Molecular Epidemiology Analysis of SARS-CoV-2 Strains Circulating in Romania during the First Months of the Pandemic.

Marius Surleac,Petre Milu,Ovidiu Vlaicu,Dragos Florea,Dimitrios Paraskevis,Anca Streinu-Cercel,Oana Sandulescu,Corina Casangiu,Simona Paraschiv,Leontina Banica,Marius Cotic,Dan Otelea

doi:10.3390/life10080152

Abstract

BACKGROUND: The spread of SARS-CoV-2 generated an unprecedented global public health crisis. Soon after Asia, Europe was seriously affected. Many countries, including Romania, adopted lockdown measures to limit the outbreak. AIM: We performed a molecular epidemiology analysis of SARS-CoV-2 viral strains circulating in Romania during the first two months of the epidemic in order to detect mutation profiles and phylogenetic relatedness. METHODS: Respiratory samples were directly used for shotgun sequencing. RESULTS: All Romanian sequences belonged to lineage B, with a different subtype distribution between northern and southern regions (subtype B.1.5 and B.1.1). Phylogenetic analysis suggested that the Romanian epidemic started with multiple introduction events from other European countries followed by local transmission. Phylogenetic links between northern Romania and Spain, Austria, Scotland and Russia were observed, as well as between southern Romania and Switzerland, Italy, France and Turkey. One viral strain presented a previously unreported mutation in the Nsp2 gene, namely K489E. Epidemiologically-defined clusters displayed specific mutations, suggesting molecular signatures for strains coming from areas that were isolated during the lockdown. CONCLUSIONS: Romanian epidemic was initiated by multiple introductions from European countries followed by local transmissions. Different subtype distribution between northern and southern Romania was observed after two months of the pandemic.

Highlights

The human population has been exposed to more than 50 emerging infectious diseases during the past half-century; 75% of them were vector-borne or zoonotically transmitted [1].The rapid spread of these emerging infectious diseases was facilitated by increased international travel as was the case with the coronavirus infectious disease 2019 (COVID-19) pandemic.Life 2020, 10, 152; doi:10.3390/life10080152 www.mdpi.com/journal/lifeA new variant of coronavirus, the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2)emerged from East Asia (Wuhan, China) at the end of 2019 [2] and spread across the world
The subtype analysis of the 25 SARS-CoV-2 sequences generated in this study indicated that all Romanian sequences belong to lineage B
All the SARS-CoV-2 sequences corresponding to viral strains circulating in the Bucharest metropolitan area (BMA) were classified as subtype B.1.1, whereas the sequences from the Suceava county outbreak were assigned as B.1.5

Summary

Introduction

The human population has been exposed to more than 50 emerging (or re-emerging) infectious diseases during the past half-century; 75% of them were vector-borne or zoonotically transmitted [1].The rapid spread of these emerging infectious diseases was facilitated by increased international travel as was the case with the coronavirus infectious disease 2019 (COVID-19) pandemic.Life 2020, 10, 152; doi:10.3390/life10080152 www.mdpi.com/journal/lifeA new variant of coronavirus, the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2)emerged from East Asia (Wuhan, China) at the end of 2019 [2] and spread across the world. The rapid spread of these emerging infectious diseases was facilitated by increased international travel as was the case with the coronavirus infectious disease 2019 (COVID-19) pandemic. A new variant of coronavirus, the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). SARS-CoV-2 causes a wide spectrum of clinical manifestations with different severities in humans, ranging from asymptomatic to life-threatening critical cases [3,4]. Romania reported the first confirmed case of SARS-CoV-2 on February 26th, 2020 [5]. 28973 new cases and 1750 COVID-19 related deaths were reported (https://gisanddata.maps.arcgis.com/ accessed on 6th of July). Many countries including Romania adopted a period of state of emergency to flatten the curve of infections and to slow down the spread of the virus. RESULTS: All Romanian sequences belonged to lineage B, with a different subtype distribution between northern and southern regions

Objectives

Methods

Results