Future COVID19 surges prediction based on SARS-CoV-2 mutations surveillance

  1. Fares Z Najar
  2. Evan Linde
  3. Chelsea L Murphy
  4. Veniamin A Borin
  5. Haun Wang
  6. Shozeb Haider
  7. Pratul K Agarwal  Is a corresponding author
  1. Oklahoma State University, United States
  2. University College London, United Kingdom

Abstract

COVID19 has aptly revealed that airborne viruses such as SARS-CoV-2 with the ability to rapidly mutate, combined with high rates of transmission and fatality can cause a deadly world-wide pandemic in a matter of weeks.1 Apart from vaccines and post-infection treatment options, strategies for preparedness will be vital in responding to the current and future pandemics. Therefore, there is wide interest in approaches that allow predictions of increase in infections ('surges') before they occur. We describe here real time genomic surveillance particularly based on mutation analysis, of viral proteins as a methodology for a priori determination of surge in number of infection cases. The full results are available for SARS-CoV-2 at http://pandemics.okstate.edu/covid19/, and are updated daily as new virus sequences become available. This approach is generic and will also be applicable to other pathogens.

Data availability

All sequences used in this work are available from GenBank. The protocol used for analysis are described in the supporting information.

The following previously published data sets were used

Article and author information

Author details

  1. Fares Z Najar

    High-Performance Computing Center, Oklahoma State University, Stillwater, United States
    Competing interests
    No competing interests declared.
  2. Evan Linde

    High-Performance Computing Center, Oklahoma State University, Stillwater, United States
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-2053-6721
  3. Chelsea L Murphy

    High-Performance Computing Center, Oklahoma State University, Stillwater, United States
    Competing interests
    No competing interests declared.
  4. Veniamin A Borin

    High-Performance Computing Center, Oklahoma State University, Stillwater, United States
    Competing interests
    No competing interests declared.
  5. Haun Wang

    School of Pharmacy, Pharmaceutical and Biological Chemistry, University College London, London, United Kingdom
    Competing interests
    No competing interests declared.
  6. Shozeb Haider

    School of Pharmacy, Pharmaceutical and Biological Chemistry, University College London, London, United Kingdom
    Competing interests
    Shozeb Haider, Reviewing editor, eLife.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-2650-2925
  7. Pratul K Agarwal

    1High-Performance Computing Center, Oklahoma State University, Stillwater, United States
    For correspondence
    pratul.agarwal@okstate.edu
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-3848-9492

Funding

No external funding was received for this work.

Reviewing Editor

  1. Jameel Iqbal, DaVita Labs, United States

Publication history

  1. Received: August 25, 2022
  2. Accepted: January 18, 2023
  3. Accepted Manuscript published: January 19, 2023 (version 1)

Copyright

© 2023, Najar et al.

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.

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  1. Fares Z Najar
  2. Evan Linde
  3. Chelsea L Murphy
  4. Veniamin A Borin
  5. Haun Wang
  6. Shozeb Haider
  7. Pratul K Agarwal
(2023)
Future COVID19 surges prediction based on SARS-CoV-2 mutations surveillance
eLife 12:e82980.
https://doi.org/10.7554/eLife.82980

Further reading

    1. Epidemiology and Global Health
    2. Medicine
    Nathan J Cheetham, Milla Kibble ... Claire J Steves
    Research Article

    Background: SARS-CoV-2 antibody levels can be used to assess humoral immune responses following SARS-CoV-2 infection or vaccination, and may predict risk of future infection. Higher levels of SARS-CoV-2 anti-Spike antibodies are known to be associated with increased protection against future SARS-CoV-2 infection. However, variation in antibody levels and risk factors for lower antibody levels following each round of SARS-CoV-2 vaccination have not been explored across a wide range of socio-demographic, SARS-CoV-2 infection and vaccination, and health factors within population-based cohorts.

    Methods: Samples were collected from 9,361 individuals from TwinsUK and ALSPAC UK population-based longitudinal studies and tested for SARS-CoV-2 antibodies. Cross-sectional sampling was undertaken jointly in April-May 2021 (TwinsUK, N = 4,256; ALSPAC, N = 4,622), and in TwinsUK only in November 2021-January 2022 (N = 3,575). Variation in antibody levels after first, second, and third SARS-CoV-2 vaccination with health, socio-demographic, SARS-CoV-2 infection and SARS-CoV-2 vaccination variables were analysed. Using multivariable logistic regression models, we tested associations between antibody levels following vaccination and: (1) SARS-CoV-2 infection following vaccination(s); (2) health, socio-demographic, SARS-CoV-2 infection and SARS-CoV-2 vaccination variables.

    Results: Within TwinsUK, single-vaccinated individuals with the lowest 20% of anti-Spike antibody levels at initial testing had 3-fold greater odds of SARS-CoV-2 infection over the next six to nine months (OR = 2.9, 95% CI: 1.4, 6.0), compared to the top 20%. In TwinsUK and ALSPAC, individuals identified as at increased risk of COVID-19 complication through the UK 'Shielded Patient List' had consistently greater odds (2- to 4-fold) of having antibody levels in the lowest 10%. Third vaccination increased absolute antibody levels for almost all individuals, and reduced relative disparities compared with earlier vaccinations.

    Conclusions: These findings quantify the association between antibody level and risk of subsequent infection, and support a policy of triple vaccination for the generation of protective antibodies.

    Funding: Antibody testing was funded by UK Health Security Agency. The National Core Studies program is funded by COVID-19 Longitudinal Health and Wellbeing - National Core Study (LHW-NCS) HMT/UKRI/MRC (MC_PC_20030 & MC_PC_20059). Related funding was also provided by the NIHR 606 (CONVALESCENCE grant COV-LT-0009). TwinsUK is funded by the Wellcome Trust, Medical Research Council, Versus Arthritis, European Union Horizon 2020, Chronic Disease Research Foundation (CDRF), Zoe Ltd and the National Institute for Health Research (NIHR) Clinical Research Network (CRN) and Biomedical Research Centre based at Guy's and St Thomas' NHS Foundation Trust in partnership with King's College London. The UK Medical Research Council and Wellcome (Grant ref: 217065/Z/19/Z) and the University of Bristol provide core support for ALSPAC.

    1. Epidemiology and Global Health
    Tina Bech Olesen, Henry Jensen ... Berit Andersen
    Research Article

    Background: In contrast to most of the world, the cervical cancer screening programme continued in Denmark throughout the COVID-19 pandemic. We examined the cervical cancer screening participation during the pandemic in Denmark.

    Methods: We included all women aged 23-64 years old invited to participate in cervical cancer screening from 2015-2021 as registered in the Cervical Cancer Screening Database combined with population-wide registries. Using a generalised linear model, we estimated prevalence ratios (PR) and 95% confidence intervals (CI) of cervical cancer screening participation within 90, 180 and 365 days since invitation during the pandemic in comparison with the previous years adjusting for age, year and month of invitation.

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    Conclusions: The overall participation in cervical cancer screening was reduced during the early phase of the pandemic. However, the decline almost diminished with longer follow-up time.

    Funding: The study was funded by the Danish Cancer Society Scientific Committee (grant number R321-A17417) and the Danish regions.