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Xiao B, Wu L, Sun Q, Shu C, Hu S. Dynamic analysis of SARS-CoV-2 evolution based on different countries. Gene 2024; 916:148426. [PMID: 38575101 DOI: 10.1016/j.gene.2024.148426] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 03/18/2024] [Accepted: 04/01/2024] [Indexed: 04/06/2024]
Abstract
Since late 2019, COVID-19 has significantly impacted the world. Understanding the evolution of SARS-CoV-2 is crucial for protecting against future infectious pathogens. In this study, we conducted a comprehensive chronological analysis of SARS-CoV-2 evolution by examining mutation prevalence from the source countries of VOCs: United Kingdom, India, Brazil, South Africa, plus two countries: United States, Russia, utilizing genomic sequences from GISAID. Our methodological approach involved large-scale genomic sequence alignment using MAFFT, Python-based data processing on a high-performance computing platform, and advanced statistical methods the Maximal Information Coefficient (MIC), and also Long Short-Term Memory (LSTM) models for correlation analysis. Our findings elucidate the dynamics of SARS-CoV-2 evolution, highlighting the virus's changing behaviour over various pandemic stages. Key results include the discovery of three temporal mutation patterns-lineage distinct, long-span, and competitive mutations-with varying levels of impact on the virus. Notably, we observed a convergence of advantageous mutations in the spike protein, especially in the later stages of the pandemic, indicating a substantial evolutionary pressure on the virus. One of the most significant revelations is the predominant role of natural immunity over vaccination-induced immunity in driving these evolutionary changes. This emphasizes the critical need for regular vaccine updates to maintain efficacy against evolving strains. In conclusion, our study not only sheds light on the evolutionary trajectory of SARS-CoV-2 but also underscores the urgency for robust, continuous global data collection and sharing. It highlights the necessity for rapid adaptations in medical countermeasures, including vaccine development, to stay ahead of pathogen evolution. This research provides valuable insights for future pandemic preparedness and response strategies.
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Affiliation(s)
- Binghan Xiao
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing, China; Sino-Danish College, University of Chinese Academy of Sciences, Beijing, China
| | - Linhuan Wu
- Microbial Resource and Big Data Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; Chinese National Microbiology Data Center (NMDC), Beijing 100101, China
| | - Qinglan Sun
- Microbial Resource and Big Data Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; Chinese National Microbiology Data Center (NMDC), Beijing 100101, China
| | - Chang Shu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.
| | - Songnian Hu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing, China.
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Ma Z, Rennert L. An epidemiological modeling framework to inform institutional-level response to infectious disease outbreaks: a Covid-19 case study. Sci Rep 2024; 14:7221. [PMID: 38538693 PMCID: PMC10973339 DOI: 10.1038/s41598-024-57488-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Accepted: 03/19/2024] [Indexed: 04/04/2024] Open
Abstract
Institutions have an enhanced ability to implement tailored mitigation measures during infectious disease outbreaks. However, macro-level predictive models are inefficient for guiding institutional decision-making due to uncertainty in local-level model input parameters. We present an institutional-level modeling toolkit used to inform prediction, resource procurement and allocation, and policy implementation at Clemson University throughout the Covid-19 pandemic. Through incorporating real-time estimation of disease surveillance and epidemiological measures based on institutional data, we argue this approach helps minimize uncertainties in input parameters presented in the broader literature and increases prediction accuracy. We demonstrate this through case studies at Clemson and other university settings during the Omicron BA.1 and BA.4/BA.5 variant surges. The input parameters of our toolkit are easily adaptable to other institutional settings during future health emergencies. This methodological approach has potential to improve public health response through increasing the capability of institutions to make data-informed decisions that better prioritize the health and safety of their communities while minimizing operational disruptions.
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Affiliation(s)
- Zichen Ma
- Department of Mathematics, Colgate University, Hamilton, NY, USA
- Center for Public Health Modeling and Response, Department of Public Health Sciences, Clemson University, 517 Edwards Hall, Clemson, SC, 29634, USA
| | - Lior Rennert
- Center for Public Health Modeling and Response, Department of Public Health Sciences, Clemson University, 517 Edwards Hall, Clemson, SC, 29634, USA.
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Hendrix N, Sidky H, Sahner DK. Influence of Prior SARS-CoV-2 Infection on COVID-19 Severity: Evidence from the National COVID Cohort Collaborative. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2023.08.03.23293612. [PMID: 38343824 PMCID: PMC10854322 DOI: 10.1101/2023.08.03.23293612] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/17/2024]
Abstract
Background A large share of SARS-CoV-2 infections now occur among previously infected individuals. In this study, we sought to determine whether prior infection modifies disease severity relative to no prior infection. Methods We used data from first and second COVID-19 episodes in the National COVID Cohort Collaborative, a nationwide collection of de-identified electronic health records. We used nested logistic regressions of monthly cohorts weighted on the inverse probability of prior infection to assess risk of hospitalization, death, and increased severity in the first versus second infection cohorts. Results We included a total of 2,058,274 individuals in the analysis, 147,592 of whom had two recorded infections. The impact of prior infection differed meaningfully between months. Prior infection was largely protective prior to March 2022, with odds ratios (ORs) as low as 0.66 (95% confidence interval: 0.51 to 0.86) in November 2021 for hospitalization. and as low as 0.23 (0.06 to 0.86) in June 2021 for death. However, prior infection was associated with an increased risk of hospitalization and death, mostly after March 2022 when the ORs were as high as 1.87 (1.26 to 2.80) and 2.99 (1.65 to 5.41) in April 2022, respectively. The overall OR for more severe disease was 1.06 (1.03 to 1.10) among previously infected individuals. Conclusion In the pandemic's first two years, previously infected patients generally had less severe disease than people without prior infection. During the Omicron era, however, previously infected patients had the same or worse severity of disease as patients without prior infection.
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Affiliation(s)
- Nathaniel Hendrix
- Center for Professionalism and Value in Health Care, American Board of Family Medicine, 1016 16th St NW Ste 800, Washington, DC 20036
| | - Hythem Sidky
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD, USA
| | - David K Sahner
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD, USA
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Ma Y, Xu S, Luo Y, Peng J, Guo J, Dong A, Xu Z, Li J, Lei L, He L, Wang T, Yu H, Xie J. Predicting the transmission dynamics of novel coronavirus infection in Shanxi province after the implementation of the "Class B infectious disease Class B management" policy. Front Public Health 2023; 11:1322430. [PMID: 38186702 PMCID: PMC10768892 DOI: 10.3389/fpubh.2023.1322430] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 11/30/2023] [Indexed: 01/09/2024] Open
Abstract
Background China managed coronavirus disease 2019 (COVID-19) with measures against Class B infectious diseases, instead of Class A infectious diseases, in a major shift of its epidemic response policies. We aimed to generate robust information on the transmission dynamics of novel coronavirus infection in Shanxi, a province located in northern China, after the implementation of the "Class B infectious disease Class B management" policy. Methods We consolidated infection data in Shanxi province from December 6, 2022 to January 14, 2023 through a network questionnaire survey and sentinel surveillance. A dynamics model of the SEIQHCVR was developed to track the infection curves and effective reproduction number (R t ). Results Our model was effective in estimating the trends of novel coronavirus infection, with the coefficient of determination (R 2 ) above 90% in infections, inpatients, and critically ill patients. The number of infections in Shanxi province as well as in urban and rural areas peaked on December 20, 2022, with the peak of inpatients and critically ill patients occurring 2 to 3 weeks after the peak of infections. By the end of January 2023, 87.72% of the Shanxi residents were predicted to be infected, and the outbreak subsequently subsided. A small wave of COVID-19 infections may re-emerge at the end of April. In less than a month, the R t values of positive infections, inpatients and critically ill patients were all below 1.0. Conclusion The outbreak in Shanxi province is currently at a low prevalence level. In the face of possible future waves of infection, there is a strong need to strengthen surveillance and early warning.
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Affiliation(s)
- Yifei Ma
- School of Public Health, Shanxi Medical University, Taiyuan, China
| | - Shujun Xu
- School of Public Health, Shanxi Medical University, Taiyuan, China
| | - Yuxin Luo
- School of Public Health, Shanxi Medical University, Taiyuan, China
| | - Junlin Peng
- School of Public Health, Shanxi Medical University, Taiyuan, China
| | - Jiaming Guo
- School of Public Health, Shanxi Medical University, Taiyuan, China
| | - Ali Dong
- Shanxi Center for Disease Control and Prevention, Taiyuan, China
| | - Zhibin Xu
- Shanxi Center for Disease Control and Prevention, Taiyuan, China
| | - Jiantao Li
- School of Management, Shanxi Medical University, Taiyuan, China
| | - Lijian Lei
- School of Public Health, Shanxi Medical University, Taiyuan, China
| | - Lu He
- School of Public Health, Shanxi Medical University, Taiyuan, China
| | - Tong Wang
- School of Public Health, Shanxi Medical University, Taiyuan, China
| | - Hongmei Yu
- School of Public Health, Shanxi Medical University, Taiyuan, China
- Shanxi Provincial Key Laboratory of Major Diseases Risk Assessment, Taiyuan, China
| | - Jun Xie
- Department of Biochemistry and Molecular Biology, Shanxi Key Laboratory of Birth Defect and Cell Regeneration, MOE Key Laboratory of Coal Environmental Pathogenicity and Prevention, Shanxi Medical University, Taiyuan, China
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Høeg TB, González-Dambrauskas S, Prasad V. The United States' decision to mask children as young as two for COVID-19 has been extended into 2023 and beyond: The implications of this policy. Paediatr Respir Rev 2023; 47:30-32. [PMID: 37183122 PMCID: PMC10129335 DOI: 10.1016/j.prrv.2023.04.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/15/2023] [Accepted: 04/20/2023] [Indexed: 05/16/2023]
Affiliation(s)
- Tracy Beth Høeg
- Department of Epidemiology and Biostatistics, University of California-San Francisco, United States.
| | - Sebastián González-Dambrauskas
- Red Colaborativa Pediátrica de Latinoamérica (LARed Network), Montevideo, Uruguay; Departamento de Pediatría y Unidad de Cuidados Intensivos de Niños del Centro Hospitalario Pereira Rossell, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - Vinay Prasad
- Department of Epidemiology and Biostatistics, University of California-San Francisco, United States
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Rennert L, Ma Z. An epidemiological modeling framework to inform institutional-level response to infectious disease outbreaks: A Covid-19 case study. RESEARCH SQUARE 2023:rs.3.rs-3116880. [PMID: 37503237 PMCID: PMC10371141 DOI: 10.21203/rs.3.rs-3116880/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Institutions have an enhanced ability to implement tailored mitigation measures during infectious disease outbreaks. However, macro-level predictive models are inefficient for guiding institutional decision-making due to uncertainty in local-level model input parameters. We present an institutional-level modeling toolkit used to inform prediction, resource procurement and allocation, and policy implementation at Clemson University throughout the Covid-19 pandemic. Through incorporating real-time estimation of disease surveillance and epidemiological measures based on institutional data, we argue this approach helps minimize uncertainties in input parameters presented in the broader literature and increases prediction accuracy. We demonstrate this through case studies at Clemson and other university settings during the Omicron BA.1 and BA.4/BA.5 variant surges. The input parameters of our toolkit are easily adaptable to other institutional settings during future health emergencies. This methodological approach has potential to improve public health response through increasing the capability of institutions to make data-informed decisions that better prioritize the health and safety of their communities while minimizing operational disruptions.
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7
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Dong T, Wang M, Liu J, Ma P, Pang S, Liu W, Liu A. Diagnostics and analysis of SARS-CoV-2: current status, recent advances, challenges and perspectives. Chem Sci 2023; 14:6149-6206. [PMID: 37325147 PMCID: PMC10266450 DOI: 10.1039/d2sc06665c] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Accepted: 05/03/2023] [Indexed: 06/17/2023] Open
Abstract
The disastrous spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has induced severe public healthcare issues and weakened the global economy significantly. Although SARS-CoV-2 infection is not as fatal as the initial outbreak, many infected victims suffer from long COVID. Therefore, rapid and large-scale testing is critical in managing patients and alleviating its transmission. Herein, we review the recent advances in techniques to detect SARS-CoV-2. The sensing principles are detailed together with their application domains and analytical performances. In addition, the advantages and limits of each method are discussed and analyzed. Besides molecular diagnostics and antigen and antibody tests, we also review neutralizing antibodies and emerging SARS-CoV-2 variants. Further, the characteristics of the mutational locations in the different variants with epidemiological features are summarized. Finally, the challenges and possible strategies are prospected to develop new assays to meet different diagnostic needs. Thus, this comprehensive and systematic review of SARS-CoV-2 detection technologies may provide insightful guidance and direction for developing tools for the diagnosis and analysis of SARS-CoV-2 to support public healthcare and effective long-term pandemic management and control.
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Affiliation(s)
- Tao Dong
- Institute for Chemical Biology & Biosensing, College of Life Sciences, Qingdao University 308 Ningxia Road Qingdao 266071 China
- School of Pharmacy, Medical College, Qingdao University 308 Ningxia Road Qingdao 266071 China
| | - Mingyang Wang
- Institute for Chemical Biology & Biosensing, College of Life Sciences, Qingdao University 308 Ningxia Road Qingdao 266071 China
| | - Junchong Liu
- Institute for Chemical Biology & Biosensing, College of Life Sciences, Qingdao University 308 Ningxia Road Qingdao 266071 China
| | - Pengxin Ma
- Institute for Chemical Biology & Biosensing, College of Life Sciences, Qingdao University 308 Ningxia Road Qingdao 266071 China
| | - Shuang Pang
- Institute for Chemical Biology & Biosensing, College of Life Sciences, Qingdao University 308 Ningxia Road Qingdao 266071 China
| | - Wanjian Liu
- Qingdao Hightop Biotech Co., Ltd 369 Hedong Road, Hi-tech Industrial Development Zone Qingdao 266112 China
| | - Aihua Liu
- Institute for Chemical Biology & Biosensing, College of Life Sciences, Qingdao University 308 Ningxia Road Qingdao 266071 China
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9
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Neumann G, Kawaoka Y. The COVID-19 Pandemic-A Potential Role for Antivirals in Mitigating Pandemics. Viruses 2023; 15:303. [PMID: 36851516 PMCID: PMC9961506 DOI: 10.3390/v15020303] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 01/17/2023] [Accepted: 01/19/2023] [Indexed: 01/24/2023] Open
Abstract
The COVID-19 pandemic has served as a stark reminder that outbreaks of novel pathogens (i.e., those not previously encountered by humans) have always plagued mankind and will continue to do so. The COVID-19 pandemic has also taught us that a single exposure to a novel pathogen is typically not sufficient to build robust population immunity that exists against common respiratory viruses. Robust population-level immunity can be achieved through repeated natural infection (typically at the cost of high mortality and overwhelmed public health resources) and/or repeated vaccination (which may be limited by vaccine availability, a country's economic resources, and/or vaccine hesitancy). Here, we suggest that the broader use of antivirals could be a mitigation strategy to limit severe disease and the burden on healthcare systems during widespread virus circulation while allowing the buildup of population immunity.
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Affiliation(s)
- Gabriele Neumann
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI 53711, USA
| | - Yoshihiro Kawaoka
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI 53711, USA
- Department of Virology, Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan
- International Research Center for Infectious Diseases, Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan
- Pandemic Preparedness, Infection and Advanced Research Center, The University of Tokyo, Tokyo 108-8639, Japan
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