Review of the SARS-CoV-2 (COVID-19) Based on Current Evidence

Review Article

Austin J Infect Dis. 2021; 8(1): 1042.

Review of the SARS-CoV-2 (COVID-19) Based on Current Evidence

Takele S* and Kedir M

National Institute for Control and Eradication of Tsetse Fly and Trypanosomosis, Ethiopia

*Corresponding author: Samson Takele, National Institute for Control and Eradication of Tsetse Fly and Trypanosomosis, Jimma Branch, Jimma, PO-Box 19917, Ethiopia

Received: December 04, 2020; Accepted: January 07, 2021; Published: January 14, 2021

Abstract

The coronaviruses are a group of RNA-containing agents known to cause respiratory illnesses in humans and animals. This virus has caused two largescale pandemics in humans in the past two decades, SARS and Middle East Respiratory Syndrome (MERS). A novel coronavirus (SARS-CoV-2) that causes the disease Coronavirus Disease 2019 (COVID-19) has been isolated from in a seafood and poultry market in the Chinese city of Wuhan in 2019. Cases have been detected in most countries worldwide, and on March 11, 2020, the World Health Organization characterized the outbreak as a pandemic. The virus spreads from person-to-person via close contact, respiratory droplets, or surface contact. The disease is mild in most people, yet may progress to pneumonia, acute respiratory distress syndrome, multi-organ dysfunction, and even death. Treatment is essentially supportive as the role of antiviral agents is yet to be established. At the moment, is known relatively little about COVID-19, except that it is a highly pathogenic and possibly zoonotic agent. Therefore, the objective of this review paper is to summarize the current published evidence on the genomic structure, pathogenesis, epidemiology, clinical characteristics, diagnosis, and prevention of SARS-CoV-2 (COVID-19).

Keywords: SARS-CoV-2; Epidemiology; Clinical characteristics; Diagnosis; Prevention

Background

Coronaviruses are a large family of viruses, which may cause illness in humans and animals [1]. In humans, several coronaviruses are known to cause respiratory infections ranging from the common cold to more severe diseases such as Middle East Respiratory Syndrome (MERS) and Severe Acute Respiratory Syndrome (SARS). The most recently discovered coronavirus causes coronavirus disease “COVID-19” and was unknown prior to the pandemic causing outbreak in Wuhan, China on December 2019 [2-5]. The most common symptoms of COVID-19 are fever, tiredness, and dry cough, although respiratory disease, and ocular, gastrointestinal, neurological, and dermatological manifestations are being increasingly recognized [6,7]. In a subset of patients, the disease can progress to pneumonia, respiratory failure, and death within one week. The virus is primarily spread between people during close contact, most often via small droplets produced by coughing, sneezing, and talking [8- 11]. As of October 11, 2020 COVID-19 has been diagnosed in more than 37,287,908 patients and associated with over 1,073,675 deaths. Cases have been reported in more than 200 countries and territories. The United States globally leads in COVID-19 cases at 7,718,947, followed by 1,568,091 in Africa, 1,285,084 in Russia, 861,112 in Spain, and 590,844 in the UK [12,13]. Although, in Africa the first case of COVID-19 was reported on February 25th, nearly 1.2 billion people remain at risk given the viruses pathogenicity [14,15]. Currently, there is no treatment specifically approved for COVID-19, and no cure for an infection, although treatments and vaccines are currently under study. Thus, the ability to limit the devastating consequences of the disease to rely on the implementation of effective preventative non-pharmaceutical interventions. Therefore, the objective of this review paper is to summarize the current published evidence on the genomic structure, pathogenesis, epidemiology, clinical characteristics, diagnosis, and prevention of SARS-CoV-2 (COVID-19).

Historical Background of Coronavirus

Coronaviruses were discovered in the early 1930s when an acute respiratory infection of domesticated chickens was shown to be caused by a virus now known as avian Infectious Bronchitis Virus (IBV) [17]. The first Human Coronaviruses (HCoV) were discovered in the 1960s. Research with human volunteers at the Common Cold Unit near Salisbury, UK, showed that colds could be induced by nasal washings that did not contain rhinoviruses. Subsequent invitro experiments, where nasal swabs from these volunteers were inoculated onto organ cultures of the respiratory tract, revealed the presence of enveloped viruses with the characteristic morphology of coronavirus. In 1968 the term coronavirus was adopted. The name “coronavirus” is derived from the Greek Korona, meaning crown [18,19]. In 1975, the Coronaviridae family was established by the International Committee on the Taxonomy of Viruses. At the 10th International Nidovirus Symposium in Colorado Springs, Colo., in June 2005, it was proposed that the Coronaviridae family be divided into two subfamilies, the Coronaviridae, and the toroviridae. Three Epidemic incidents of human coronavirus have been reported in world history. The first, In November 2002, a viral respiratory disease (SARS-CoV) appeared in southern China and quickly spread to other countries, leading to over 8,000 confirmed cases at the end of the epidemic in 2004, with a mortality rate of ~9.6%. The second, MERSCoV has caused two major outbreaks in Saudi Arabia (2012) and South Korea (2015), with the global confirmed cases exceeding 2,000 and a mortality rate of ~35% (10). Similar to SARS-CoV, MERSCoV originated in bats, but it later adapted to dromedary camels as intermediate hosts [20-22]. Currently, a novel and highly pathogenic coronavirus (SARS-CoV-2) has caused an outbreak in Wuhan city, Hubei province of China since December 2019, and soon spread nationwide and spilled over to other countries around the world, and it contributes to causing more than 37 millions of people to suffer and more than one million people to die [23,24].

Morphological Structure of SARS-CoV-2 (COVID-19)

All known coronaviruses share a similar structure made of four main structural proteins: Spike (S), Membrane (M), Envelope (E), and Nucleocapsid (N) proteins. More recently, however, it has become clear that some Coronavirus (CoVs) do not require the full ensemble of structural proteins to form a complete, infectious virion, suggesting that some structural proteins might be dispensable or that these CoVs might encode additional proteins with overlapping compensatory functions [6,25,26]. While the exact functions of most accessory proteins are still currently being researched on, it is recognized that the structural proteins aid the viral infection of host cells and subsequent replication [27]. Individually, each protein primarily plays a role in the structure of the virus particle, but they are also involved in other aspects of the replication cycle. The S-protein is responsible for attachment to host receptors, M protein helps shape the virion particles and binding to nucleocapsid, E-protein plays a role in the assembly and release of particles while N-protein aids with the binding of the genome to a replication transcription complex which is required for the replication of genomic material [28,29]. Isolated from a COVID-19 pneumonia patient, a worker in the Wuhan seafood market, the complete genome of Wuhan-Hu-1 coronavirus, one strain of SARS-CoV-2, is 29.9 kb. While SARS-CoV and MERS-CoV have positive-sense RNA genomes of 27.9 kb and 30.1 kb, respectively [26].

Genomic Structure of SARS-CoV-2 (COVID-19)

The genetic information of any life is protected in its genome, and annotation is the initial step to interpret the sequence. The genome of SARS-CoV-2 is a single-stranded positive-sense RNA of 30kb (29891 nucleotides) encoding 9860 amino acids. G+C content varies from 32 to 43% [30]. There are 12 functional Open Reading Frames (ORFs) along with a set of nine sub genomic mRNAs carrying a conserved leader sequence, nine transcriptionregulatory sequences, and 2 terminal untranslated regions [31]. The genome of this virus lacks the haemagglutinin-esterase gene, which is characteristically found in lineage a βCoV. Two-thirds of viral RNA, mainly located in the first ORF translates two polyproteins, pp1a and pp1ab, and encodes 16 Non-Structural Proteins (NSP), while the remaining ORFs encode accessory and structural proteins. The 16 non-structural proteins include two viral cysteine proteases, namely, NSP3 (papain-like protease) and NSP5 (main protease), NSP12 (RNA-dependent RNA polymerase, NSP13 (helicase), and other NSPs which are likely involved in the transcription and replication of the virus The remaining portion of the viral genome codes for four structural proteins E, M, S, and E along with a number of accessory proteins that interfere with the host immune response (Figure 1A & Figure 2B) [32,33]. The organization of the coronavirus genome is 5'-leader-UTR-replicase-S (Spike)-E (Envelope)-M (Membrane)-N (Nucleocapsid)-3'UTR-poly (A) tail with accessory genes interspersed within the structural genes at the 3' end of the genome [34,35]. Given the high sequence similarity between the SARS-CoV-2 and the SARS-like bat CoVs from Hipposideros bats in China, the natural host of the SARS-CoV-2 may be the Hipposideros bat. The discovery that pangolin coronavirus genomes have 85.5 to 92.4% sequence similarity to SARS-CoV-2 suggests pangolins should be considered as possible hosts in the emergence of SARS-CoV-2 [36,37]. SARS-CoV-2 is closer to the SARS-like bat CoVs in terms of the whole genome sequence. However, mutations are observed in NSP2, NSP3 and the spike protein, that play a significant role in infectious capability and differentiation mechanism of SARS-CoV-2 strains, namely L-type and S-type. It was found that L lineage was more prevalent than the S lineage within the limited patient samples that were examined. The implication of these evolutionary changes on disease etiology remains unclear. Coronavirus mainly recognizes the corresponding receptor on the target cell through the S protein on its surface and enters into the cell, then causing the occurrence of infection. A structure model analysis shows that SARS-CoV-2 binds ACE2 with above 10 folds higher affinity than SARS-CoV, but higher than the threshold required for virus infection [38,39]. The detailed mechanism about whether the SARS-CoV-2 would infect humans via binding of S-protein to ACE2, how strong the interaction is for risk of human transmission, and how SARS-CoV-2 causes pathological mechanisms of organ damage remains unknown, which need more studies to elaborate [24] (Table 1).