Evidence brief of SARS-CoV-2 incubation periods
August 2021
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Table of contents
- Introduction
- Key points
- Overview of the evidence
- Methods
- Evidence Tables
- Table 1. Evidence of incubation period for VOCs (n=4): alpha (n=2), delta (n=3)
- Table 2. Estimates of incubation period for the original variants prior to the emergence of VOCs from systematic reviews (n=9), meta-analyses (n=2), rapid reviews (n=1) and scoping reviews (n=1) and select primary research not included in the syntheses (n=2)
- References
Introduction
What is the incubation period for SARS-CoV-2 and has it changed with variants of concern (VOC)?
The incubation period is defined as the time between exposure to an infectious pathogen and symptom onset. The incubation period of SARS-CoV-2 determined by the World Health Organization (WHO) and the European Centers for Disease Control (ECDC) is 0-14.0 days, the US Centers for Disease Control and Prevention (CDC) is 2.0-14.0 days and the Public Health Agency of Canada is 1.0-14.0 days. A comparison across what was known on incubation periods for other coronaviruses reported the average incubation periods of SARS was 4.6 days (95% CI: 3.8‐5.8 d) and MERS was 5.2 days (95% CI: 1.9‐14.7 d)Footnote 1. This review summarizes the incubation period of the original SARS-CoV-2 variants prior to the emergence of variants of concern (VOC) from several systematic reviews that included studies from the first 12 months of the pandemic (Table 2) and more recent research that has focused on establishing the incubation period of the VOCs (Table 1).
SARS-CoV-2 VOCs are circulating variants that have been flagged by national or global public health organizations. There are currently four VOCs: B.1.1.7 (Alpha), B.1.351 (Beta), P.1 (Gamma) and B.1.617.2 (Delta). VOCs are of concern when compared to the original SARS-CoV-2 variants, as their complement of mutations lead to increased transmissibility, increased virulence (morbidity or mortality), changes in clinical disease presentation, immune evasion, reduced effectiveness of treatments, vaccines and/or public health measures and/or are associated with diagnostic detection failures Footnote 2Footnote 3 Footnote 4. Canada has established a national definition for VOCs3. In May 2021, the WHO released a naming system for VOCs and variants of interest (VOIs) using Greek letters to improve the ease of communication on variants and potential stigma related to places where variants were first identified. This naming system has been adopted in this report2.
This evidence brief focuses on the evidence up to August 17th, 2021 on incubation periods for SARS-CoV-2 and whether there is evidence that the incubation period for any VOC is different than previously circulating variants. In this summary, "original variant" refers to any variant that was not designated as a VOC or VOI.
Key points
Incubation period for the original SARS-CoV-2 variants (prior to VOCs)
Highlights from the current literature include:
- The incubation period of SARS-CoV-2 based on a range of estimates from meta-analyses of studies conducted in 2020 prior to the emergence of VOCs estimated pooled mean incubation periods of 4.9-6.9 days (9 meta-analyses) and pooled median incubation periods of 4.8-5.9 days (8 meta-analyses) (Table 2).
- The largest meta-analysis included 99 studies with a range of 2.33-17.60 days incubation period reported across studies and the pooled mean incubation period 6.38 days (95%CI 5.79-6.97) and median 5.41 days (95%CI 4.74-6.07) had high between study heterogeneity Footnote 5.
- In most meta-analyses the incubation period mean estimate is longer than the median estimate because there appears to be a few cases in each dataset with very long incubation periods, which causes a right skew in the data, also known as over dispersion in the tail of incubation periods. Long incubation periods are well documented particularly for immunocompromised populations, which have been covered in previous reviews and can be requested by contacting ocsoevidence-bcscdonneesprobantes@phac-apsc.gc.ca.
- Two reviews reported evidence of a longer incubation period in children compared to adults: median, 7.3 days in children vs. 5.8 days in adults Footnote 6, median 10 days vs. 7 days, respectively Footnote 7.
- The majority (up to 90%) of the studies included in the meta-analyses were from China and represented data collected in the first half of 2020 Footnote 8Footnote 9. The incubation period estimated prior to the end of January 2020 was shorter than after January 2020 in these studies, which was hypothesized to represent a bias in the data as cases were increasing exponentially9.
- The Canadian model estimating incubation period over the pandemic up to November 2020 reported a mean of 6.89 days, a median of 6 days and 90th, 95th, 99th percentiles of 11, 12, 13.5 days. The results suggested a slight increase in the incubation period over timeFootnote 10.
Incubation period for VOCs
Highlights from the current literature include:
- Four studies were found on the incubation period for VOCs; one that looked at Alpha, two that looked at Delta, and one that looked at both Alpha and Delta (Table 1). No studies reporting on the incubation period for Beta or Gamma were found.
- The two studies included in this summary on Alpha incubation period found it could be shorter than original strains by 2 days. The first study is a small retrospective cohort study in Japan that reported incubation period of Alpha was shorter compared to other strains (mean: 3.53 days vs. 5.71 days / median 3.0 days vs. 5.0 days) Footnote 11. The other was a surveillance report from England that reported the median incubation period for Alpha was 4 days and no mean incubation period was provided Footnote 12. Both results indicate that Alpha incubation period may be shorter, however there is low confidence in these estimates, which are likely to change as additional research is published.
- The three studies on Delta incubation period included two contact tracing investigations from Guangdong, China. All results indicated that Delta incubation period may be shorter, however the difference may not be significant and there is low confidence in these estimates, which are likely to change as additional research is published. The first study reported the mean incubation period was 5.8 days (95%CI 5.2-6.4) and the latent period was 4.0 days (95%CI 3.5-4.4) Footnote 13. The latent period is defined as the time from acquiring infection to infectiousness onset. The other study estimated time to first positive PCR test, latent period rather than incubation period, in quarantined cases with Delta compared to a sample of cases from the initial epidemic wave in 2020: median 4 days (IQR 3-5) vs. 6 days (IQR 5-8), respectivelyFootnote 11. The third estimate was a surveillance report from England that reported the median incubation period for Delta was 4 daysFootnote 12.
Overview of the evidence
Thirteen reviews on incubation periods prior to the emergence of VOCs were included in this review including systematic reviews and meta-analysis (n=9), meta-analyses (n=2), a rapid review (n=1), and a scoping review (n=1). In addition, one recently published primary research study and one quantitative model using Canadian data were included for information on pre-VOC incubation period estimates as they were not included in the 13 reviews (Table 2). Studies reporting on incubation period for any VOC were reported in four studies or reports (Table 1).
Most incubation period data comes from public health contact tracing investigations mainly from studies done in Asia. One study reported contact tracing surveillance data for VOCs in the UK. Contact tracing investigations are at high risk of bias due to their retrospective nature. The data may also be affected by the fact that people do not know with certainty when or where they were exposed. The systematic reviews were not evaluated by the AMSTAR-2, a tool for evaluating systematic reviews, however the methods synopsis indicates the missing steps of each systematic review. The quality of the reviews was highly variable in both conduct and reporting across reviews. The systematic reviews and meta-analyses that are included in this brief overlap with the studies that were included. The quantitative model uses Canadian data to estimate the incubation period in the Canadian context. This model would be sensitive to the quality of the data used to develop the model.
The evidence for the non-VOC incubation period is abundant but not conclusive and the evidence for the VOC incubation period is sparse. This has resulted in large knowledge gaps on all SARS-CoV-2 viruses. Additional cohort studies are needed to assess early signals that the incubation period for original variants have evolved over time and to establish incubation periods for all the VOCs including pediatric studies to assess the early signal that children exposed to VOCs have a longer incubation period than adults.
Methods
A daily scan of the literature (published and pre-published) is conducted by the Emerging Science Group, PHAC. The scan has compiled COVID-19 literature since the beginning of the outbreak and is updated daily. Searches to retrieve relevant COVID-19 literature are conducted in Pubmed, Scopus, BioRxiv, MedRxiv, ArXiv, SSRN, Research Square and cross-referenced with the COVID-19 information centers run by Lancet, BMJ, Elsevier, Nature and Wiley. The daily summary and full scan results are maintained in a Refworks database and an excel list that can be searched. Targeted keyword searching was conducted within these repositories to identify relevant citations on COVID-19 and SARS-CoV-2. Search terms used included: (incubation period and (review or "variant of concern terms")). This review contains research published up to August 17, 2021.
A Google search and search of targeted government websites was conducted to find publicly available reports, protocols and clinical data pertinent to the evidence questions. Search terms used included: COVID-19 and incubation period. Searches were conducted and websites accessed on August 17, 2021.
Each potentially relevant reference was examined to confirm it had relevant data, and relevant citations were explored for further detail; relevant data was extracted into the review.
Acknowledgments
Prepared by: Kusala Pussegoda and Lisa Waddell, National Microbiology Laboratory Emerging Science Group, Public Health Agency of Canada.
Editorial review, science to policy review, peer-review by a subject matter expert and knowledge mobilization of this document was coordinated by the Office of the Chief Science Officer: ocsoevidence-bcscdonneesprobantes@phac-aspc.gc.ca
Evidence Tables
Study | Method | Key outcomes |
---|---|---|
Primary literature on alpha and delta | ||
Homma (2021)Footnote 11 Retrospective cohort study Japan |
A small retrospective cohort that included 30 Alpha cases from March 2021 and compared them to other SARS-CoV-2 strains from Mar 2020-Jan 2021. |
|
Li (2021) Footnote 14 Outbreak investigation China |
A study from China reported a shorter time interval between exposure and first PCR positive test in quarantined cases involved in an outbreak of Delta across the province of Guangdong (n=34) compared to cases caused by 19A/19B genetic strains during the early 2020 epidemic (n=29). |
|
Kang (2021)Footnote 13 Outbreak investigation China |
The transmission and epidemiological characteristics of the outbreak in Southern China is described. |
|
Public Health England (2021)Footnote 12 Surveillance data analysis UK |
Contact tracing surveillance data from the UK between March 29 and June 9, 2021. |
|
CI = Confidence interval, IQR= Interquartile range, PCR= Polymerase Chain Reaction |
Study | Method | Key outcomes |
---|---|---|
Reviews (n=13) | ||
Song (2021)Footnote 7 Systematic review NA |
This systematic review conducted a search up to 10 March 2021 on COVID-19 family clusters. Eighteen studies (published Jan-May 2020) involving 34 children and 98 adults from 28 families were included. Incubation period was reported in 31 children and 72 adults. No risk of bias assessment conducted. |
|
Elias (2021)Footnote 5 Short communication Meta-analysis Jan 2021 |
A systematic search was carried out on studies published from 1 January 2020 to 10 January 2021 reporting the SARS-CoV-2 incubation period. No studies on VOCs were identified. There is no systematic review protocol or risk of bias assessment reported. The meta-analysis included 99 studies, of which 23 (23.2%) were cohort studies, 61 (61.6%) were case series, and 15 (15.2%) were modeling studies. Results of meta-analysis available here. |
|
Li (2021)Footnote 15 Scoping review NA |
This scoping review conducted a search up to 10 December 2020. There were 1920 confirmed cases included. Individual patient analysis was conducted by transforming case data to be double interval-censored, which was considered to be best for obtaining a precise estimate. An accelerated failure time model was used to estimate the time to event distribution. This scoping review included a search, inclusion/exclusion criteria and data extraction and analysis. Thus, other than the omission of a risk of bias assessment resembles a systematic review more than a scoping review. |
|
Dhouib (2021)Footnote 8 Systematic review and meta-analysis NA |
This systematic review was conducted with a search from December 2019 to December 1, 2020. Forty-two studies were included and consisted of 9 strong, 19 moderate, and 14 weak quality studies. The meta-analysis included 10 studies on mean incubation period. This systematic review has a registered protocol CRD42020196347, included a risk of bias and SIGN assessment of the certainty of the evidence. Random effects meta-analysis was conducted. |
|
Xin (2021)Footnote 9 Systematic review and meta-analysis NA |
This systematic review included a search conducted from 1 February 2020 and 25 September 2020. The meta-analysis included 31 studies that reported mean incubation period and 41 studies that reported median incubation period. The search strategy is presented, articles were evaluated with the STROBE checklist for quality and a random effects meta-analyses and meta-regression were conducted. |
|
Daley (2020) Footnote 16 Systematic Review NA |
The systematic review search was conducted 18 July 2020 and included 21 studies reporting incubation period. There is no protocol, a brief search description, no risk of bias assessment and the statistical analysis was averaging. |
|
Alene (2021)Footnote 17 Systematic review and meta-analysis NA |
This systematic review was conducted on studies published up to 30 June 2020. Search, screening and data extractions details provided. Risk of bias was assessed using the Ottawa-Newcastle Scale. Random effects meta-analysis included 14 studies on mean incubation period. |
|
Wei (2020)Footnote 6 Systematic review and meta-analysis NA |
The systematic review search was conducted up to 26 April 2020. 56 studies were included in the meta-analysis (4095 observations). Methods for the search, selection, data extraction and quality assessment (AHRQ) of studies are described. Random effects meta-analysis was conducted. Bayesian meta-analysis was also employed to better simulate the distribution of the incubation period. Meta-regression was used to explore heterogeneity. |
|
McAloon (2020)Footnote 18 Rapid review and meta-analysis NA |
Rapid review and meta-analysis included a search conducted 8 April 2020. 24 studies were included for review, 9 of them were analyzed. The search, selection criteria, data extraction details and quality assessment using the Ottawa-Newcastle scale was described. Random effects meta-analysis was conducted. |
|
Quesada (2021)Footnote 19 Systematic review and meta-analysis NA |
This systematic review was conducted with a search up to 21 March 2020. The meta-analysis included 7 studies. Search, selection strategies and meta-analysis methods are reported. Quality assessment was not done. |
|
Khalili (2020)Footnote 20 Systematic review and meta-analysis NA |
A systematic review was conducted up to 11 March 2020. 18 studies were included in the meta-analysis of incubation period, only 2 were from outside China. Search, selection strategies and meta-analysis methods are reported. Quality assessment was not done. |
|
Lauer (2020)Footnote 21 Meta-analysis NA |
Pooled analysis of 181 cases reported Jan 4 - Feb 24, 2020 outside of Hubei province. The analysis in this paper is individual patient data meta-analysis. However the data was scraped from many different sources. |
|
Lin (2020)Footnote 22 Systematic Review NA |
Search date was Feb 21, 2020. 8 mathematical or statistical models that estimated incubation period were included. The search strategy, selection criteria and data extraction are described. The ISPOR-SMDM Modelling Good Research Practices Task Force tool was used to evaluate the models. Estimates are descriptively summarized. |
|
Primary literature (n=1) | ||
Huang (2021) Footnote 23 Retrospective cohort China |
787 cases from outside Wuhan with sufficient information about exposure and symptom onset were identified from a national database of cases during 2020 in China. An interval-censored data estimation methods was used to study the data and factors that may explain the variability in incubation period. A gamma distribution best fit the data which was right skewed. |
|
Model (n=1) | ||
Paul (2021)Footnote 10 Model Canada |
SEIR model of the Canadian epidemic was developed to estimate the incubation period up to Nov 2020. |
|
CI = Confidence interval NR = Not reported, NA = country not applicable, IQR = Interquartile range |
References
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-
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-
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-
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-
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-
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-
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-
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