Early chains of transmission of COVID-19 in France
This article has been Reviewed by the following groups
Listed in
- Evaluated articles (ScreenIT)
- Evaluated articles (NCRC)
Abstract
Introduction
SARS-CoV-2, which causes COVID-19, has spread rapidly across the world. A dedicated surveillance system was implemented in France in January 2020 to improve early detection of cases and their contacts and limit secondary transmission. Our objective was to use contact-tracing data collected during this initial phase of the epidemic to better characterize SARS-CoV-2 transmission.
Methods
We analysed data collected during contact tracing and retrospective epidemiological investigations in France from 24 January to 30 March 2020. We assessed the secondary clinical attack rate and characterized the risk of a contact becoming a case. We described chains of transmission and estimated key parameters of spread.
Results
Over the study period, 6,082 contacts of 735 confirmed cases were traced. The overall secondary clinical attack rate was 4.1% (95%CI 3.6-4.6) and increased with age of the index case and of the contact. Family contacts were at higher risk of becoming cases (adjusted odds ratio 2.1 (95%CI 1.4-3.0)) while nosocomial contacts were at lower risk (adjusted odds ratio 0.3 (95%CI 0.1-0.7)), compared to coworkers/friends. We identified 328 infector/infectee pairs, 49% of which were family members. The distribution of secondary cases was highly over-dispersed with 80% of secondary cases being caused by 10% of cases. The mean serial interval was 5.1 days (interquartile range 2-8 days) in contact-tracing pairs where late transmission events may be censored, and 6.8 (3-8) days in pairs investigated retrospectively.
Conclusion
This study contributes to improving our knowledge of SARS-CoV-2 transmission, such as the importance of superspreading events. Contact-tracing data are challenging to collect but are key to better understand emerging pathogens.
Funding statement
This work was supported by the LabEx “Integrative Biology of Emerging Infectious Diseases (IBEID)” (Grant Number ANR-10-LABX-62-IBEID), Santé Publique France, the INCEPTION project (PIA/ANR-16-CONV-0005), and the European Union’s Horizon 2020 research and innovation program under grants 101003589 (RECOVER) and 874735 (VEO).
Article activity feed
-
Our take
The objective of this study, available as a preprint and thus not yet peer-reviewed, was to describe the secondary clinical attack rate and its variation across age-group, geographic region, and other factors in France during the beginning of the pandemic (January-March 2020). They estimated an attack rate of 4.1% for secondary cases, and a tertiary attack rate of 2.3%. They also estimated the rate was higher at the beginning compared to the end of the study period, and that older individuals aged 75+ were more likely to transmit COVID-19 than younger individuals. However, they used individual-based surveillance that did not identify asymptomatic cases and only provided confirmatory testing to cases with clinical diagnosis from symptoms, and also had difficulty contacting individuals hospitalized. Therefore, secondary …
Our take
The objective of this study, available as a preprint and thus not yet peer-reviewed, was to describe the secondary clinical attack rate and its variation across age-group, geographic region, and other factors in France during the beginning of the pandemic (January-March 2020). They estimated an attack rate of 4.1% for secondary cases, and a tertiary attack rate of 2.3%. They also estimated the rate was higher at the beginning compared to the end of the study period, and that older individuals aged 75+ were more likely to transmit COVID-19 than younger individuals. However, they used individual-based surveillance that did not identify asymptomatic cases and only provided confirmatory testing to cases with clinical diagnosis from symptoms, and also had difficulty contacting individuals hospitalized. Therefore, secondary and tertiary transmission were likely underestimated as the symptomatic extremes (e.g., mild disease and severe disease) were missing in their analysis.
Study design
prospective-cohort
Study population and setting
The study sought to describe the secondary clinical attack rate and transmission among PCR-confirmed COVID-19 cases identified early in the pandemic in France. From January 24, 2020 to March 30, 2020, the study included any clinical COVID-19 cases identified in the hospital or in the community. Presumed cases were isolated after diagnosis. Cases were administered a questionnaire including sociodemographic characteristics, clinical presentation, and history of exposure. Contacts of confirmed cases were identified through standard contact tracing methods, and only contacts with COVID-19 symptoms were given a PCR test for SARS-CoV-2 infection. Their contacts were then also traced. Possible exposure was grouped into 3 categories (negligible, low, moderate/high) and only contacts with low to moderate/high exposure were followed up. Due to limits in staffing that reduced the timeliness of entry into the web database, the database of contacts was not exhaustive and represented only a sample of all contact tracing. Contact patterns were described using an age-specific contact matrix using French population-based data from another study (COMES-F in 2012). The clinical secondary attack rate and risk factors for secondary transmission were also estimated using logistic regression.
Summary of main findings
During the study period, 735 confirmed cases were successfully traced resulting in identification of 6,028 individual contacts. Cases had an average of 8.3 contacts traced (median: 4, range: 0 - 146). Of the 6,028 contacts, 248 were secondary cases, with an estimated clinical attack rate of 4.1% (95% CI: 3.6 – 4.6). The tertiary clinical attack rate (that is, the secondary attack rate among secondary cases) was 2.3% (95% CI: 1.4 – 3.6). This decreased over time, with an estimated attack rate of 6.8% in the first week of the pandemic, and 1.8% in weeks 12-13. There was also geographic and age-based variation, with individuals 75+ years of age having the highest estimated attack rate (6.2%, 95% CI; 4.3 – 8.7). The attack rate was also highest among family member contacts (7.9%, 95% CI: 6.6 – 9.3), and coworkers/friend (3.4%, 95% CI: 2.5 – 4.4). Estimating chains of transmission, 329 connections were identified between cases, with the largest cluster identified in Oise, France, with 39 cases across 5 familial generations identified, beginning with a pair of cases identified 25 February 2020.
Study strengths
The study made use of extensive contact tracing efforts across France in order to identify chains of transmission across the 735 indexed cases and their 6028 contacts. Based on their comprehensive questionnaire, they were able to examine differences between contacts and their modeling was able to identify a large family cluster in northern France.
Limitations
The study was limited by the human resources available to them—the authors note that they were not able to input and follow-up with every contact in their web database due to the limits of their staff. This highlights the importance of public health departments being well-resourced during critical periods. Additionally, they noted that the workload differed by region, and areas with higher case burdens were less likely to be able to successful trace all contacts compared to less affected regions. Additionally, their testing protocol only included symptomatic cases, which means this study was not reflective of asymptomatic cases or a population-based surveillance strategy that would be more representative of the general population. Additionally, they reported difficulty in identifying contacts from hospitalized individuals, and thus the findings may not have reflected more severe cases of disease.
Value added
The study shows the importance of extensive contact tracing efforts and describes a high attack rate during the early pandemic.
-
SciScore for 10.1101/2020.11.17.20232264: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement not detected. Randomization not detected. Blinding not detected. Power Analysis not detected. Sex as a biological variable not detected. Table 2: Resources
No key resources detected.
Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:Our study has several limitations. Data collected during outbreaks are often noisy and incomplete due to the difficult conditions in which they are collected. Case definitions and protocols evolved during the study period to …
SciScore for 10.1101/2020.11.17.20232264: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement not detected. Randomization not detected. Blinding not detected. Power Analysis not detected. Sex as a biological variable not detected. Table 2: Resources
No key resources detected.
Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:Our study has several limitations. Data collected during outbreaks are often noisy and incomplete due to the difficult conditions in which they are collected. Case definitions and protocols evolved during the study period to adapt to the changing epidemic situation and new knowledge about the virus and its transmission. More importantly, there are major practical challenges associated with contact tracing, in particular the difficulty of both identifying all potential contacts of an individual and then closely monitoring those contacts during the recommended follow-up period of 14 days, with limited human resources. We showed that the proportion of traced cases and the secondary clinical attack rate declined over time, and varied across regions. This likely reflects variations in data quality and completeness, rather than the true evolution of the epidemiological situation due to control measures. Indeed, contact tracing could not be scaled up to meet the exponentially growing burden during the early phase of the epidemic, and investigation teams were quickly overwhelmed with the influx of new cases. Moreover, the work overload was heterogeneous between regions, depending on the local epidemiological situation, and data may therefore vary in quality and consistency. The northeast quarter of France was the most severely affected (especially Ile-de-France and Grand Est regions), while the rest of the country was less overwhelmed (19). However, in a sensitivity analysis, our ris...
Results from TrialIdentifier: No clinical trial numbers were referenced.
Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
Results from JetFighter: We did not find any issues relating to colormaps.
Results from rtransparent:- Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
- Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
- No protocol registration statement was detected.
-
