1. Introduction
Coronavirus Disease- 2019 (COVID-19) originated from a sea food market at Wuhan city (the capital of Hubei province at the south east of China) and spread rapidly in more than 200 countries. On 2 Jul 2020, the total confirmed cases reached more than 10.5 million and 512000 deaths. The symptoms of COVID 19 include cough, fever, headache, fatigue, sore throat and malaise. The disease can be complicated to pneumonia and severe acute respiratory syndrome [1-3]. The COVID 19 is transmitted through direct or indirect contact with respiratory droplets and biological samples such as urine, saliva and stool [4]. However, some studies proved the presence of the virus in air samples and one study stated that the virus from air samples is viable for up to three hours [5-8].
Coronavirus 19 is named by the WHO and the International Committee on Taxonomy of Viruses (ICTV) as SARS-CoV-2 and is grouped in the same class of SARS-CoV [9]. The two viruses belong to the family: Coronaviridae; subfamily: Orthocoronavirinae; genus: betacoronavirus; subgenus: sarbecovirus; species: Severe Acute Respiratory Syndrome- related coronavirus. The bat coronavirus (BatCoV RaTG13) was isolated from the bat genus Rhinolophus affinis. As the SARS-CoV-2 and SARS-CoV, The bat coronavirus (BatCoV RaTG13) belongs to the beta coronaviruse and it has 96% genome sequence identity compared to the genome of SARS-CoV-2 [10].
The SARS-CoV-2, SARS-CoV, and the bat coronavirus (BatCoV RaTG13) have the same virion structure. They have an RNA with nucleocapsid protein and an envelope. The viral envelope contains a bi-lipid membrane and three proteins: the spike protein, envelope protein and membrane protein [11].
The three viruses contain two major genes: The orf 1ab and 1a (two third) and the structural and accessory proteins gene (one third). The Orf 1ab and 1a genes are translated and hydrolyzed to produced 16 nonstructural proteins (nsp1- nsp16) while the translation of the second gene produces the structural proteins spike (S), envelope (E), membrane (M), and nucleocapsid (N); and the accessory proteins orf3a, orf3b, orf6, orf7a, orf7b, orf8a, orf8b, orf9b and orf10. The number and type of the accessory proteins differs according to the virus [10, 12-16].
Regarding the NS3, NS6, NS7a, NS7b and NS8 of the BatCoV RaTG13, some published articles named them as nonstructural proteins [16-17] and others named them as accessory proteins [18,19]. Because these proteins are located in the gene of the structural and accessory proteins, they are considered as accessory proteins and compared to the accessory proteins of SARS-CoV-2.
This article investigated the protein sequence identity and similarity percentages of SARS-CoV-2 compared to the proteins of SARS-CoV and the BatCoV RaTG13.