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Zhang Q, Zhang M, Hu J, He G, Zhou Y, Chen X, Zhuang Y, Rong Z, Yin L, Zhao J, Huang Z, Zeng W, Li X, Zhu Z, Tang Y, Quan Y, Li Y, Zhang L, Fu D, Li Y, Xiao J. Spatial-temporal clustering of an outbreak of SARS-CoV-2 Delta VOC in Guangzhou, China in 2021. Front Public Health 2022; 10:1050096. [PMID: 36568757 PMCID: PMC9780675 DOI: 10.3389/fpubh.2022.1050096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 11/23/2022] [Indexed: 12/13/2022] Open
Abstract
Background In May 2021, the SARS-CoV-2 Delta variant led to the first local outbreak in China in Guangzhou City. We explored the epidemiological characteristics and spatial-temporal clustering of this outbreak. Methods Based on the 153 cases in the SARS-CoV-2 Delta variant outbreak, the Knox test was used to analyze the spatial-temporal clustering of the outbreak. We further explored the spatial-temporal clustering by gender and age groups, as well as compared the changes of clustering strength (S) value between the two outbreaks in Guangzhou. Results The result of the Knox analysis showed that the areas at short distances and brief periods presented a relatively high risk. The strength of clustering of male-male pairs was higher. Age groups showed that clustering was concentrated in cases aged ≤ 18 years matched to 18-59 years and cases aged 60+ years. The strength of clustering of the outbreak declined after the implementation of public health measures. The change of strength of clustering at time intervals of 1-5 days decreased greater in 2021 (S = 129.19, change rate 38.87%) than that in 2020 (S = 83.81, change rate 30.02%). Conclusions The outbreak of SARS-CoV-2 Delta VOC in Guangzhou has obvious spatial-temporal clustering. The timely intervention measures are essential role to contain this outbreak of high transmission.
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Affiliation(s)
- Qian Zhang
- School of Public Health, Guangdong Pharmaceutical University, Guangzhou, China,Guangdong Provincial Institute of Public Health, Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, China
| | - Meng Zhang
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, China,Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Guangzhou, China
| | - Jianxiong Hu
- Guangdong Provincial Institute of Public Health, Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, China
| | - Guanhao He
- Guangdong Provincial Institute of Public Health, Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, China
| | - Yan Zhou
- Guangdong Provincial Institute of Public Health, Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, China,School of Public Health, Southern Medical University, Guangzhou, China
| | - Xuguang Chen
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, China,Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Guangzhou, China
| | - Yali Zhuang
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, China,Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Guangzhou, China
| | - Zuhua Rong
- Guangdong Provincial Institute of Public Health, Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, China
| | - Lihua Yin
- Guangdong Provincial Institute of Public Health, Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, China
| | - Jianguo Zhao
- Guangdong Provincial Institute of Public Health, Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, China
| | - Zitong Huang
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, China,School of Public Health, Sun Yat-sen University, Guangzhou, China
| | - Weilin Zeng
- Guangdong Provincial Institute of Public Health, Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, China
| | - Xing Li
- Guangdong Provincial Institute of Public Health, Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, China
| | - Zhihua Zhu
- Guangdong Provincial Institute of Public Health, Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, China
| | - Yerong Tang
- School of Public Health, Sun Yat-sen University, Guangzhou, China,Arboviral Disease Prevention Department, Yunnan Institute of Parasitic Diseases, Puer, China
| | - Yi Quan
- Guangdong Provincial Institute of Public Health, Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, China,School of Public Health, Southern Medical University, Guangzhou, China
| | - Yihan Li
- Guangdong Provincial Institute of Public Health, Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, China,School of Public Health, Southern Medical University, Guangzhou, China
| | - Li Zhang
- Guangdong Provincial Institute of Public Health, Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, China,School of Public Health, Southern Medical University, Guangzhou, China
| | - Di Fu
- Department of Public Health and Preventive Medicine, School of Medicine, Jinan University, Guangzhou, China
| | - Yan Li
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, China,Guangdong Workstation for Emerging Infectious Disease Control and Prevention, Guangzhou, China,*Correspondence: Yan Li
| | - Jianpeng Xiao
- Guangdong Provincial Institute of Public Health, Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, China,Jianpeng Xiao
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de Souza AS, de Freitas Amorim VM, Guardia GDA, dos Santos FF, Ulrich H, Galante PAF, de Souza RF, Guzzo CR. Severe Acute Respiratory Syndrome Coronavirus 2 Variants of Concern: A Perspective for Emerging More Transmissible and Vaccine-Resistant Strains. Viruses 2022; 14:827. [PMID: 35458557 PMCID: PMC9029021 DOI: 10.3390/v14040827] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Revised: 03/29/2022] [Accepted: 04/01/2022] [Indexed: 02/06/2023] Open
Abstract
Novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern (VOC) are constantly threatening global public health. With no end date, the pandemic persists with the emergence of novel variants that threaten the effectiveness of diagnostic tests and vaccines. Mutations in the Spike surface protein of the virus are regularly observed in the new variants, potentializing the emergence of novel viruses with different tropism from the current ones, which may change the severity and symptoms of the disease. Growing evidence has shown that mutations are being selected in favor of variants that are more capable of evading the action of neutralizing antibodies. In this context, the most important factor guiding the evolution of SARS-CoV-2 is its interaction with the host's immune system. Thus, as current vaccines cannot block the transmission of the virus, measures complementary to vaccination, such as the use of masks, hand hygiene, and keeping environments ventilated remain essential to delay the emergence of new variants. Importantly, in addition to the involvement of the immune system in the evolution of the virus, we highlight several chemical parameters that influence the molecular interactions between viruses and host cells during invasion and are also critical tools making novel variants more transmissible. In this review, we dissect the impacts of the Spike mutations on biological parameters such as (1) the increase in Spike binding affinity to hACE2; (2) bound time for the receptor to be cleaved by the proteases; (3) how mutations associate with the increase in RBD up-conformation state in the Spike ectodomain; (4) expansion of uncleaved Spike protein in the virion particles; (5) increment in Spike concentration per virion particles; and (6) evasion of the immune system. These factors play key roles in the fast spreading of SARS-CoV-2 variants of concern, including the Omicron.
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Affiliation(s)
- Anacleto Silva de Souza
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo 05508-000, Brazil; (A.S.d.S.); (V.M.d.F.A.); (R.F.d.S.)
| | - Vitor Martins de Freitas Amorim
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo 05508-000, Brazil; (A.S.d.S.); (V.M.d.F.A.); (R.F.d.S.)
| | - Gabriela D. A. Guardia
- Centro de Oncologia Molecular, Hospital Sírio Libanes, São Paulo 01308-060, Brazil; (G.D.A.G.); (F.F.d.S.); (P.A.F.G.)
| | - Filipe F. dos Santos
- Centro de Oncologia Molecular, Hospital Sírio Libanes, São Paulo 01308-060, Brazil; (G.D.A.G.); (F.F.d.S.); (P.A.F.G.)
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo 05508-000, Brazil;
| | - Henning Ulrich
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo 05508-000, Brazil;
| | - Pedro A. F. Galante
- Centro de Oncologia Molecular, Hospital Sírio Libanes, São Paulo 01308-060, Brazil; (G.D.A.G.); (F.F.d.S.); (P.A.F.G.)
| | - Robson Francisco de Souza
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo 05508-000, Brazil; (A.S.d.S.); (V.M.d.F.A.); (R.F.d.S.)
| | - Cristiane Rodrigues Guzzo
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo 05508-000, Brazil; (A.S.d.S.); (V.M.d.F.A.); (R.F.d.S.)
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