Introduction
Coronaviridae family is a single-strand, positive-sense, enveloped RNA virus family(Su et al., 2016) that can be found circulating in a wide range of avian and mammal species hosts.(Cavanagh, 2007; Ismail, Tang, & Saif, 2003) In December 2019, a patient was found to have pneumonia caused by an unknown betacoronavirus. By using unbiased sequencing of the sample from the patient, a novel coronavirus was determined. According to the latest official name by the International Committee on Taxonomy of Viruses (ICTV), it should be called Severe Acute Respiratory Syndrome Coronavirus 2, SARS-CoV-2 in abbreviation. Then within the same month, in late December, there are already been a crowd of patients that had been diagnosed with infecting the pathogen. (W. M. H. Commission, 2019; Zhu et al., 2020) The widely believed origin, seafood wholesale market in Wuhan, Hubei Province, China, was proven wrong according to the official announcement.(rfi, 2020) The origin of the virus is still a mystery.
SARS-CoV-2 is identified to be a betacoronavirus that belongs to the subgenus sarbecovirus of Coronaviridae family (Beta-CoV lineage B) based on the Phylogenetic analysis.(David S. Hui et al., 2020; R. Lu et al., 2020; Wong, Li, Lau, & Woo, 2019) Therefore, similar to other coronaviruses, it is a positive-sense single-stranded RNA (+ssRNA) virus with an envelope, and its granules are round or oval in shape with a diameter of 50 to 200 nm.(Zhe, 2020) Typical betacoronavirus structures (S gene, E gene and M gene etc.) was found by Zhu et al.(Zhu et al., 2020) and Zhou et al.(P. Zhou et al., 2020a) Notably, S (spike) protein is one of the main proteins of the virus with its gene coding always used for virus typing.(Zhe, 2020) The protein itself could be divided into two domains, S1 domain and S2 domain. Each domain is responsible for different functions, where S1 domain is responsible for receptor binding and S2 domain is responsible for cell membrane fusion.(He et al., 2004; F. Li, 2016) The protein also plays a key role in determining the host’s ability of transmission and tropism.(G. Lu, Wang, & Gao, 2015; Q. Wang, Wong, Lu, Yan, & Gao, 2016)
It has been confirmed that, through numerous reports from all over the world, the virus has a person-to-person transmission route.(Chan et al., 2020; Rothe et al., 2020; Wired., 2020; Zhe, 2020) The sources of infection seen so far are mainly patients with new coronavirus infection. Asymptomatic infection can also be a source of infection.(N. H. Commission, 2020) Respiratory droplets and close contact transmission are the main routes of transmission. There is the possibility of aerosol transmission in a relatively closed environment for a long-time exposure to high concentrations of aerosol. Population in crowdedness is also under risk is generally susceptible.(N. H. Commission, 2020)
According to the up-to-date studies, the basic reproduction number (R0) of the virus has been estimated to be 1·4 - 3·9 with the incubation period is about 1-14 days, mostly 3-7 days, and an average 4·8 days.(Q. Li et al., 2020; Riou & Althaus, 2020; Rothe et al., 2020) The fatality rate is about 2% with fever, dry cough and fatigue as the main manifestations. Its viral diagnostic method had already been developed basing on PCR and RT-PCR.(Corman et al., 2020; Jonsdottir & Dijkman, 2016; Liu et al., 2019; Zhu et al., 2020) Since the E gene and the RdRp gene are comparatively more sensitive, they were chosen for further evaluation for detection.(Corman et al., 2020) Whist, development of its vaccine is also already on the way.(Steenhuysen, 2020)
As of 12 April 2020, the Coronavirus disease 2019 (COVID-19) Situation Report from WHO(WHO, 2020) reported that 1,610,909 confirmed (89,657 new) and 99,690 deaths (6,892 new) cases globally, and 83,369 confirmed (64 new) in China with 3,349 deaths (4 new). These figures show that China has roughly controlled the epidemic, but the situation in the rest of the world is becoming less and less optimistic as there are more concentrated outbreaks are taking place.
Since considerable studies had already been carried out based on the analysis of SARS-CoV-2’s genome sequence and its comparison with that of the other SARS-like virus, let us review in detail and, hopefully, they might provide us with some key features for answering some of the crucial questions relating to its origin, epidemiology, and treatment to better contain the virus. Basing on that, clues on how to develop a fast and accurate viral diagnostic method and the way of treating it may also be provided.