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      Crucial control measures to contain China's first Delta variant outbreak

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          Abstract

          The SARS-CoV-2 B.1.617.2 (Delta) variant flared up in late May in Guangzhou, China. Transmission characteristics of Delta variant were analysed for 153 confirmed cases and two complete transmission chains with seven generations were fully presented. A rapid transmission occurred in five generations within 10 days. The basic reproduction number (R 0) was 3.60 (95% confidence interval: 2.50–5.30). After redefining the concept of close contact, the proportion of confirmed cases discovered from close contacts increased from 43% to 100%. With the usage of a yellow health code, the potential exposed individuals were self-motivated to take a nucleic acid test and regained public access with a negative testing result. Facing the massive requirement of screening, novel facilities like makeshift inflatable laboratories were promptly set up as a vital supplement and 17 cases were found, with 1 pre-symptomatic. The dynamic adjustment of these three interventions resulted in the decline of Rt from 5.00 to 1.00 within 9 days. By breaking the transmission chain and eliminating the transmission source through extending the scope of the close-contact tracing, health-code usage and mass testing, the Guangzhou Delta epidemic was effectively contained.

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          Early Transmission Dynamics in Wuhan, China, of Novel Coronavirus–Infected Pneumonia

          Qun Li, Xuhua Guan, Peng Wu … (2020)
          Abstract Background The initial cases of novel coronavirus (2019-nCoV)–infected pneumonia (NCIP) occurred in Wuhan, Hubei Province, China, in December 2019 and January 2020. We analyzed data on the first 425 confirmed cases in Wuhan to determine the epidemiologic characteristics of NCIP. Methods We collected information on demographic characteristics, exposure history, and illness timelines of laboratory-confirmed cases of NCIP that had been reported by January 22, 2020. We described characteristics of the cases and estimated the key epidemiologic time-delay distributions. In the early period of exponential growth, we estimated the epidemic doubling time and the basic reproductive number. Results Among the first 425 patients with confirmed NCIP, the median age was 59 years and 56% were male. The majority of cases (55%) with onset before January 1, 2020, were linked to the Huanan Seafood Wholesale Market, as compared with 8.6% of the subsequent cases. The mean incubation period was 5.2 days (95% confidence interval [CI], 4.1 to 7.0), with the 95th percentile of the distribution at 12.5 days. In its early stages, the epidemic doubled in size every 7.4 days. With a mean serial interval of 7.5 days (95% CI, 5.3 to 19), the basic reproductive number was estimated to be 2.2 (95% CI, 1.4 to 3.9). Conclusions On the basis of this information, there is evidence that human-to-human transmission has occurred among close contacts since the middle of December 2019. Considerable efforts to reduce transmission will be required to control outbreaks if similar dynamics apply elsewhere. Measures to prevent or reduce transmission should be implemented in populations at risk. (Funded by the Ministry of Science and Technology of China and others.)
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            Genomic characterisation and epidemiology of 2019 novel coronavirus: implications for virus origins and receptor binding

            Roujian Lu, Xiang Zhao, Juan Li … (2021)
            Summary Background In late December, 2019, patients presenting with viral pneumonia due to an unidentified microbial agent were reported in Wuhan, China. A novel coronavirus was subsequently identified as the causative pathogen, provisionally named 2019 novel coronavirus (2019-nCoV). As of Jan 26, 2020, more than 2000 cases of 2019-nCoV infection have been confirmed, most of which involved people living in or visiting Wuhan, and human-to-human transmission has been confirmed. Methods We did next-generation sequencing of samples from bronchoalveolar lavage fluid and cultured isolates from nine inpatients, eight of whom had visited the Huanan seafood market in Wuhan. Complete and partial 2019-nCoV genome sequences were obtained from these individuals. Viral contigs were connected using Sanger sequencing to obtain the full-length genomes, with the terminal regions determined by rapid amplification of cDNA ends. Phylogenetic analysis of these 2019-nCoV genomes and those of other coronaviruses was used to determine the evolutionary history of the virus and help infer its likely origin. Homology modelling was done to explore the likely receptor-binding properties of the virus. Findings The ten genome sequences of 2019-nCoV obtained from the nine patients were extremely similar, exhibiting more than 99·98% sequence identity. Notably, 2019-nCoV was closely related (with 88% identity) to two bat-derived severe acute respiratory syndrome (SARS)-like coronaviruses, bat-SL-CoVZC45 and bat-SL-CoVZXC21, collected in 2018 in Zhoushan, eastern China, but were more distant from SARS-CoV (about 79%) and MERS-CoV (about 50%). Phylogenetic analysis revealed that 2019-nCoV fell within the subgenus Sarbecovirus of the genus Betacoronavirus, with a relatively long branch length to its closest relatives bat-SL-CoVZC45 and bat-SL-CoVZXC21, and was genetically distinct from SARS-CoV. Notably, homology modelling revealed that 2019-nCoV had a similar receptor-binding domain structure to that of SARS-CoV, despite amino acid variation at some key residues. Interpretation 2019-nCoV is sufficiently divergent from SARS-CoV to be considered a new human-infecting betacoronavirus. Although our phylogenetic analysis suggests that bats might be the original host of this virus, an animal sold at the seafood market in Wuhan might represent an intermediate host facilitating the emergence of the virus in humans. Importantly, structural analysis suggests that 2019-nCoV might be able to bind to the angiotensin-converting enzyme 2 receptor in humans. The future evolution, adaptation, and spread of this virus warrant urgent investigation. Funding National Key Research and Development Program of China, National Major Project for Control and Prevention of Infectious Disease in China, Chinese Academy of Sciences, Shandong First Medical University.
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              Reduced sensitivity of SARS-CoV-2 variant Delta to antibody neutralization

              Delphine Planas, David Veyer, Artem Baidaliuk … (2021)
              The SARS-CoV-2 B.1.617 lineage was identified in October 2020 in India1-5. Since then, it has become dominant in some regions of India and in the UK, and has spread to many other countries6. The lineage includes three main subtypes (B1.617.1, B.1.617.2 and B.1.617.3), which contain diverse mutations in the N-terminal domain (NTD) and the receptor-binding domain (RBD) of the SARS-CoV-2 spike protein that may increase the immune evasion potential of these variants. B.1.617.2-also termed the Delta variant-is believed to spread faster than other variants. Here we isolated an infectious strain of the Delta variant from an individual with COVID-19 who had returned to France from India. We examined the sensitivity of this strain to monoclonal antibodies and to antibodies present in sera from individuals who had recovered from COVID-19 (hereafter referred to as convalescent individuals) or who had received a COVID-19 vaccine, and then compared this strain with other strains of SARS-CoV-2. The Delta variant was resistant to neutralization by some anti-NTD and anti-RBD monoclonal antibodies, including bamlanivimab, and these antibodies showed impaired binding to the spike protein. Sera collected from convalescent individuals up to 12 months after the onset of symptoms were fourfold less potent against the Delta variant relative to the Alpha variant (B.1.1.7). Sera from individuals who had received one dose of the Pfizer or the AstraZeneca vaccine had a barely discernible inhibitory effect on the Delta variant. Administration of two doses of the vaccine generated a neutralizing response in 95% of individuals, with titres three- to fivefold lower against the Delta variant than against the Alpha variant. Thus, the spread of the Delta variant is associated with an escape from antibodies that target non-RBD and RBD epitopes of the spike protein.
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                Author and article information

                Contributors
                Lei Luo
                Zifeng Yang
                Jingyi Liang
                Yu Ma
                Hui Wang
                Chitin Hon
                Mei Jiang
                Zhengshi Lin
                Wenda Guan
                Zhitong Mai
                Yongming Li
                Kailin Mai
                Zhiqi Zeng
                Chuanmeizi Tu
                Jian Song
                Bin Liu
                Yong Liu
                Jianfeng He
                Huiyuan Li
                Bosheng Li
                Hang Dong
                Yutian Miao
                Shujun Fan
                Lirui Fan
                Xingyi Liang
                Ke Li
                Chun Chen
                Huihong Deng
                Zhicong Yang
                Nanshan Zhong
                Journal
                Journal ID (nlm-ta): Natl Sci Rev
                Journal ID (iso-abbrev): Natl Sci Rev
                Journal ID (publisher-id): nsr
                Title: National Science Review
                Publisher: Oxford University Press
                ISSN (Print): 2095-5138
                ISSN (Electronic): 2053-714X
                Publication date Collection: April 2022
                Publication date (Electronic): 18 January 2022
                Publication date PMC-release: 18 January 2022
                Volume: 9
                Issue: 4
                Electronic Location Identifier: nwac004
                Affiliations
                Institute of Public Health, Guangzhou Medical University & Guangzhou Center for Disease Control and Prevention , Guangzhou 510440, China
                State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University , Guangzhou 510120, China
                Guangzhou Laboratory , Bio-Island, Guangzhou 510320, China
                Guangzhou Key Laboratory for Clinical Rapid Diagnosis and Early Warning of Infectious Diseases , Guangzhou 51000, China
                State Key Laboratory of Quality Research in Chinese Medicine, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology , Taipa 999078, China
                State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University , Guangzhou 510120, China
                Guangzhou Laboratory , Bio-Island, Guangzhou 510320, China
                Macau Institute of Systems Engineering, Macau University of Science and Technology , Taipa 999078, China
                Institute of Public Health, Guangzhou Medical University & Guangzhou Center for Disease Control and Prevention , Guangzhou 510440, China
                Institute of Public Health, Guangzhou Medical University & Guangzhou Center for Disease Control and Prevention , Guangzhou 510440, China
                Macau Institute of Systems Engineering, Macau University of Science and Technology , Taipa 999078, China
                State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University , Guangzhou 510120, China
                State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University , Guangzhou 510120, China
                Guangzhou Laboratory , Bio-Island, Guangzhou 510320, China
                State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University , Guangzhou 510120, China
                Guangzhou Laboratory , Bio-Island, Guangzhou 510320, China
                Guangzhou Key Laboratory for Clinical Rapid Diagnosis and Early Warning of Infectious Diseases , Guangzhou 51000, China
                State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University , Guangzhou 510120, China
                Guangzhou Laboratory , Bio-Island, Guangzhou 510320, China
                State Key Laboratory of Quality Research in Chinese Medicine, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology , Taipa 999078, China
                State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University , Guangzhou 510120, China
                Guangzhou Laboratory , Bio-Island, Guangzhou 510320, China
                State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University , Guangzhou 510120, China
                Guangzhou Laboratory , Bio-Island, Guangzhou 510320, China
                State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University , Guangzhou 510120, China
                Guangzhou Laboratory , Bio-Island, Guangzhou 510320, China
                State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University , Guangzhou 510120, China
                Guangzhou Laboratory , Bio-Island, Guangzhou 510320, China
                State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University , Guangzhou 510120, China
                Guangzhou Laboratory , Bio-Island, Guangzhou 510320, China
                State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University , Guangzhou 510120, China
                Guangzhou Laboratory , Bio-Island, Guangzhou 510320, China
                State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University , Guangzhou 510120, China
                Kingmed Virology Diagnostic & Translational Center, Guangzhou Kingmed Center for Clinical Laboratory Co., Ltd, Guangzhou 510330 , China
                Guangdong Center for Disease Control and Prevention , Guangzhou 511430, China
                Kingmed Virology Diagnostic & Translational Center, Guangzhou Kingmed Center for Clinical Laboratory Co., Ltd, Guangzhou 510330 , China
                Guangdong Center for Disease Control and Prevention , Guangzhou 511430, China
                Institute of Public Health, Guangzhou Medical University & Guangzhou Center for Disease Control and Prevention , Guangzhou 510440, China
                Institute of Public Health, Guangzhou Medical University & Guangzhou Center for Disease Control and Prevention , Guangzhou 510440, China
                Institute of Public Health, Guangzhou Medical University & Guangzhou Center for Disease Control and Prevention , Guangzhou 510440, China
                Institute of Public Health, Guangzhou Medical University & Guangzhou Center for Disease Control and Prevention , Guangzhou 510440, China
                Department of Urban and Rural Planning, Shunde Urban and Rural Planning Information Research Center , Foshan 528300, China
                Institute of Public Health, Guangzhou Medical University & Guangzhou Center for Disease Control and Prevention , Guangzhou 510440, China
                Institute of Public Health, Guangzhou Medical University & Guangzhou Center for Disease Control and Prevention , Guangzhou 510440, China
                Guangdong Center for Disease Control and Prevention , Guangzhou 511430, China
                Institute of Public Health, Guangzhou Medical University & Guangzhou Center for Disease Control and Prevention , Guangzhou 510440, China
                State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University , Guangzhou 510120, China
                Guangzhou Laboratory , Bio-Island, Guangzhou 510320, China
                Author notes
                Corresponding author. E-mail: nanshan@ 123456vip.163.com

                Lei Luo, Zifeng Yang, Jingyi Liang, Yu Ma, Hui Wang, Chitin Hon and Mei Jiang are equally contributed to this work.

                Article
                Publisher ID: nwac004
                DOI: 10.1093/nsr/nwac004
                PMC ID: 9046578
                PubMed ID: 35497644
                SO-VID: 01aa4eed-2eb8-4b2d-a3c4-d9535f669625
                Copyright © © The Author(s) 2022. Published by Oxford University Press on behalf of China Science Publishing & Media Ltd.
                License:

                This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.

                History
                Date received : 27 September 2021
                Date revision received : 11 December 2021
                Date accepted : 22 December 2021
                Date: 27 April 2022
                Page count
                Pages: 10
                Funding
                Funded by: National Key Research and Development Program of China, DOI 10.13039/501100012166;
                Award ID: 2021YFF0306006
                Funded by: Key Research and Development Project of Jiangsu Province, DOI 10.13039/501100013058;
                Award ID: 2021A1111120009
                Categories
                Subject: RESEARCH ARTICLE
                Subject: Special Section: SARS-CoV-2
                Subject: Clinical Medicine
                Subject: AcademicSubjects/MED00010
                Subject: AcademicSubjects/SCI00010

                Keywords: covid-19,public health,control measure,close contact,mass testing
                Data availability:
                Keywords: covid-19, public health, control measure, close contact, mass testing

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