ABSTRACT
IntroductionThe SARS-CoV-2 pandemic has been associated with the occurrence since summer 2020 of several viral variants that overlapped or succeeded each other in time. Those of current concern harbor mutations within the spike receptor binding domain (RBD) that may be associated with viral escape to immune responses. In our geographical area a viral variant we named Marseille-4 harbors a S477N substitution in this RBD. Materials and methodsWe aimed to implement an in-house one-step real-time reverse transcription-PCR (qPCR) assay with a hydrolysis probe that specifically detects the SARS-CoV-2 Marseille-4 variant. ResultsAll 6 cDNA samples from Marseille-4 variant strains identified in our institute by genome next-generation sequencing (NGS) tested positive using our Marseille-4 specific qPCR, whereas all 32 cDNA samples from other variants tested negative. In addition, 39/42 (93%) respiratory samples identified by NGS as containing a Marseille-4 variant strain and 0/26 samples identified as containing non-Marseille-4 variant strains were positive. Finally, 1,585/2,889 patients SARS-CoV-2-diagnosed in our institute, 10/277 (3.6%) respiratory samples collected in Algeria, and none of 207 respiratory samples collected in Senegal, Morocco, or Lebanon tested positive using our Marseille-4 specific qPCR. DiscussionOur in-house qPCR system was found reliable to detect specifically the Marseille-4 variant and allowed estimating it is involved in more than half of our SARS-CoV-2 diagnoses since December 2020. Such approach allows the real-time surveillance of SARS-CoV-2 variants, which is warranted to monitor and assess their epidemiological and clinical characterics based on comprehensive sets of data.
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; 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.
Subject(s)
COVID-19ABSTRACT
Background: We share our experience in COVID-19 pneumonia management at Saint George Hospital University Medical Center (SGHUMC) in Lebanon. In the absence of a standard of care, early diagnosis and opt-in therapy with Hydroxychloroquine and Azithromycin were offered. Methods: We reviewed records of COVID-19 pneumonia patients from March 16-April 26 2020. Based on NEWS score, we stratified patients as A: low B: medium, and C: high clinical severity and obtained pharmacotherapy data. Chest-CT-severity-score (CTSS) was used. We defined clinical cure as resolution of symptoms and biomarkers and virologic cure as a PCR above 35 cycles(Ct). Results: We recorded 21 COVID-19 pneumonia patients of whom 19 opted for treatment. Clinical symptoms and laboratory markers at presentation did not significantly correlate with severity. Lower initial viral load significantly correlated with lower levels of clinical and radiological severity (p=0.038). Virologic cure, Ct>35, by day 10, was only 33% in high severity significantly less than categories A and B. We observed 100% clinical cure at day 10 in Category-A, 67% in B, and 33% in C(p<0.05). Patients with the lowest severity had the fastest virologic cure in a mean of 5.8 days from diagnosis, shortest hospitalization and earlier radiological improvement(p<0.005). Ultimately, 18 patients were discharged home in good condition and one remains in the ICU. Conclusion: Viral dynamics matter in COVID-19 pneumonia. An early control of replication may be crucial in averting complications. Early administration of Hydroxychloroquine and Azithromycin potentially explains our 94.7% success rate in treating a fairly complex cohort of COVID-19 pneumonia.