COVID-19 Outbreak: An Overview

Abstract

Background: In late December 2019, Chinese health authorities reported an outbreak of pneumonia of unknown origin in Wuhan, Hubei Province.

Summary: A few days later, the genome of a novel coronavirus was released (http://viro-logical.org/t/novel-2019-coronavirus-genome/319; Wuhan-Hu-1, GenBank accession No. MN908947) and made publicly available to the scientific community. This novel coronavirus was provisionally named 2019-nCoV, now SARS-CoV-2 according to the Coronavirus Study Group of the International Committee on Taxonomy of Viruses. SARS-CoV-2 belongs to the Coronaviridae family, Betacoronavirus genus, subgenus Sarbecovirus. Since its discovery, the virus has spread globally, causing thousands of deaths and having an enormous impact on our health systems and economies. In this review, we summarize the current knowledge about the epidemiology, phylogenesis, homology modeling, and molecular diagnostics of SARS-CoV-2. Key Messages: Phylogenetic analysis is essential to understand viral evolution, whereas homology modeling is important for vaccine strategies and therapies. Highly sensitive and specific diagnostic assays are key to case identification, contact tracing, identification of the animal source, and implementation of control measures.

Keywords: COVID-19; Pandemic; Phylogenesis; Protein modeling; Real-time polymerase chain reaction; SARS-CoV-2.

Fig. 1

HHpred mapping of the homologous structures of all proteins coded by the 2019-nCoV genome. Numbers below the open rectangles refer to all open reading frames (ORFs) detected. Red strips represent the PDB (Protein Data Bank) homologous structures. PDB codes are reported within the corresponding red stripes. Details are given in Table 1.

Fig. 2

Phylogenetic tree of all the 2019-nCov sequences available on February 9, 2020 (n = 74, cartooned outbreak clade), plus n = 1 Bat CoV-like sequence, n = 5 Human SARS, n = 4 Bat SARS-like sequences, and n = 2 from MERS. Numbers along the branches represent a bootstrap value >0.90. The scale bar represents expected substitutions per nucleotide site.

Fig. 3

Maximum clade credibility phylogeny estimated using all the complete and near-complete 2019-nCov genome sequences available up to February 9, 2020 (n = 74). Clade posterior probabilities are shown at well-supported nodes. The colors represent different locations.