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

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 5th 2020 -June 14th 2020. We used the LightMix(R) Modular SARS-CoV-2 (COVID19) E, N, and RdRP-genes (Tib Molbiol, Berlin, Germany). Week one of epidemiologic surveillance began on March 31st 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.