Extinction of COVID-19 Clusters in a Lebanese Village: A Quick, Adapted Molecular and Contact tracing

  1. Amanda Chamieh
  2. Rania Warrak
  3. Lucie Tawk
  4. Omar Zmerli
  5. Claude Afif
  6. Jean-Marc Rolain
  7. Eid Azar

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Abstract

There is growing evidence of cluster transmission and superspreading of SARS-CoV-2, implying heterogeneous dispersion. We discuss the successful containment of COVID-19 local outbreak in Bcharreh, the small town of 4500 inhabitants, in Northern Lebanon. We look at the dynamics of cluster transmission and viral load evolution throughout the outbreak.

SARS-CoV-2 PCR test was proposed to all exposed individuals. Persons under investigation that tested negative by PCR were periodically retested. We define: a cluster as more than 3 people with a common suspicious or confirmed SARS-CoV-2 positive contact, clinical cure as the resolution of symptoms, and virologic cure as SARS-CoV-2 PCR Cycle threshold(Ct) >35. We analyzed all obtained Ct into corresponding clusters and performed a time series analysis.

A total of 713/871 SARS-CoV-2 PCR tests were performed at Saint George Hospital University Medical Center (SGHUMC) from April 5 th 2020 -June 14 th 2020. We used the LightMix® Modular SARS-CoV-2 (COVID19) E, N, and RdRP-genes (Tib Molbiol, Berlin, Germany). Week one of epidemiologic surveillance began on March 31 st when the first case was detected. A strict lockdown was imposed on Bcharreh village 5 days later, on top of the national lockdown. We identified 4 different clusters ranging from 3 to 27 cases and 3 sporadic unrelated cases.

Almost 70% of each cluster was diagnosed within 7 days. After 2 weeks, we saw a significant increase in the average initial diagnostic Ct 27.9 to 34.72 (P<0.0001). A total of 73/74 SARS-CoV-2 PCR positive individuals achieved cure (98.6%). We recorded one death of a 90-year-old man with multiple comorbidities.

In explosive new epidemics, we can derive from previous experience and not be blinded by it. To safely navigate out of the lockdown, focus on where new transmission is likely to emerge and accordingly target available diagnostic technologies.

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  1. ScreenIT

    SciScore for 10.1101/2020.11.28.20240077: (What is this?)

    Please note, not all rigor criteria are appropriate for all manuscripts.

    Table 1: Rigor

    Institutional Review Board Statementnot detected.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.
    Sex as a biological variablenot 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:
    The common limitation in facing emerging pathogens such as SARS-CoV-2 is the unknown epidemiologic characteristics and transmissibility that may impede and complicate effective control strategies. More than often, this leads to delays in proper management and an overwhelmed healthcare system. The various proposed mathematical models and projections may be misleading and far from real life empiric experience. Most models for SARS-CoV-2 were based on assumptions from the 1918 Flu pandemic, which we know follows a homogenous transmission with a dispersion factor k of 1. This means that clusters had very little role in the 1918 Flu pandemic, contradicting the transmission pattern of the current COVID-19 pandemic(3,19). We also know that the higher the proportion of non-transmitting individuals, i.e. the more over dispersed, the more likely that disease extinction occurs and the chain of transmission dies out. However, if an outbreak does result, it is much more explosive than predicted by Ro. So, a disease with high over dispersion that does not result in an outbreak probably lacked the superspreading event. This is where lockdown and social distancing come in. In addition, this may explain why the introduction of SARS-CoV-2 in France dating back to December 2019 did not result in an outbreak at that time(20). After 2 weeks, we saw a significant decrease in the average initial diagnostic Ct (P<0.0001) probably affected by the lockdown, and preventive measures such as mask use, so...

    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.

    About SciScore

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  2. Version published to 10.1101/2020.11.28.20240077v1 on medRxiv