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

Version history

  1. Received: August 25, 2022
  2. Preprint posted: September 7, 2022 (view preprint)
  3. Accepted: January 18, 2023
  4. Accepted Manuscript published: January 19, 2023 (version 1)
  5. Version of Record published: February 2, 2023 (version 2)

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.

Metrics

  • 1,490
    views
  • 186
    downloads
  • 3
    citations

Views, downloads and citations are aggregated across all versions of this paper published by eLife.

Download links

A two-part list of links to download the article, or parts of the article, in various formats.

Downloads (link to download the article as PDF)

Open citations (links to open the citations from this article in various online reference manager services)

Cite this article (links to download the citations from this article in formats compatible with various reference manager tools)

  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

Share this article

https://doi.org/10.7554/eLife.82980

Further reading

    1. Epidemiology and Global Health
    Xiaoxin Yu, Roger S Zoh ... David B Allison
    Review Article

    We discuss 12 misperceptions, misstatements, or mistakes concerning the use of covariates in observational or nonrandomized research. Additionally, we offer advice to help investigators, editors, reviewers, and readers make more informed decisions about conducting and interpreting research where the influence of covariates may be at issue. We primarily address misperceptions in the context of statistical management of the covariates through various forms of modeling, although we also emphasize design and model or variable selection. Other approaches to addressing the effects of covariates, including matching, have logical extensions from what we discuss here but are not dwelled upon heavily. The misperceptions, misstatements, or mistakes we discuss include accurate representation of covariates, effects of measurement error, overreliance on covariate categorization, underestimation of power loss when controlling for covariates, misinterpretation of significance in statistical models, and misconceptions about confounding variables, selecting on a collider, and p value interpretations in covariate-inclusive analyses. This condensed overview serves to correct common errors and improve research quality in general and in nutrition research specifically.

    1. Ecology
    2. Epidemiology and Global Health
    Emilia Johnson, Reuben Sunil Kumar Sharma ... Kimberly Fornace
    Research Article

    Zoonotic disease dynamics in wildlife hosts are rarely quantified at macroecological scales due to the lack of systematic surveys. Non-human primates (NHPs) host Plasmodium knowlesi, a zoonotic malaria of public health concern and the main barrier to malaria elimination in Southeast Asia. Understanding of regional P. knowlesi infection dynamics in wildlife is limited. Here, we systematically assemble reports of NHP P. knowlesi and investigate geographic determinants of prevalence in reservoir species. Meta-analysis of 6322 NHPs from 148 sites reveals that prevalence is heterogeneous across Southeast Asia, with low overall prevalence and high estimates for Malaysian Borneo. We find that regions exhibiting higher prevalence in NHPs overlap with human infection hotspots. In wildlife and humans, parasite transmission is linked to land conversion and fragmentation. By assembling remote sensing data and fitting statistical models to prevalence at multiple spatial scales, we identify novel relationships between P. knowlesi in NHPs and forest fragmentation. This suggests that higher prevalence may be contingent on habitat complexity, which would begin to explain observed geographic variation in parasite burden. These findings address critical gaps in understanding regional P. knowlesi epidemiology and indicate that prevalence in simian reservoirs may be a key spatial driver of human spillover risk.