Modeling the onset of symptoms of COVID-19: Effects of SARS-CoV-2 variant

PLoS Comput Biol. 2021 Dec 16;17(12):e1009629. doi: 10.1371/journal.pcbi.1009629. eCollection 2021 Dec.


Identifying order of symptom onset of infectious diseases might aid in differentiating symptomatic infections earlier in a population thereby enabling non-pharmaceutical interventions and reducing disease spread. Previously, we developed a mathematical model predicting the order of symptoms based on data from the initial outbreak of SARS-CoV-2 in China using symptom occurrence at diagnosis and found that the order of COVID-19 symptoms differed from that of other infectious diseases including influenza. Whether this order of COVID-19 symptoms holds in the USA under changing conditions is unclear. Here, we use modeling to predict the order of symptoms using data from both the initial outbreaks in China and in the USA. Whereas patients in China were more likely to have fever before cough and then nausea/vomiting before diarrhea, patients in the USA were more likely to have cough before fever and then diarrhea before nausea/vomiting. Given that the D614G SARS-CoV-2 variant that rapidly spread from Europe to predominate in the USA during the first wave of the outbreak was not present in the initial China outbreak, we hypothesized that this mutation might affect symptom order. Supporting this notion, we found that as SARS-CoV-2 in Japan shifted from the original Wuhan reference strain to the D614G variant, symptom order shifted to the USA pattern. Google Trends analyses supported these findings, while weather, age, and comorbidities did not affect our model's predictions of symptom order. These findings indicate that symptom order can change with mutation in viral disease and raise the possibility that D614G variant is more transmissible because infected people are more likely to cough in public before being incapacitated with fever.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • COVID-19 / diagnosis*
  • COVID-19 / epidemiology
  • COVID-19 / virology*
  • China / epidemiology
  • Computational Biology
  • Cough / etiology
  • Diarrhea / etiology
  • Fever / etiology
  • Humans
  • Japan / epidemiology
  • Models, Biological*
  • Mutation
  • Nausea / etiology
  • Pandemics
  • SARS-CoV-2* / genetics
  • SARS-CoV-2* / pathogenicity
  • Time Factors
  • United States / epidemiology
  • Vomiting / etiology

Supplementary concepts

  • SARS-CoV-2 variants

Grants and funding

We acknowledge funding support by the Dr. Peter N. Schlegel, M.D., Family Endowed Fellowship Fund awarded to JRL; Hsieh Family Foundation and Kathy & Richard Leventhal Research Fund awarded to PK. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.