Dataset Information

Viral infection and transmission in a large, well-traced outbreak caused by the SARS-CoV-2 Delta variant.

ABSTRACT: The SARS-CoV-2 Delta variant has spread rapidly worldwide. To provide data on its virological profile, we here report the first local transmission of Delta in mainland China. All 167 infections could be traced back to the first index case. Daily sequential PCR testing of quarantined individuals indicated that the viral loads of Delta infections, when they first become PCR-positive, were on average ~1000 times greater compared to lineage A/B infections during the first epidemic wave in China in early 2020, suggesting potentially faster viral replication and greater infectiousness of Delta during early infection. The estimated transmission bottleneck size of the Delta variant was generally narrow, with 1-3 virions in 29 donor-recipient transmission pairs. However, the transmission of minor iSNVs resulted in at least 3 of the 34 substitutions that were identified in the outbreak, highlighting the contribution of intra-host variants to population-level viral diversity during rapid spread.

SUBMITTER: Li B

PROVIDER: S-EPMC8786931 | biostudies-literature | 2022 Jan

REPOSITORIES: biostudies-literature

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Viral infection and transmission in a large, well-traced outbreak caused by the SARS-CoV-2 Delta variant.

Li Baisheng B Deng Aiping A Li Kuibiao K Hu Yao Y Li Zhencui Z Shi Yaling Y Xiong Qianling Q Liu Zhe Z Guo Qianfang Q Zou Lirong L Zhang Huan H Zhang Meng M Ouyang Fangzhu F Su Juan J Su Wenzhe W Xu Jing J Lin Huifang H Sun Jing J Peng Jinju J Jiang Huiming H Zhou Pingping P Hu Ting T Luo Min M Zhang Yingtao Y Zheng Huanying H Xiao Jianpeng J Liu Tao T Tan Mingkai M Che Rongfei R Zeng Hanri H Zheng Zhonghua Z Huang Yushi Y Yu Jianxiang J Yi Lina L Wu Jie J Chen Jingdiao J Zhong Haojie H Deng Xiaoling X Kang Min M Pybus Oliver G OG Hall Matthew M Lythgoe Katrina A KA Li Yan Y Yuan Jun J He Jianfeng J Lu Jing J

Nature communications 20220124 1

The SARS-CoV-2 Delta variant has spread rapidly worldwide. To provide data on its virological profile, we here report the first local transmission of Delta in mainland China. All 167 infections could be traced back to the first index case. Daily sequential PCR testing of quarantined individuals indicated that the viral loads of Delta infections, when they first become PCR-positive, were on average ~1000 times greater compared to lineage A/B infections during the first epidemic wave in China in e ...[more]

PMID: 35075154

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Project description:BackgroundIn early March 2022, a major outbreak of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron variant spread rapidly throughout Shanghai, China. Here we aimed to provide a description of the epidemiological characteristics and spatiotemporal transmission dynamics of the Omicron outbreak under the population-based screening and lockdown policies implemented in Shanghai.MethodsWe extracted individual information on SARS-CoV-2 infections reported between January 1 and May 31, 2022, and on the timeline of the adopted non-pharmaceutical interventions. The epidemic was divided into three phases: i) sporadic infections (January 1-February 28), ii) local transmission (March 1-March 31), and iii) city-wide lockdown (April 1 to May 31). We described the epidemic spread during these three phases and the subdistrict-level spatiotemporal distribution of the infections. To evaluate the impact on the transmission of SARS-CoV-2 of the adopted targeted interventions in Phase 2 and city-wide lockdown in Phase 3, we estimated the dynamics of the net reproduction number (Rt ).FindingsA surge in imported infections in Phase 1 triggered cryptic local transmission of the Omicron variant in early March, resulting in the largest outbreak in mainland China since the original wave. A total of 626,000 SARS-CoV-2 infections were reported in 99.5% (215/216) of the subdistricts of Shanghai until the end of May. The spatial distribution of the infections was highly heterogeneous, with 37% of the subdistricts accounting for 80% of all infections. A clear trend from the city center towards adjacent suburban and rural areas was observed, with a progressive slowdown of the epidemic spread (from 463 to 244 meters/day) prior to the citywide lockdown. During Phase 2, Rt remained well above 1 despite the implementation of multiple targeted interventions. The citywide lockdown imposed on April 1 led to a marked decrease in transmission, bringing Rt below the epidemic threshold in the entire city on April 14 and ultimately leading to containment of the outbreak.InterpretationOur results highlight the risk of widespread outbreaks in mainland China, particularly under the heightened pressure of imported infections. The targeted interventions adopted in March 2022 were not capable of halting transmission, and the implementation of a strict, prolonged city-wide lockdown was needed to successfully contain the outbreak, highlighting the challenges for containing Omicron outbreaks.FundingKey Program of the National Natural Science Foundation of China (82130093); Shanghai Rising-Star Program (22QA1402300).

Dataset Information

Viral infection and transmission in a large, well-traced outbreak caused by the SARS-CoV-2 Delta variant.

Publications

Viral infection and transmission in a large, well-traced outbreak caused by the SARS-CoV-2 Delta variant.

Similar Datasets

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