IMR Press / FBE / Volume 13 / Issue 1 / DOI: 10.2741/874

Frontiers in Bioscience-Elite (FBE) is published by IMR Press from Volume 13 Issue 2 (2021). Previous articles were published by another publisher on a subscription basis, and they are hosted by IMR Press on as a courtesy and upon agreement with Frontiers in Bioscience.

Open Access Review
Insights into the COVID-19 pandemic: Origin, pathogenesis, diagnosis, and therapeutic interventions
Show Less
1 Department of Environmental Health, College of Public Health, Imam Abdulrahman Bin Faisal University, P.O.Box 1982, Dammam 31441, Saudi Arabia
Front. Biosci. (Elite Ed) 2021 , 13(1), 117–139;
Published: 1 October 2020

Coronavirus disease (COVID-19) is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), a member of the human coronavirus (HCoV) family that targets the lower part of the respiratory tract and causes severe acute respiratory syndrome (SARS). In a short span of time, this infection has led to a global pandemic and has become a significant threat to the existence of present human society. Currently, there are no treatments for this infection and the measures established across various countries such as social distancing, usage of mask to prevent entry of the virus into the respiratory tract, quarantine, and containment together have reduced the prevalence of this disease and mortality in highly susceptible individuals. Here, we examine the structure, replication cycle, phylogeny and genomic organization of this virus and discuss the role of spike (S) protein of the virus, an important structure that interacts with the host ACE2 receptor facilitating viral entry. Further, we explore the epidemiology, symptoms of the disease, describe the reverse transcriptase-polymerase chain reaction (RT-PCR) that establishes the diagnosis of the disease and also review its unique diagnostic features in the chest CT-Scan. Finally, we review the current approaches to develop therapies and vaccines as a measure for disease prevention and control.

S spike protein
Genomic Organization
Transmission Diagnosis

An emerging infectious disease causing severe acute respiratory syndrome (SARS) was recently detected in Wuhan, China (1-3). According to the Coronavirus Study Group (CSG), the novel virus is named as SARS coronavirus 2 (SARS-CoV-2) (4) and the resulting disease as Coronavirus disease (COVID-19). Due to the COVID-19 outbreak, there is an increasing interest to comprehensively understand the phylogeny, epidemiology and pathogenesis of the virus caused by the growing concern for people’s health.

Several members of the coronavirus families cause many zoonotic diseases such as enteritis in cows, pigs, pangolins, and birds, as well as lung diseases in chicken (5-7). In the past decade, two outbreaks have been caused by beta coronaviruses, namely, SARS-CoV-1 and MERS-CoV, causing global anxiety without widespread effects (8). However, the recent disease caused by the newly identified novel coronavirus SARS-CoV-2 has been declared as a global pandemic that brings about severe acute respiratory disease (9). This pandemic has attracted a greater attention of the scientific community, health organizations, and policy makers because of the serious threat it poses to global health, social, and economic systems. The main aim of this review was to update information concerning the COVID-19 outbreak with a special emphasis on the COVID-19 genome highlighting its structure, genomic organization and its mechanism of replication. Further, the virulence of COVID -19 in humans and the role of ACE2 in its pathogenesis have been comprehensively covered. This review also intends to fill in the gaps in knowledge regarding epidemiology, methods of SARS-CoV-2 infection, diagnosis, possible therapeutics and vaccines. Finally, major challenges that hinder the measures to control or prevent viral transmission from person-to-person at the national and international levels have also been discussed.


Due to the recent COVID-19 outbreak, there has been a considerable interest in knowing the phylogeny of SARS-CoV-2 or HCoV-19 virus (10-11). Generally, coronaviruses are zoonotic viruses belonging to the order Nidovirales that includes three families, namely, Coronaviridae, Arteriviridae, and Roniviridae. Coronaviridae is subsequently divided into the following two subfamilies: Torovirinae and Coronavirinae. On the basis of serological analysis and phylogeny, members of the latter subfamily are further categorized into four groups: alpha, beta, gamma, and delta coronaviruses (4).

Seven coronaviruses are known to cause infections in humans ranging from mild to severe respiratory symptoms. Of these, four are endemic human coronaviruses HCoV-229E (alpha), HCoV-NL63 (alpha), HCoV-OC43, and HCoV-HKU1 (beta), which are responsible for mild common cold symptoms mostly in lung infections and are mostly associated with bats, rodents, cows and pigs (12). The remaining three are the most dangerous viral candidates that cause severe lower respiratory infections, such as the two epidemic-causing coronaviruses SARS-CoV and MERS-CoV, and a third novel pandemic-causing coronavirus, SARS-CoV-2, belonging to the beta coronavirus group. Remarkably, bats could be the natural reservoirs of the three human coronaviruses with palm civet, dromedary camels or pangolin acting as intermediate amplifying and transmitting host, respectively (5-6,12).

4.1. Organization and Structure of SARS-CoV-2 genome

Like other human coronaviruses, the enveloped positive-sense RNA viruses such as SARS-CoV-2 is composed of approximately 30 kilobase (kb) genome (13). Organizational structure of the SARS-CoV-2 genome encompasses six open reading frames (ORFs) (Figure 1). Two-thirds of the genome contains the first translated ORF (ORF1a/b), that comprises of 16 highly conserved nonstructural polyproteins (nsps1-16), encoding the replication-transcription (RTC) complex in the double-membrane vesicles (DMVs). A group of nested single stranded RNA genome (sgRNA) sequences are synthesized by RTC in a discontinuous transcription manner due to the interception of ORFs by transcriptional regulatory sequences. The remaining one third of the genome encodes various structural proteins, responsible for nucleocapsid polymorphisms that act as an adaptive response to new hosts. This region of the genome is coded by four main ORFs to synthesize the viral structure proteins: S, M, E and N as well as other sgRNAs accessory genes (Figure 1) (6, 13-14).

Figure 1

Genome organization of human coronavirus COVID-19. The genome size is approximately 30 kilobase (kb). The two-third region encodes for the two main overlapping open reading frames (ORF 1a/b) encode conserved nonstructural polyproteins required for replication-transcription complex (RTC) and virus synthesis (above). The last third of the genome coded for the main structural component proteins including S, E, M and N and a set of accessory genes including ORF3a, 3b, ORF6, ORF7a, 7b, ORF8a, 8b and 9b.

Results of the genomic sequence analysis indicated that the genomic organizational structure of the SARS-CoV-2 coronavirus is highly similar to beta coronaviruses genomes. Chan et al. (15) mentioned that the genetic material of the novel coronavirus has approximately 89% and 82% identity with bat SARS-like-CoVZXC21 and human SARS-CoV, respectively. Phylogenetically, the genome sequence of the novel coronavirus that came from Wuhan city, was very close to Bat SARS-like viruses, such as SL-ZC45 and SL-ZXC21 (87.6 and 87.7%, respectively), and more distantly related to SARS and MERS (79% and 51.8%, respectively) (16). Moreover, Rothan and Byrareddy (10) revealed that the novel COVID-19 virus has approximately 80% and 50% identity to SARS and MERS of bat origin, respectively.

Interestingly, no modifications were recorded for nonstructural proteins NSP7, NSP13 and the structured and accessory proteins p6 and 8b. However, key modifications were recorded for nonstructural proteins NSP2, NSP3 and the structured spike protein underpinning subdomain, i.e., RBD (17). Indeed, Chan et al. (15) reported that this external subdomain shows 40% identity in amino acid sequences in comparison with sequences of SARS-related coronaviruses. Also, several scientists revealed that mutations in NSP2 and NSP3, as well as exposure of certain spike protein sites to selective pressure, could play a crucial role in enhancing COVID-19 infectivity, differentiation and adaption to new host (18-19). Interestingly, genome analyses of 558 SARS-CoV-2 coronaviruses indicated that the genes encoding spike proteins and nucleoproteins as well as RNA dependent (RD) RNA-polymerase and primase undergo frequent mutations that could allow better tracking of the virus epidemics (20).

On the other hand, the comparative genome analysis by Andersen et al (21) revealed that SARS-CoV-2 originated through natural selection and not from a laboratory manipulation. This could be attributed to the high affinity of SARS-CoV-2 receptor-binding domain to human ACE2 receptor protein in animal host or in human after zoonotic transfer (3, 21-22). Moreover, Tang et al. (23) revealed that the genomic variation between SARS-CoV-2 and bat SARSr-CoV (RaTG13) is only 4% and 17% at neutral sites. Likewise, changes in high affinity of the receptor-binding domain of the spike protein in SARS-CoV-2 and from pangolin virus SARSr-CoVs are mainly due to mutations and natural selection. Interestingly, the higher degree of bat ACE2 receptor homology with other animals indicates that it is an intermediate host for COVID-19 (24). Collectively, these results could be used for arguments denying the rumors about SARS-CoV-2’s use as a biological weapon. Analyses of 103 genomes of the novel virus revealed the possible existence of two types of COVID-19 coronavirus, namely, 70% L type and 30% S ancestral type (23). Moreover, human interventions might contribute to a highly select for the L type, leading to more severity and aggressiveness of COVID-19. However, more studies should be performed on the genomic and epidemiological levels to support this finding.

4.2. Replication of SARS-CoV-2

As previously described, coronaviruses are a unique group of spherically enveloped particles harboring a single stranded positive-sense RNA genome (+ssgRNA) along with a nucleoprotein and a protein capsid. Characteristic club-shaped glycoprotein spikes project from the virus envelop and interestingly carry the main antigenic determinants or “epitopes” recognized by the antibodies. The positive-sense RNA is characterized by the presence of 5’ terminal cap and a poly A tail structure, thus having the ability to acts as an mRNA for subsequent transcription (7, 22, 25). Similar to other human coronaviruses, the major distinctive feature of the COVID-19 viral replication is the direct translation of the upstream open reading frame (ORF) into replicase-transcriptase protein. This region comprises two-thirds of the viral genome and involves two main ORFs (ORF1a and ORFb1) and 16 other non-structural proteins. The last one-third of the genome contains four genes that code for the structural proteins including the spike, envelope, membrane and nucleocapsid (7, 25).

The life cycle of SARS-CoV-2 in humans begins with the attachment of the viral spikes to an ACE2 cellular receptor (Figure 2). Using cryo-EM, Song et al. (26) have recorded that in the prefusion conformation structure of SARS-CoV-2 spike proteins, S proteins are observed to have high affinity for the cellular receptor protein ACE2, compared to the previously reported coronaviruses. Following their entry, the viral genome is unveiled with ORF1a and ORF 1ab being translated to the two polyproteins pp1a and ab, that further undergo proteolysis by papain-like (PLpro) and chymotrypsin-like proteases to yield 16 nonstructural proteins (16 nsps). These protein elements constitute the RNA replicase-transcriptase protein complex and controls single stranded RNA genome (sgRNA) production, replication and transcription. The positive-sense RNA genome (+gRNA) is produced by replication and a set of nested 7-9 sgRNA are formed through discontinuous transcription. The sgRNAs are translated into structural and nonstructural proteins from the transcription of the first ORF close to 5’ end. Subsequently, +gRNA and nucleocapsids are assembled in the host cytosol and bud into the lumen of Endoplasmic reticulum-Golgi intermediate compartment (ERGIC). Mature viral particles are then released from the host cell via its internal membrane through exocytosis (Figure 2) (5, 13).

Figure 2

Schematic diagram showing the replication cycle of SARS-CoV-2 in a host cell. SARS-CoV-2 attached to the host cell through spikes that bind to ACE2 cellular receptor. Following entry, positive-sense genomic viral RNA (+gRNA) is exposed in the cytoplasm. ORF1a and ab are translated to produce pp1a and pp1ab polyproteins, undergo proteolysis to yield 16 nonstructural proteins (16 nsps) that comprises RNA replicase-transcriptase protein complex. This complex controls -gRNA production, transcription and replication. The +gRNA is produced by replication and group of 7-9 nested sgRNA are formed by discontinuous transcription. Those sgRNAs translated into structural and nonstructural proteins from the first ORF close to 5’ end. Subsequently, +gRNA and nucleocapsids are assembled in the cytoplasm, followed by budding into ERGIC lumen. Finally, mature virus particle released from the host cell through exocytosis.

5.1. Transmission of COVID-19

Epidemiologic studies indicated that the outbreak started from a seafood market selling live animals in Wuhan, China; subsequently transmitted to humans and further spread from person-to-person (1, 10, 22, 27). For COVID-19, the main route of human transmission occurs through respiratory tracts via droplets, respiratory secretions and direct contact (22, 28). When the infected person coughs, sneezes, or talks, he/she can transmit the disease through aerosolized droplets that can travel indoor for meters, even in minuscule quantities (29-30). Though the rate of viral transmission by the notably symptomatic diseased individual is high, the extent of the transmission is highly unreliable especially due to the location and medical interventions of the COVID-19 patient (1,31-32).

Furthermore, SARS-CoV-2 infections can also be transmitted to the major routes of viral entry such as eyes, nose, or mouth by touching previously contaminated surfaces. Epidemiology of the virus depends on several factors including viral load in upper respiratory tract and capability of asymptomatic carriers to transmit the disease (33-35). Transmission of COVID-19 by asymptomatic individuals has been reported but needs to be investigated further (28, 36-37).

A study conducted to evaluate the viral transmission caused due to the stability of the COVID-19 virus in aerosols and surfaces, reported that it was highly probable. According to van Doremalen et al. (34) the virus remains viable for at least 3 hours in aerosols and surfaces. In the same study, SARS-CoV-2 wasn’t detected after 4 hours on certain metal surfaces such as copper, whereas viable SARS-CoV-2 was detected till 24 hours on cardboard. Serological analyses have detected the viral genomic material in blood and stool specimens (9,26 24) and the probability of isolating the virus from fecal swabs and blood of COVID-19 patients indicate the existence of other means of viral transmission (38).

5.2. Pathogenesis of COVID-19

As the case with other coronaviruses, COVID-19 is transmitted primarily through airborne droplets to the nasal mucosa. However, the pathogenicity of this virus is highly complicated. The virus replicates specifically in cells of the ciliated epithelium (specifically the lung AT2 alveolar epithelial cells), causing severe damage and inflammation that sometimes manifests as a “cytokine storm” (5,39). High levels of plasma pro-inflammatory cytokines have been reported in many COVID-19 patients with severe respiratory syndromes (10). Unfortunately, the cell damage activates an inflammatory response, hence increased nasal secretions, local inflammation and swelling. In most cases, IL-6 production by leukocytes induces B lymphocyte differentiation, thermoregulation, bone maintenance and regulation of the central nervous system (CNS). Interestingly, as the levels of interleukin rise during COVID-19, underlying diseases such as autoimmune disorders and certain types of cancer are aggravated, thereby increasing the health risk and virus virulence in patients with such underlying conditions (39).

5.3. Role of ACE2 in SARS-CoV-2 infection

Several scientists have reported ACE2 to act as a host receptor in acute lung diseases and as a potential therapeutic target against COVID-19 (40-43). ACE2 expression has been reported to play a crucial role in many diseases such as myocardial disease, respiratory diseases, gastrointestinal diseases, kidney and liver damage, even provides receptor-mediated entry for SARS-CoV-2 and thereby increasing the risk of COVID-19 (42). Fang et al. (44) reported that renin-angiotensin system (RAS) is important for the cardiovascular regulatory system and helps in maintaining blood pressure homeostasis. Angiotensin II, a negative regulator of RAS, is generated by the ACE from angiotensin I in the lung blood capillaries and contributes towards the pathogenesis of many inflammatory lung diseases such as acute respiratory distress syndrome (ARDS). Recently, ACE2 was recognized as a key receptor in SARS infections, including COVID-19. Protective action of ACE2 in case of lung infections as observed in model animal with ARDS, encouraged scientists to use ACE2 as a novel treatment approach for many respiratory infections (42). On the other hand, Fang et al. (44) concluded that patients suffering from hypertension and diabetes have an increased risk for COVID-19, as they show an increased ACE2 expression in the epithelial cells of lungs and other organs including intestine, kidney, and blood vessels. This is because, the treatment for hypertension with ACE inhibitors and diabetes with angiotensin II type-I receptor blockers (ARBs) increases ACE2 expression and subsequently the risk for COVID-19 (44). Additionally, since smoking can upregulate ACE2 receptor expression, it could be a potential risk for the COVID-19 disease (45). On the contrary, Kuster et al. (46) revealed that the inhibition of the RAS might be protective toward COVID-19.

5.4. Role of S spike protein in SARS-CoV-2 infection

The receptor binding and membrane fusion processes of SARS-CoV-2 coronavirus are mediated by trimeric S spike glycoproteins. The gene coding for the S spike protein is organized up-stream of a signal peptide (SP) followed by the main sequence of S spike protein (Figure 3). Proteases such as trypsin and cathepsin L cleave the S protein into two major subunits, S1 and S2. The process of infection and pathogenesis has been reported to start with the recognition and binding of the S1 subunit in RBD through its receptor-binding motif (RBM), to the ACE2 receptor of the host cell. Subsequently, the viral progression and its transmembrane fusion are mediated by conformational changes in S2 subunit due to conserved fusion peptide (FP) (47-48). Xia et al. (49) were able to design an inhibitory drug that inhibits spike protein and interferes with membrane fusion.

Figure 3

Genomic organization of SARS-CoV-2 S spike protein. The upstream region coded by a signal peptide followed by two major subunits S1 and S2. S1 protein subunit contains N-terminal domain NTD), the receptor-binding domain (RBD) that incorporates the receptor-binding motif that binds specifically with ACE2 receptor protein. S2 contain a short fusion protein (FP) followed by two heptad repeats (HR1 and HR2), transmembrane domain (TM) and an intracellular cytoplasmic protein (CM). Sites of expected mutations along the S spike protein encoding genomic from different virus isolates.

Alignment studies between SARS-CoV-2 and SARS-like BatCoV-RaTG13 coronavirus, revealed a high similarity in the S protein (Figure 4) (47,50). By comparing the S protein sequence of 2019-nCoV with SARS-GZ02, Pradhan et al. (51) detected four unique insertions showing high similarity to the variable regions (V1, V4, and V5) of HIV1 envelope glycoprotein gp120 or HIV-1 Gag of certain unique strains from three different countries, namely, Thailand, Kenya, and India, supporting the speculation that 2019-nCoV is a recombinant virus. As shown in Figure 4, three of those insertions already exist in SARS-like BatCoV-RaTG13 and bears no similarity with any sequence from HIV-1. In concordance with this finding, Xiao et al. (52) demonstrated that there was no evidence that those sequences were HIV-1 specific or that the 2019-nCoV viruses obtained these insertions from HIV-1. These results collectively indicate the natural genetic variation in the S protein gene and eliminate reservations regarding SARS-CoV-2 being a synthetic virus. Only a four amino acid residue, 681PRRA684, has been recorded as a unique insert among all the known SARS-CoV-2 coronaviruses (Figure 4) (47). Together with this, the conserved R685 amino acid could be recognized as the site for proteolytic action for S1/S2 cleavage. Nevertheless, a recombinant viral construct with the SARS-CoV backbone encoding S protein from bat SHC014 has been able to demonstrate the potential to use multiple human ACE2 receptor orthologs for its entry and doesn’t respond to any neutralization vaccines, providing previously unknown insights regarding the evolution and pathogenicity of SARS-CoV-2 coronavirus (53). Interestingly, a highly conserved unique 111-fragment has been detected in all verified S proteins of human coronaviruses except MERS (data not shown), and therefore, could be possibly used as a therapeutic target while designing vaccines (50).

Figure 4

Multiple amino acid sequence alignment between SARS-CoV-2 and other coronaviruses using CLUSTAL Omega online tool, EMBL-EBI UK, Four unique sequences highlighted, the first showed high similarity with Bat SARS-like BaTG13.

Analyses of COVID-19 genomes from different isolates revealed several mutations up- and down-stream of the receptor binding domain (RBD) (Figure 3). These mutations have a direct influence on the secondary structure of the S1 domain and on the interaction of the S spike protein with ACE2 receptor. Several substitutions were detected during multiple alignments of various genomic sequences of spike proteins from several isolates (Figure 5). Mutations in positions Q271R and D614G, in the S1 domain of SARS-CoV-2 S spike domain were detected in isolates from many countries, with the latter being more frequent in isolates from regions such as North America, Europe and in countries like India (Table 1) (54-56). It is assumed that the D614G mutation, in which aspartic acid is changed to glycine, could lead to a conformational change in the spike protein that reduces the interaction between the S1 and S2 subunits, enabling the detachment of S1 from the viral-membrane-bound S2 (57).

Figure 5

Multiple sequence alignment of amino acid (A) and nucleotide (B) sequences of the S spike protein (surface glycoprotein) of SARS-CoV-2 and other coronaviruses using CLUSTAL Omega online tool, EMBL-EBI, UK, S spike protein sequences accession numbers from GenBank, NIH, USA. Alpha-3 country code: according to ISO 3166 international standard. The red arrow reveals the position of the most frequent D614G substitution in amino acids and nucleotide sequences of the spike protein gene in different isolates from North America, Europe and India.

Table 1 Distribution of mutations along S spike protein encoding sequence in SARS-CoV-2 coronavirus isolates from different sources after multiple sequence alignment of the amino acid sequences using Clustal Omega alignment tool
Accession Number/ Country Type of amino acid mutation (substitutions or deletions)
L5F1 Y28N H49Y1 S71F N74K Y1441 I197V S221W S247R Q271R1 R407I1 K574X D614G1 V621I V772I A930V1 V1064L D1259H1
QHS34546-IND L Y H S N -3 I S S Q I2 K D V V A V D
QIZ13179-USA L Y H F2 N Y I S S Q R K D V V A V D
QIS60906-USA F2 Y H S N Y I S S Q R K D V V A V D
QIS30165-USA L Y H S N Y I S S Q R K D V V A V D
QIS60582-USA L Y H S N Y I S S Q R K D V V A V H2
QIZ16509-TUR L Y H S N Y I S S Q R K D V I2 A V D
QIZ16559-GRC L Y H S N Y V2 S S Q R K D V V A V D
QHU79173-FIN L Y Y2 S N Y I S S Q R K D V V A V D
QIA98583-IND L Y H S N Y I S S Q R K D V V V2 V D
QHR84449-AUS L Y H S N Y I S S Q R K D V V A V D
QHZ00379-KOR L Y H S N Y I W2 R Q R K D V V A V D
0QIO04367-CHN L Y H S K2 Y I S S Q R K D V V A V D
QHD43416-CHN L Y H S N Y I S S Q R K D V V A V D
QHR63290-CHN L N2 H S N Y I S S Q R K D V V A V D
QIA20044-CHN L Y H S N Y I S S Q R K D V V A V D
QJA42177-USA L Y H S N Y I S S Q R K G2 V V A L2 D
QIZ13789-USA L Y H S N Y I S S Q R K G2 I2 V A V D
QIU78719-ESP L Y H S N Y I S S Q R X2 G2 V V A V D
QJC19491-IND L Y H S N Y I S S R2 R K G2 V V A V D
QIX12148-FRA L Y H S N Y I S S Q R K G2 V V A V D
QIK50427-CAN L Y H S N Y I S S Q R K G2 V V A V D
1Position of the most frequent mutations in COVID-19 coronavirus spike protein gene recorded by many scientists (53-55). Types of mutations; 2Substitution mutation and 3Deletion mutation. Amino acids symbols; L: Leucine; Y: Tyrosine; H: Histidine; S: Serine; F: Phenylalanine; N: Asparagine; I: Isoleucine; W: Tryptophan; Q: Glutamine; R: Arginine; K: Lysine; X: Stop codon; D: Aspartic acid; G: Glycine; V: Valine; A: Alanine. S spike protein sequences accession numbers from GenBank, NIH, USA. Alpha-3 country code: according to ISO 3166 international standard. Multiple sequence alignment was carried out using Clustal Omega alignment tool
6.1. Symptoms of COVID-19

COVID-19, caused by a member of the coronaviruses, shares common symptoms with other beta coronavirus infections. The major symptoms of this disease include fever, dry cough, fatigue, and mostly appear after approximately 5-6 days after contracting the disease (1,58-59). Cascella et al. (39) reported that a fever with cough as well as rhonchi or coarse breathing sounds coming from lungs were the main signs of severe COVID-19. Phlegm production, headache, hemoptysis, diarrhea, dyspnea, and lymphocytopenia could also be observed (1,60). Rothana and Byrareddy (10) reported diarrhea to be a major gastrointestinal symptom developed in COVID-19 patients. However, fluctuations in the incidence of gastrointestinal symptoms have also been recorded (61). Development of various diagnostic methods, to detect the virus transmitted through several means, is urgently required to minimize the viral transmission. Also, a comprehensive epidemiological investigation together with modern diagnostic methods could help in the early detection of asymptomatic carriers (37).

6.2. Molecular detection of SARS-CoV-2 using RT-PCR

There is an accelerated effort to develop diagnostic methods to use for the detection of SARS-CoV-2. Several scientists have worked on designing primers for the molecular detection of the virus, just by utilizing the COVID-19 genomic data published in open access databases. Due to the close relation between SARS coronavirus and 2019-nCoV, it has been possible to design probes to detect the recent virus (62). Colson et al. (63) described the timeline for COVID-19 virus detection by an ultra-rapid diagnostic molecular method (RT-PCR) in 3 hours, complete genome sequencing in 11 hours and culture isolation in 72 hours. As with other acute respiratory infections, RT-PCR is recorded as the most efficient method of virus detection, specifically in secretions. A wide number of scientists have hastened the process of designing RT-PCR based tests that use specific probes to detect the virus. To understand the efficacy of these diagnostic kits, molecular diagnosis of the novel SARS-CoV-2 was carried out in 19 patients using three different fluorescent RT-PCR kits. While the virus was detectable in 47.4% of patients’ oropharyngeal samples, 90% had the virus in their stools and none in their blood and urine samples. Unfortunately, since 52.6% of the patients were undiagnosed by these molecular detection kits, other diagnostic methods like, Chest CT scan should be used for virus detection (64).

6.3. Diagnosis of COVID-19 by Chest CT-Scan

Since COVID-19 mainly attacks the lower respiratory system, this can be visualized by CT chest scan to further confirm the disease. The most common symptoms of coronaviruses that can be detected on the chest CT scans are mutual-sided ground-glass opacities (19 16, 58-59). In fact, the chest CT scans of some COVID-19 patients show the occurrence of grand-glass opacities in their lungs (65-66). Indeed, several marginal ground-glass opacities were observed in the subpleural regions of lungs bilaterally with an increased inflammation and no improvement even with interferon inhalation. In most cases dyspnea with hypoxemia has been associated with deep infiltration in the superior sections of the lung (67).

Usually, the chest CT scan for the diagnosis of confirmed COVID-19 patients revealed ground-glass opacities accompanied by deprived consolidative bilateral deviations, coinciding with viral pneumonia (68-69). As compared to RT-PCR, the chest CT scan shows a high sensitivity towards SARS-CoV-2 diagnosis (70). This comparative diagnostic study showed that amongst all COVID-19 patients, 59% have been recorded as RT-PCR-positive, while 88% were chest CT scan-positive. In fact, the sensitivity of the chest CT scan in diagnosis of SARS-CoV-2 was 97% based on positive RT-PCR. Among the negative RT-PCR patients, 75% recorded positive results in CT scan. In conclusion, the chest CT scan is recommended as a more practical approach for diagnosing COVID-19 early due to its better sensitivity, consistency, and reliability.


Finding a vaccine for the coronavirus has become a public health priority. Simultaneously, there is also a progressive increase in research led by several pharmaceutical companies to design a suitable drug and find new vaccines for COVID-19. The discovery of new vaccines is an overwhelming process and takes a very long time for their approval. Due to the surge in number of SARS-CoV-2-infected patients and the consequent public health emergency, there is an urgent need to identify proper treatment options for appropriate administration. Due to the lack of specific drugs or vaccines against SARS-CoV-2 infection, treatment of symptoms and offering respiratory support are the most available options in terms of medical intervention (14). Most of the current efforts targeting research and development of a new drug depend on the strong similarity between SARS-CoV and SARS-CoV-2 specifically in viral entry, replication and genomic organization. Liu et al. (71) has highlighted the major therapeutics and vaccines that have been already approved or under investigation for COVID-19 treatment.

Many antiviral drugs used for influenza and certain inhibitors are commonly recommended for therapeutic use against COVID-19 (10). Adenosine nucleotide analogue Remdesivir, with a broad antiviral activity against RNA viruses, and chloroquine, commonly used in the treatment of malaria, showed great activity against SARS-CoV-2 infection (14 21). Similar strategies have been used to deal with other coronavirus infections that cause severe acute respiratory diseases like SARS and MERS (72). Moreover, protease inhibitors such as Lopinavir/Ritonavir, commonly used in HIV treatment, demonstrated to have a potential against SARS-CoV and MERS-CoV, and hence, these could also be used for COVID-19 treatment (73-75). These drugs together with aerosol inhalation of interferon-alpha have been used for treating the disease symptoms to clinically manage the COVID-19 patients (58). Other broad-spectrum antiviral drugs include, Neuraminidase inhibitors, peptide (EK1), RNA synthesis inhibitors, such as, Nitazoxanide, Favipiravir, Nafamostat have also been recommended (14,72) (Table 2). The transfer of plasma from convalescent COVID-19 patients (supposed to contain antibodies against COVID-19), is an endorsed COVID-19 treatment measure that has been used to suppress the disease in its early stages (76). Through the identification of the first viral genome and molecular modelling, the drug Baricitinib has been identified, and is predicted to interrupt the viral entry and assembly in the lung cells (74) (Table 2). Finally, discovering suitable therapeutics and vaccines require a larger allocation of funds and more importantly a significant interest in reestablishing the general health of the public to overcome the COVID-19 outbreak.

Table 2 List of most commonly used antiviral drugs against COVID-19
Drug Description/Mode of Action Reference Disease or Target Reference(s)
Chloroquine and hydroxychloroquine 9-aminoquinolin, elevates endosomal pH, immunomodulator, autophagic blocker Malaria, autoimmune disease 39,82,83,84
Remdesivir (GS-5734) Nucleotide analogue product, inhibitor of RNA polymerase Interfere with viral entry With activity against Ebola and other RNA viruses 39, 85, 86, 87
lopinavir/ritonavir Protease inhibitor, block HIV-1 protease action leading to viral immaturity AIDS, SARS, MERS 39, 88, 89
Ribavirin Synthetic guanosine nucleoside, interfering with the synthesis of viral mRNA HCV, SARS, MERS 87, 90
Tolicizumab Immunotherapy, humanized IgG1 moAB against the IL-6 receptor Treatment of rheumatoid arthritis 39
Arbidol Angiotensin-converting enzyme 2 (ACE 2), viral receptor protein that binds to viral S protein Influenza virus, SARS-CoV-2 22, 91
Camostat mesylate Host-cell mediated Serine 2 Transmembrane protease, facilitate binding to ACE2 and intervening with replication process SARS-CoV-2 and other HCoVs 71
Favipiravir Nucleoside analogue, acts as RNA polymerase inhibitor (RdRp inhibitor), preventing viral reproduction Ebola, influenza A(H1N1) 22, 87
Nafamostat Synthetic serine protease inhibitor, blocks membrane fusion by reducing the release of cathepsin B; anticoagulant activities Influenza, MERS, Ebola 87, 92, 93
Shufeng Jiedu Capsule (SFJDC, a traditional Chinese medicine) Anitviral compounds from plants, blocks viral 3CL protease and inhibits RdRp activity Active against human viruses including SARS, influenza, and HCoVs 22, 84
Nitazoxanide Antiprotozoal agent, modulating biological activities and replication of various microbes Human and animal coronaviruses 87
convalescent plasma convalescent plasma containing neutralizing antibody antibodies against COVID-19 80
Baricitinib inhibition of clathrin-mediated endocytosis, interrupt virus entry and assembly processes in lung cells COVID-19 78, 94

Currently, most countries have been observed to direct their efforts in controlling the COVID-19 outbreak through strict protective measures that enable reduction of the viral spread (Figure 6). At an individual level, considerable measures must be taken to restrict person-to-person transmission of the virus (1). Some of the more efficient non-therapeutic interventions to prevent COVID-19 spread in society are maintaining hand hygiene, social distancing and quarantining, all of which could reduce the number of secondary infections (77). However, the usage of masks to reduce viral transmission remains controversial (78). The impact of non-pharmaceutical interventions to prevent viral transmission was investigated using mathematical models. These models highlighted the crucial importance of traditional public health outbreak responses such as social distancing, contact-tracing, quarantine, and face masks in determining the future of the COVID-19 pandemic (79). If such measures were proven to be inefficient, “community-wide containment’ is recommended to control the further spread of COVID-19 (80).

Figure 6

Pathogenesis, symptomatology, diagnostic and non-therapeutic intervesions of COVID-19.

Besides hand washing and social distancing, efforts should be made to get rid of virus laden air droplets especially indoors by allowing proper ventilation (30). Also, priority must be given to the most vulnerable candidates including elderly people, patients with cardiovascular diseases, hypertension and diabetes due to their weak immune system (10). Apart from the practical guidelines provided by the world health organization (WHO) for risk assessment of COVID-19 outbreaks, public should be routinely reminded and encouraged to use hand sanitizers and disinfectants. More importantly, physical contact with contaminated materials like feces and urine should be avoided (31). Some of the major challenges include tracing the suspected cases and determining the severity of cases among those tested positive without obvious clinical signs of the disease and more specifically the ability of asymptomatic carriers for disease transmission (33,35-36). Along with the WHO technical guidelines regarding mass gatherings, special attention should be given to points of entry based on the susceptibility to COVID-19 outbreak. The impact of international air travel in dissemination of COVID-19 has been reported by Bogoch et al. (81) during the early stages of the outbreak. Therefore, the most characteristic action taken by nearly all countries is to halt transport and travel and enforce strict quarantine measures in all aspects of community living.

Nowadays, there is an excessive anxiety about the global preparedness in facing international challenges to respond effectively in curtailing the COVID-19 outbreak. The major points of contention exposed by the SARS-CoV-2 outbreak include communities’ response; political, structural, institutional, and environmental preparedness; and scientific and technical readiness required to address the SARS-CoV-2 pathogen-related issues. With respect to the international level, the most overwhelming effect would be on the low-income or poor countries, countries with weak health care systems, and even those that endure conflicts. The situation in such countries would be highly critical due to the inherent difficulties they face for viral detection and containment. Therefore, to bridge this, there is a concerted effort by several countries to discover effective diagnostic drugs and vaccines to overcome this public health outbreak.


This work was funded by the Deanship of Scientific Research, Imam Abdulrahman Bin Faisal University, Eastern Province, Saudi Arabia (Grant application No. Covid19-2020-017-CPH).


Severe Acute Respiratory Syndrome Coronavirus


Middle East Respiratory Syndrome Coronavirus


coronavirus disease-19, a disease caused by SARS-CoV-2


human coronavirus


angiotensin-converting enzyme 2


endoplasmic reticulum-Golgi intermediate compartment


replication-transcription complex


double-membrane vesicles










interleukin 6


negative-sense genomic RNAs


subgenomic RNA


positive-sense genomic RNA


receptor-binding domain


receptor-binding motif


acute respiratory distress syndrome

A (H1N1)

Influenza A virus “swine flu”, hemagglutinin Type 1 and Neuraminidase Type 1


Acquired Immune Deficiency Syndrome


Human Immunodeficiency virus

LiQ GuanX WuP WangX ZhouL TongY RenR LeungKSM LauEHY WongJY XingX XiangN WuY LiC ChenQ LiD LiuT ZhaoJ LiuM TuW ChenC JinL YangR WangQ ZhouS WangR LiuH LuoY LiuY ShaoG LiH TaoZ YangY DengZ LiuB MaZ ZhangY ShiG LamTTY WuJT GaoGF CowlingBJ YangB LeungGM FengZ Early transmission dynamics in Wuhan, China, of novel coronavirus-infected pneumonia. N Engl 0J Med202038211991207DOI: 10.1056/NEJMoa2001316
WuF ZhaoS YuB ChenY-M WangW SongZ-G HuY TaoZ-W TianJ-H PeiY-Y YuanM-L ZhangY-L DaiF-H LiuY WangQ-M ZhengJ-J XuL HolmesEC ZhangY-Z A new coronavirus associated with human respiratory disease in China. Nature2020579265269DOI: 10.1038/s41586-020-2008-3
ZhouP YangX-L WangX-G HuB ZhangL ZhangW SiH-R ZhuY LiB HuangC-L ChenH-D ChenJ LuoY GuoH JiangR-D LiuM-Q ChenY ShenX-R WangX ZhengX-S ZhaoK ChenQ-J DengF LiuL-L YanB ZhanF-X WangY-Y XiaoG-F ShiZ-L A pneumonia outbreak associated with a new coronavirus of probable bat origin. Nature2020579270273DOI: 10.1038/s41586-020-2012-7
GorbalenyaAE BakerSC BaricRS GrootRJ de DrostenC GulyaevaAA HaagmansBL LauberC LeontovichAM NeumanBW PenzarD PerlmanS PoonLLM SamborskiyD SidorovIA SolaI ZiebuhrJ Severe acute respiratory syndrome-related coronavirus: classifying 2019-nCoV and naming it SARS-CoV-2. Nat Microbiol20205536544DOI: 10.1038/s41564-020-0695-z
FehrAR CoronavirusesS Perlma An overview of their replication and pathogenesis. Methods Mol Biol20151282123DOI: 10.1007/978-1-4939-2438-7_1
CormanVM MuthD NiemeyerC DrostenC Hosts and sources of endemic human coronaviruses. Adv Virus Res3018100163188DOI: 10.1016/bs.aivir.2018.01.001
LimYX NgYL TamJP CoronavirusesDX Liu: Human A review of virus-host interactions. Diseases201643128DOI: 10.3390/diseases4030026
WolfeND DunavanCP DiamondJ Origins of major human infectious diseases. Nature2007447279283DOI: 10.1038/nature05775
ZhuN ZhangD WangW LiX YangB SongJ ZhaoX HuangB ShiW LuR NiuP ZhanF MaX WangD XuW WuG GaoGF TanW A novel coronavirus from patients with pneumonia in China, 2019. N Engl J Med 3822020727733DOI: 10.1056/NEJMoa2001017
RothanHA ByrareddySN The epidemiology and pathogenesis of coronavirus disease (COVID- 19) outbreak. J Autoimmun202010914DOI: 10.1016/j.jaut.2020.102433
JiangS ShiZ ShuY SongJ GaoGF TanW GuoD A distinct name is needed for the new coronavirus. Lancet Infect Dis202039510228949DOI: 10.1016/S0140-6736(20)30419-0
HuB ZengL-P YangX-L GeX-Y ZhangW LiB XieJ ShenX ZhangY-Z WangN LuoD-S ZhengXS WangM-N DaszakP WangL- CuiJ ShiZL Discovery of a rich gene pool of bat SARS-related coronaviruses provides new insights into the origin of SARS coronavirus. PLoS Pathog20171311e1006698DOI: 10.1371/journal.ppat.1006698
ChenY LiuD GuoD Emerging coronaviruses: Genome structure, replication, and pathogenesis. J Med Virol202092418423DOI: 10.1002/jmv.25681
HuD ZhuC AiL HeT WangY YeF YangL DingC ZhuX LvR ZhuJ HassanB FengY TanW WangC Genomic characterization and infectivity of a novel SARS-like coronavirus in Chinese bat. Emerg Microbes Infect20187154DOI: 10.1038/s41426-018-0155-5
ChanJ F-W KokK-H ZhuZ ChuH ToKK-W YuanS YuenK-Y Genomic characterization of the 2019 novel human-pathogenic coronavirus isolated from a patient with atypical pneumonia after visiting Wuhan. Emerg Microbes Infect202091221236DOI: 10.1080/22221751.2020.1719902
RenLL WangYM WuZQ XiangZC GuoL XuT JiangYZ XiongX LiY LiX LiH FanGH GuXY XiaoY GaoH XuJY YangF WangXM WuC ChenL LiuYW LiuB YangJ WangXR DongJ LiL HuangCL ZhaoJP HuY ChengZS LiuLL QianZH QinC JinQ CaoB WangJW Identification of a novel coronavirus causing severe pneumonia in human: a descriptive study. Chin Med J2020133910151024DOI: 10.1097/CM9.0000000000000722
WuA PengY HuangB DingX WangX NiuP MengJ ZhuZ ZhangZ WangJ ShengJ QuanL XiaZ TanW ChengG JiangT Genome composition and divergence of the novel coronavirus (2019-nCoV) originating in China. Cell Host Microbe2020273325328DOI: 10.1016/j.chom.2020.02.001
AngelettiS BenvenutoD BianchiM GiovanettiM PascarellaS COVID-2019M Ciccozzi the role of the nsp2 and nsp3 in its pathogenesis. J Med Virol2020926584588DOI: 10.1002/jmv.25719
Lv L Li G Chen J Liang X Li Y Comparative genomic analysis revealed specific mutation pattern between human coronavirus SARS-CoV-2 and Bat-SARSr-CoV RaTG13. bioRxiv 2020.02.27 2020 969006
YinC Genotyping coronavirus SARS-CoV-2: methods and Implications. arXiv 2003202010965DOI: 10.1016/j.ygeno.2020.04.016
AndersenKG RambautA LipkinWI HolmesEC GarryRF The proximal origin of SARS-CoV-2. Nat Med202026450452DOI: 10.1038/s41591-020-0820-9
GuoY-R CaoQ-D HongZ-S TanY-Y ChenS-D JinH-J TanK-S WangD-Y YanY The origin, transmission and clinical therapies on coronavirus disease 2019 (COVID-19) outbreak - an update on the status. Mil Med Res202071110DOI: 10.1186/s40779-020-00240-0
TangX WuC LiX SongY YaoX WuX DuanY ZhangH WangY QianZ CuiJ LuJ On the origin and continuing evolution of SARS-CoV-2. Natl Sci Rev20200112DOI: 10.1093/nsr/nwaa036
CuiJ LiF ShiZL Origin and evolution of pathogenic coronaviruses. Nat Rev Microbiol201917181192DOI: 10.1038/s41579-018-0118-9
Long SS Prober CG Fischer M Principles and practice of pediatric infectious diseases, 5th Edn, Elsevier 2018
SongW GuiM WangX XiangY Cryo-EM structure of the SARS coronavirus spike glycoprotein in complex with its host cell receptor ACE2. PLoS Pathog201848119DOI: 10.1371/journal.ppat.1007236
PhanLT NguyenTV LuongQC NguyenTV NguyenHT LeHQ NguyenTT CaoTM PhamQD Importation and human-to-human transmission of a novel coronavirus in Vietnam. N Engl J Med2020382872874DOI: 10.1056/NEJMc2001272
WuP HaoX LauEHY WongJY LeungKSM WuJT CowlingBJ LeungGM Real-time tentative assessment of the epidemiological characteristics of novel coronavirus infections in Wuhan, China, as at 22 January 2020. Euro Surveill 25 (3), pii=20202000044DOI: 10.2807/1560-7917. ES.2020.25.3.2000044
Lee PI Hsueh PR Emerging threats from zoonotic coronaviruses-from SARS and MERS to 2019-nCoV. J Microbiol Immunol Infect pii:S1684-1182(20) 2020 30011 6
MorawskaL CaoJ Airborne transmission of SARS-CoV-2: The world should face the reality. Environ Intern2020139105730DOI: 10.1016/j.envint.2020.105730
AssiriA Al-TawfiqJA Al-RabeeahAA Al-RabiahFA Al-HajjarS Al-BarrakA FlembanH Al-NassirWN BalkhyHH Al-HakeemRF MakhdoomHQ ZumlaAI MemishZA Epidemiological, demographic, and clinical characteristics of 47 cases of Middle East respiratory syndrome coronavirus disease from Saudi Arabia: a descriptive study. Lancet Infect Dis201313752761DOI: 10.1016/S1473-3099(13)70204-4
LeeN HuiD WuA ChanP CameronP JoyntGM AhujaA YungMY LeungCB ToKF LuiSF SzetoCC ChungS SungJJ A major outbreak of severe acute respiratory syndrome in Hong Kong. N Engl J Med200334819861994DOI: 10.1056/NEJMoa030685
RotheC SchunkM SothmannP BretzelG FroeschlG WallrauchC ZimmerT ThielV JankeC GuggemosW SeilmaierM DrostenC VollmarP ZwirglmaierK ZangeS WölfelR HoelscherM Transmission of 2019-nCoV infection from an asymptomatic contact in Germany. N Engl J Med202038210970971DOI: 10.1056/NEJMc2001468
DoremalenN van BushmakerT MorrisDH HolbrookMG GambleA WilliamsonBN TaminA HarcourtJL ThornburgNJ GerberSI Lloyd-SmithJO WitE de MunsterVJ Aerosol and surface stability of SARS-CoV-2 as compared with SARS-CoV-1. N Engl J Med202038215641567DOI: 10.1056/NEJMc2004973
ZouL RuanF HuangM LiangL HuangH HongZ YuJ KangM SongY XiaJ GuoQ SongT HeJ YenHL PeirisM WuJ SARS-CoV-2 viral load in upper respiratory specimens of infected patients. N Engl J Med202038211771179DOI: 10.1056/NEJMc2001737
BaiY YaoL WeiT TianF JinD-Y ChenL WangM Presumed asymptomatic carrier transmission of COVID-19. JAMA20203231414061407DOI: 10.1001/jama.2020.2565
LuS LinJ ZhangZ XiaoL JiangZ ChenJ HuC LuoS Alert for non-respiratory symptoms of coronavirus disease 2019 (COVID-19) patients in epidemic period: A case report of familial cluster with three asymptomatic COVID-19 patients. J Med Virol202032190904DOI: 10.1002/jmv.25776
ZhangW DuRH LiB ZhengXS YangXL HuB WangY-Y XiaoG-Fu YanB ShiZ-L ZhouP Molecular and serological investigation of 2019-nCoV infected patients: implication of multiple shedding routes. Emerg Microbes Infect2020913869DOI: 10.1080/22221751.2020.1729071
Cascella M Rajnik M Cuomo A Dulebohn SC Napoli RD Features, evaluation and treatment coronavirus (COVID-19). In: StatPearls [Internet]. Treasure Island (FL): Stat Pearls Publishing; 2020
KubaK koImaiY PenningerJM Angiotensin-converting enzyme 2 in lung diseases. Curr Opin Pharmacol200663271276DOI: 10.1016/j.coph.2006.03.001
JiaH Pulmonary angiotensin-converting enzyme 2 (ACE2) and inflammatory lung disease. Shock201646323948DOI: 10.1097/SHK.0000000000000633
Li S Tang Z Li Z Liu X Searching therapeutic strategy of new coronavirus pneumonia from angiotensin-converting enzyme 2: the target of COVID-19 and SARS-CoV. Eur J Clin Microbiol Infect Dis 2020 39 6 1021 1026
LuR ZhaoX LiJ NiuP YangB WuH WangW SongH HuangB ZhuN BiY MaX ZhanF WangL HuT ZhouH HuZ ZhouW ZhaoL ChenJ MengY WangJ LinY YuanJ XieZ MaJ LiuW J WangD XuW HolmesEC GaoGF WuG ChenW ShiW TanW Genomic characterization and epidemiology of 2019 novel coronavirus: implications for virus origins and receptor binding. Lancet 395 (10224),2020565574DOI: 10.1016/S0140-6736(20)30251-8
FangL KarakiulakisG RothM Are patients with hypertension and diabetes mellitus at increased risk for COVID-19 infection?. Lancet Respir Med202084E21DOI: 10.1016/S2213-2600(20)30116-8
BrakeSJ BarnsleyK LuW McAlindenKD EapenMS SohalSS Smoking upregulates angiotensin-converting enzyme-2 receptor: a potential adhesion site for novel coronavirus SARS-CoV-2 (Covid-19). J Clin Med202093841DOI: 10.3390/jcm9030841
KusterGM PfisterO BurkardT ZhouQ TwerenboldR HaafP WidmerAF SARS-CoV2S Osswald should inhibitors of the renin-angiotensin system be withdrawn in patients with COVID-19?. Eur Heart J2020ehaa235013DOI: 10.1093/eurheartj/ehaa235
JaimesJA AndréNM ChappieJS MilletJK WhittakerGR Phylogenetic analysis and structural modeling of SARSCoV-2 spike protein reveals an evolutionary distinct and proteolytically sensitive activation loop. J Molec Biol20204321033093325DOI: 10.1016/j.jmb.2020.04.009
SongZ XuY BaoL ZhangL YuP QuY ZhuH ZhaoW HanY QinC From SARS to MERS, thrusting coronaviruses into the spotlight. Viruses201911159DOI: 10.3390/v11010059
XiaS LiuM WangC XuW LanQ FengS QiF BaoL DuL LiuS QinC SunF ShiZ ZhuY JiangS LuL Inhibition of SARS-CoV-2 (previously 2019-nCoV) infection by a highly potent pan-coronavirus fusion inhibitor targeting its spike protein that harbors a high capacity to mediate membrane fusion. Cell Res202030343355DOI: 10.1038/s41422-020-0305-x
Bassa BV Brown OR Comparative analysis of coronaviridae nucleocapsid and surface glycoprotein sequences. Front Biosci Landmark 2020 25 1894 1900
PradhanP PandeyAK MishraA GuptaP TripathiPK MenonMB GomesJ VivekanandanP KunduB Uncanny similarity of unique inserts in the 2019-nCoV spike protein to HIV-1 gp120 and Gag. bioRxiv2020DOI: 10.1101/2020.01.30.927871
XiaoC LiX LiuS SangY GaoS-J GaoF HIV-1 did not contribute to the 2019-nCoV genome. Emerg Microbes Infect20209378381DOI: 10.1080/22221751.2020.1727299
MenacheryVD YountBL DebbinkK AgnihothramS GralinskiLE PlanteJA GrahamRL ScobeyT GeX-Y DonaldsonEF RandelSH LanzavecchiaA MarascoWA ShiZ-L BaricRS A SARS-like cluster of circulating bat coronaviruses shows potential for human emergence. Nat Med2015211215081513DOI: 10.1038/nm.3985
KorberB FischerWM GnanakaranS YoonH TheilerJ AbfaltererW FoleyB GiorgiEE BhattacharyaT ParkerMD PartridgeDC EvansCM SilvaT de LaBrancheCC MontefioriDC Spike mutation pipeline reveals the emergence of a more transmissible form of SARS-CoV-2. bioRxiv 2020.04.292020069054DOI: 10.1101/2020.04.29.069054
BanerjeeAK BegumF ThagrikiD TripathiPP RayU Novel mutations in the S1 domain of COVID 19 spike protein of isolate from Gujarat origin, western India. Preprints20202020040450DOI: 10.20944/preprints202004.0450.v1
SahaP BanerjeeAK TripathiPP SrivastavaAK RayU A virus that has gone viral: amino acid mutation in S protein of Indian isolate of coronavirus COVID-19 might impact receptor binding and thus infectivity. bioRxiv 2020.04.072020029132DOI: 10.1101/2020.04.07.029132
PachettiM MariniB BenedettiF GiudiciF MauroE StoriciP MasciovecchioC AngelettiS CiccozziM GalloRC ZellaD IppodrinoR Emerging SARS-CoV-2 mutation hot spots include a novel RNA-dependent-RNA polymerase variant. J Transl Med202018179DOI: 10.1186/s12967-020-02344-6
GaoJ TianZ BreakthroughX Yang Chloroquine phosphate has shown apparent efficacy in treatment of COVID-19 associated pneumonia in clinical studies. Biosci Trends20201417273DOI: 10.5582/bst.2020.01047
HuangY TuM WangS ChenS ZhouW ChenD ZhouL WangM ZhaoY ZengW HuangQ XuH LiuZ GuoL Clinical characteristics of laboratory confirmed positive cases of SARS-CoV2 infection in Wuhan, China: A retrospective single center analysis. Travel Med Infect Dis2020101606DOI: 10.1016/j.tmaid.2020.101606
WangW TangJ WeiF Updated understanding of the outbreak of 2019 novel coronavirus (2019-nCoV) in Wuhan, China. J Med Virol 92 (4),2020441447DOI: 10.1002/jmv.25689
KotfisK COVID-19K Skonieczna-Żydecka gastrointestinal symptoms and potential sources of 2019-nCoV transmission. Anaesthesiol Intensive Ther202052DOI: 10.5114/ait.2020.93867
CormanVM LandtO KaiserM MolenkampR MeijerA ChuDKW BleickerT BrüninkS SchneiderJ SchmidtML MuldersDGJC HaagmansBL VeerB van der Detection of 2019 novel coronavirus (2019-nCoV) by real-time RT-PCR. Euro Surveil20202532000045DOI: 10.2807/1560-7917. ES.2020.25.3.2000045
Colson P Lagier J Baudoin J Khalil JB Scola B La Raoult D Ultrarapid diagnosis, microscope imaging, genome sequencing, and culture isolation of SARS-CoV-2. Eur J Clin Microbiol Infect Dis 2020
XieC JiangL HuangG PuH GongBo LinH MaShi ChenX LongB SiG YuH JiangL YangX ShiY YangZ Comparison of different samples for 2019 novel coronavirus detection by nucleic acid amplification tests. Int J Infect Dis202093264267DOI: 10.1016/j.ijid.2020.02.050
GuanW NiZ YuHu LiangW OuC HeJ LiuL ShanH LeiC HuiDSC DuB LiL ZengG YuenK-Y ChenR TangC WangT ChenP XiangJ LiS WangJ-L LiangZ PengY WeiL LiuY PengHH Y-h P WangJ-M LiuJ ChenZ LiG ZhengZ QiuS LuoJ YeC ZhuS ZhongN Clinical characteristics of coronavirus disease 2019 in China. N Engl J Med2020113DOI: 10.1101/2020.02.06.20020974
HuangC WangY LiX RenL ZhaoJ HuY ZhangL FanG XuJ GuX ChengZ YuT XiaJ WeiY WuW XieX YinW LiH LiuM XiaoY GaoH GuoL XieJ WangG JiangR GaoZ JinQ WangJ CaoB Clinical features of patients infected with 2019 novel coronavirus in Wuhan, China. Lancet 395 (10223),2020497506DOI: 10.1016/S0140-6736(20)30183-5
LeiJ LiJ LiX QiX CT imaging of the 2019 novel coronavirus (2019-nCoV) early transmission dynamics in Wuhan, China, of novel coronavirus-infected pneumonia. Radiology2020200236DOI: 10.1148/radiol.2020200236
ShiH HanX JiangN CaoY AlwalidO GuJ FanY ZhengC Radiological findings from 81 patients with COVID-19 pneumonia in Wuhan, China: a descriptive study. Lancet Infect Dis2020204425434DOI: 10.1016/S1473-3099(20)30086-4
ZhaoW ZhongZ XieX YuQ LiuJ Relation between chest CT findings and clinical conditions of coronavirus disease (COVID-19) pneumonia: a multicenter study. AJR Am J Roentgenol2020316DOI: 10.2214/AJR.20.23287
AiT YangZ HouH ZhanC ChenC LvW TaoQ SunZ XiaL Correlation of chest CT and RT-PCR testing in coronavirus disease 2019 (COVID-19) in China: a report of 1014 cases. Radiology2020200642DOI: 10.1148/radiol.2020200642
LiuC ZhouQ GarnerLV WatkinsSP CarterLJ SmootJ GreggAC DanielsAD JerveyS AlbaiuD Research and development on therapeutic agents and vaccines for COVID-19 and related human coronavirus diseases. ACS Cent Sci202063315331DOI: 10.1021/acscentsci.0c00272
ZumlaA ChanJF AzharEI HuiDS YuenKY Coronaviruses - drug discovery and therapeutic options. Nat Rev Drug Discov201615532747DOI: 10.1038/nrd.2015.37
LimJ JeonS ShinHY KimMJ SeongYM LeeWJ ChoeKW KangYM LeeB ParkSJ Case of the index patient who caused tertiary transmission of COVID-19 infection in Korea: the application of lopinavir/ritonavir for the treatment of COVID-19 infected pneumonia monitored by quantitative RT-PCR. J Korean Med Sci2020356e79DOI: 10.3346/jkms.2020.35.e79
RichardsonP GriffinI TuckerC SmithD OechsleO PhelanA StebbingJ Baricitinib as potential treatment for 2019-nCoV acute respiratory disease. Lancet Infect Dis2020201719DOI: 10.1016/S0140-6736(20)30304-4
ZhavoronkovA AladinskiyV ZhebrakA ZagribelnyyB TerentievV BezrukovDS PolykovskiyD ShayakhmetovR FilimonovA OrekhovP YanY PopovaO VanhaelenQ AliperA IvanenkovY Potential COVID-2019 3C-like protease inhibitors designed using generative deep learning approaches. ChemRxiv2020DOI: 10.26434/chemrxiv.11829102
ChenL XiongJ BaoL ShiY Convalescent plasma as a potential therapy for COVID-19. Lancet Infect Dis2020204398400DOI: 10.1016/S1473-3099(20)30141-9
GünerR HasanoğluI COVID-19F Aktaş Prevention and control measures in community. Turk J Med Sci 50 (SI-1),2020571577DOI: 10.3906/sag-2004-146
ChengVC WongSC ChuangVW SoSY ChenJH SridharS ToKK ChanJF HungIF HoPL YuenKY The role of community-wide wearing of face mask for control of coronavirus disease 2019 (COVID-19) epidemic due to SARS-CoV-2. J Infect S0163-4453(20)2020302358DOI: 10.1016/j.jinf.2020.04.024
NgonghalaCN IboiE EikenberryS ScotchM MacIntyreCR BondsMH GumelAB Mathematical assessment of the impact of non-pharmaceutical interventions on curtailing the 2019 novel coronavirus. Math Biosci2020325108364DOI: 10.1016/j.mbs.2020.108364
Wilder-SmithA FreedmanDO Isolation, quarantine, social distancing and community containment: pivotal role for old style public health measures in the novel coronavirus (2019-nCoV) outbreak. J Travel Med2020272taaa020DOI: 10.1093/jtm/taaa020
BogochII WattsBA Thomas-BachliA HuberC KraemerMUG KhanK Pneumonia of unknown etiology in Wuhan, China: potential for international spread via commercial air travel. J Trav Med2020722DOI: 10.1093/jtm/taaa008
SavarinoA BoelaertJR CassoneA MajoriG CaudaR Effects of chloroquine on viral infections: an old drug against today's diseases?. Lancet Infect Dis20033117227DOI: 10.1016/S1473-3099(03)00806-5
GaoX YuanZ YangD LiH ZhangY GaoP LiuX ZhaoW XiaoT DuanX A family cluster of severe acute respiratory syndrome coronavirus 2 infections. Eur J Clin Microbiol Infect Dis202015DOI: 10.21203/
WangZ ChenX LuY ChenF ZhangW Clinical characteristics and therapeutic procedure for four cases with 2019 novel coronavirus pneumonia receiving combined Chinese and Western medicine treatment. Biosci Trends20201416468DOI: 10.5582/bst.2020.01030
WitE de FeldmannF CroninJ JordanR OkumuraA ThomasT ScottD CihlarT FeldmannH Prophylactic and therapeutic remdesivir (GS-5734) treatment in the rhesus macaque model of MERS-CoV infection. Proc Natl Acad Sci20201171267716776DOI: 10.1073/pnas.1922083117
GordonCJ TchesnokovEP FengJY PorterD GotteA The antiviral compound remdesivir potently inhibits RNA-dependent RNA polymerase from middle east respiratory syndrome coronavirus. J Biol Chem20202951547734779DOI: 10.1074/jbc. AC120.013056
WangM CaoR ZhangL YangX LiuJ XuM Remdesivir and chloroquine effectively inhibit the recently emerged novel coronavirus (2019-nCoV) in vitro. Cell Res202030269271DOI: 10.1038/s41422-020-0282-0
CvetkovicRS Lopinavir/ritonavirKL Goa a review of its use in the management of HIV infection. Drugs2003638769802DOI: 10.2165/00003495-200363080-00004
ChuCM ChengVC HungIF WongMM ChanKH ChanKS KaoRY PoonLL WongCL GuanY PeirisJS YuenKY Role of lopinavir/ritonavir in the treatment of SARS: initial virological and clinical findings. Thorax20045932526DOI: 10.1136/thorax.2003.012658
ArabiYM ShalhoubS MandourahY Al-HameedF Al-OmariA QasimE Al JoseJ AlraddadiB AlmotairiA KhatibK Al AbdulmomenA QushmaqI SindiAA MadyA SolaimanO Al-RaddadiR MaghrabiK RagabA MekhlafiGA Al BalkhyHH HarthyA Al KharabaA GramishJA Al-AithanAM Al-DawoodA MersonL HaydenFG FowlerR Ribavirin and interferon therapy for critically ill patients with middle east respiratory syndrome: a multicenter observational study. Clin Infect Dis201970918371844DOI: 10.1093/cid/ciz544
DongL HuS GaoJ Discovering drugs to treat coronavirus disease 2019 (COVID-19). Drug Discov Ther20201415860DOI: 10.5582/ddt.2020.01012
HsiehHP HsuJT Strategies of development of antiviral agents directed against influenza virus replication. Curr Pharm Des20071334353142DOI: 10.2174/138161207782794248
NishimuraH YamayaM A synthetic serine protease inhibitor, nafamostat mesilate, is a drug potentially applicable to the treatment of ebola virus disease. Tohoku J Exp Med201523714550DOI: 10.1620/tjem.237.45
StebbingJ PhelanA GriffinV TuckerC OechsleO SmithD COVID-19P. Richardson combining antiviral and anti-inflammatory treatments. Lancet Infect Dis2020204400402DOI: 10.1016/S1473-3099(20)30132-8
Publisher’s Note: IMR Press stays neutral with regard to jurisdictional claims in published maps and institutional affiliations.
Back to top