Whole genome sequencing and phylogenetic classification of Tunisian SARS-CoV-2 strains from patients of the Military Hos
- PDF / 1,503,881 Bytes
- 5 Pages / 595.276 x 790.866 pts Page_size
- 5 Downloads / 147 Views
SHORT REPORT
Whole genome sequencing and phylogenetic classification of Tunisian SARS‑CoV‑2 strains from patients of the Military Hospital in Tunis Susann Handrick1 · Malena Bestehorn‑Willmann1 · Simone Eckstein1 · Mathias C. Walter1 · Markus H. Antwerpen1 · Habiba Naija2 · Kilian Stoecker1 · Roman Wölfel1 · Mohamed Ben Moussa2 Received: 2 July 2020 / Accepted: 12 September 2020 © The Author(s) 2020
Abstract In the present work, two complete genome sequences of SARS-CoV-2 were obtained from nasal swab samples of Tunisian SARS-CoV-2 PCR-positive patients using nanopore sequencing. The virus genomes of two of the patients examined, a Tunisian soldier returning from a mission in Morocco and a member of another Tunisian family, showed significant differences in analyses of the total genome and single nucleotide polymorphisms (SNPs). Phylogenetic relationships with known SARS-CoV-2 genomes in the African region, some European and Middle Eastern countries and initial epidemiological conclusions indicate that the introduction of SARS-CoV-2 into Tunisia from two independent sources was travel-related. Keywords SARS-CoV-2 · COVID-19 · RT-qPCR · Sequencing · Tunisia · Morocco The current global spread of the newly emerged severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of coronavirus disease 2019 (COVID19), has led to worldwide social and economic disruption. The virus was first described in December 2019 in Wuhan, China, and has since spread into a pandemic. As a result, healthcare systems in almost all countries of the world are facing unprecedented challenges. A few clinically approved drugs have been shown to exhibit anti-SARS-CoV-2 activity, but none have yet been proven to be sufficiently effective in treating COVID-19 patients, nor are vaccines available [1]. By August 2020, the World Health Organization (WHO) had reported more than 21.99 million infected individuals and 775,893 deaths worldwide. In the African Region, 966,352 confirmed cases have been reported [2], but many cases Edited by Hartmut Hengel. Susann Handrick and Malena Bestehorn-Willmann have contributed equally. Roman Wölfel and Mohamed Ben Moussa are shared last authors. * Susann Handrick [email protected] 1
Bundeswehr Institute of Microbiology, Munich, Germany
Department of Virology, Military Hospital of Instruction of Tunis, Tunis, Tunisia
2
remain undetected, probably due to insufficient diagnostic capacity, limited contact tracing and the oftentimes unspecific symptoms of affected patients. Diagnostic tests for SARS-CoV-2 have been carried out in Tunisia since early February 2020. On 2 March 2020, the first case of COVID-19, a Tunisian patient from Italy, was reported [3, 4]. Since then, the number of positively-tested SARS-CoV-2 patients has been increasing. By 18 August 2020, a total of 117,086 tests were performed and 2427 SARS-CoV-2 positive cases were reported by the Tunisian Ministry of Health. Of these positive cases, 60 patients died [5]. So far, only a few whole genome sequences
Data Loading...
