

National Centre for Infectious Diseases, Singapore

Matthias Paul HS Toh

National Centre for Infectious Diseases, Singapore

Yi Ding Lim

Ministry of Health, Singapore

Pei Hua Lee

National Centre for Infectious Diseases, Singapore

Tau Hong Lee

National Centre for Infectious Diseases, Singapore

Po Ying Chia

National Centre for Infectious Diseases, Singapore; Tan Tock Seng Hospital; Nanyang Technological University (NTU) - Lee Kong Chian School of Medicine

Sebastian Maurer-Stroh

Agency for Science, Technology and Research (A*STAR) - Bioinformatics Institute

Raymond Tzer Pin Lin

National Centre for Infectious Diseases, Singapore

Yee-Sin Leo

National Centre for Infectious Diseases, Singapore; Tan Tock Seng Hospital; National University of Singapore (NUS) - Saw Swee Hock School of Public Health; Nanyang Technological University (NTU) - Lee Kong Chian School of Medicine; National University of Singapore (NUS) - Yong Loo Lin School of Medicine

Vernon J. Lee

Ministry of Health, Singapore; National University of Singapore (NUS) - Saw Swee Hock School of Public Health

David Chien Lye

National Centre for Infectious Diseases, Singapore

Barnaby E. Young

National Centre for Infectious Diseases, Singapore

More...

Abstract

Background: The impact of SARS-CoV-2 variants of concern (VOCs) on disease severity is unclear. In this retrospective cohort 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 SARS-CoV-2 patients with VOC infection admitted to our centre between 20-December-2020 and 12-May-2021 were analysed. Outcomes were compared with a cohort of 846 patients admitted January-April 2020.

Findings: There were 838 VOC infections in Singapore in the study period. After adjusting for age and gender, B.1.617.2 infection 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 patients with VOCs were admitted to our centre. After adjusting for age, gender, comorbidities, and vaccination, aOR for pneumonia with B.1.617.2 was 1·88 [95% CI 0·95-3·76]) compared with wild-type. B.1.617.2 was associated with significantly lower PCR Ct values and significantly longer duration of Ct value ≤30 (estimated median duration 18 days for B.1.617.2, 13 days for wild-type). Vaccine breakthrough cases were less severe.

Interpretation: 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 a strong impetus for the rapid implementation of vaccination programmes.

Funding Information: National Medical Research Council grants COVID19RF-001 and COVID19RF-008.

Declaration of Interests: BEY reports personal fees from Roche and Sanofi, outside the submitted work. All other authors declare no competing interests.

Ethics Approval Statement: Informed consent for retrospective data collection was waived as approved by the institutional review board (NHG-DSRB reference number 2020/01122).

Keywords: COVID-19; SARS-CoV-2; B.1.1.7; B.1.351; B.1.617; variants of concern; severity; mortality

Suggested Citation

Ong, Sean Wei Xiang and Chiew, Calvin J. and Ang, Li Wei and Mak, Tze-Minn and Cui, Lin and Toh, Matthias Paul HS and Lim, Yi Ding and Lee, Pei Hua and Lee, Tau Hong and Chia, Po Ying and Maurer-Stroh, Sebastian and Lin, Raymond Tzer Pin and Leo, Yee-Sin and Lee, Vernon J. and Lye, David Chien and Young, Barnaby E., 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). Available at SSRN: https://ssrn.com/abstract=3861566 or http://dx.doi.org/10.2139/ssrn.3861566

Sean Wei Xiang Ong

National Centre for Infectious Diseases, Singapore

Singapore

Calvin J. Chiew

National Centre for Infectious Diseases, Singapore

Singapore

Li Wei Ang

National Centre for Infectious Diseases, Singapore ( email )

Tze-Minn Mak

National Centre for Infectious Diseases, Singapore

Singapore

Lin Cui

National Centre for Infectious Diseases, Singapore ( email )

Singapore

Matthias Paul HS Toh

National Centre for Infectious Diseases, Singapore

Singapore

Yi Ding Lim

Ministry of Health, Singapore ( email )

College of Medicine
16 College Road
Singapore, 169854
Singapore

Pei Hua Lee

National Centre for Infectious Diseases, Singapore

Singapore

Tau Hong Lee

National Centre for Infectious Diseases, Singapore

Singapore

Po Ying Chia

National Centre for Infectious Diseases, Singapore

Singapore

Tan Tock Seng Hospital

11 Jalan Tan Tock Seng
308433
Singapore

Nanyang Technological University (NTU) - Lee Kong Chian School of Medicine

Singapore

Sebastian Maurer-Stroh

Agency for Science, Technology and Research (A*STAR) - Bioinformatics Institute ( email )

30 Biopolis Street
#07-01 Matrix
Singapore, 138671
China

Raymond Tzer Pin Lin

National Centre for Infectious Diseases, Singapore ( email )

Yee-Sin Leo

National Centre for Infectious Diseases, Singapore ( email )

Singapore

Tan Tock Seng Hospital

11 Jalan Tan Tock Seng
308433
Singapore

National University of Singapore (NUS) - Saw Swee Hock School of Public Health

16 Medical Drive
#10-01
117597
Singapore

Nanyang Technological University (NTU) - Lee Kong Chian School of Medicine

Singapore

National University of Singapore (NUS) - Yong Loo Lin School of Medicine

Singapore

Vernon J. Lee

Ministry of Health, Singapore ( email )

Singapore

National University of Singapore (NUS) - Saw Swee Hock School of Public Health ( email )

16 Medical Drive
#10-01
117597
Singapore

David Chien Lye

National Centre for Infectious Diseases, Singapore ( email )

Singapore

Barnaby E. Young (Contact Author)

National Centre for Infectious Diseases, Singapore ( email )

Singapore

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