The COVID-19 Pandemic: A Comprehensive Review of Taxonomy, Genetics, Epidemiology, Diagnosis, Treatment, and Control

Yosra A Helmy, Mohamed Fawzy, Ahmed Elaswad, Ahmed Sobieh, Scott P Kenney, Awad A Shehata, Yosra A Helmy, Mohamed Fawzy, Ahmed Elaswad, Ahmed Sobieh, Scott P Kenney, Awad A Shehata

Abstract

A pneumonia outbreak with unknown etiology was reported in Wuhan, Hubei province, China, in December 2019, associated with the Huanan Seafood Wholesale Market. The causative agent of the outbreak was identified by the WHO as the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), producing the disease named coronavirus disease-2019 (COVID-19). The virus is closely related (96.3%) to bat coronavirus RaTG13, based on phylogenetic analysis. Human-to-human transmission has been confirmed even from asymptomatic carriers. The virus has spread to at least 200 countries, and more than 1,700,000 confirmed cases and 111,600 deaths have been recorded, with massive global increases in the number of cases daily. Therefore, the WHO has declared COVID-19 a pandemic. The disease is characterized by fever, dry cough, and chest pain with pneumonia in severe cases. In the beginning, the world public health authorities tried to eradicate the disease in China through quarantine but are now transitioning to prevention strategies worldwide to delay its spread. To date, there are no available vaccines or specific therapeutic drugs to treat the virus. There are many knowledge gaps about the newly emerged SARS-CoV-2, leading to misinformation. Therefore, in this review, we provide recent information about the COVID-19 pandemic. This review also provides insights for the control of pathogenic infections in humans such as SARS-CoV-2 infection and future spillovers.

Keywords: COVID-19; One Health; SARS-CoV-2; control; diagnosis; epidemiology; genetics; outbreak; pneumonia; public health; treatment.

Conflict of interest statement

The authors declare no conflict of interest.

Figures

Figure 1
Figure 1
Genome organization of SARS CoV-2 and its encoded proteins. The orf1ab gene constitutes two-thirds of the genome, encodes a total of 16 non-structural proteins (NSPs) within the pp1ab gene, as shown in yellow, which are nsp1 (180 aa), nsp2 (638 aa), nsp3 (1945 aa), nsp4 (500 aa), nsp5 (306 aa), nsp6 (290 aa), nsp7 (83 aa), nsp8 (198 aa), nsp9 (113 aa), nsp10 (139 aa), nsp11 (13 aa), nsp12 (932 aa), nsp13 (601 aa), nsp14 (527 aa), nsp15 (346 aa), and nsp16 (298 aa). The other third of SARS CoV-2 includes four genes (in green) that encode four structural proteins (S, M, E, N), and six accessory genes (in blue) that encode six accessory proteins (orf3a, orf6, orf7a, orf7b, orf8, and orf10).
Figure 2
Figure 2
Phylogenetic tree based on the complete genome sequences of 45 selected coronaviruses from 18 countries including the SARS-CoV-2, SARS-CoV, HCoV, bat SARS, SARS-like CoV, and MERS-CoV. The tree was constructed in IQ-TREE using the maximum likelihood method, ModelFinder, and ultrafast bootstrap approximation (1000 replicates). The tree is drawn to scale, with branch lengths (numbers below the branches) measured in the number of substitutions per site. Branch lengths less than 0.3 are not shown. Numbers above the branches represent the percentage of replicate trees in which the associated viruses clustered together in the bootstrap test. The tree is rooted with two human coronavirus species from the genus Alphacoronavirus as an outgroup (HCoV-229E and HCoV-NL63).
Figure 3
Figure 3
The transmission cycle of coronaviruses including MERS-CoV, SARS-CoV, and SARSCoV-2. The transmission of the virus to humans occurs by direct contact with infected animals. The continuous line represents direct transmission.
Figure 4
Figure 4
Lung of a 51-year-old male patient with a history of hepatitis C and symptoms of dry cough and shortness of breathing for three weeks. No recent travel or known contacts with infected subjects. Axial (A) and coronal computed tomography (CT) (B) of chest without contrast revealed bilateral peribronchial and subpleural consolidative opacities noted throughout both lungs (green arrow). There were scattered nodular consolidative opacities in a peribronchial distribution (orange arrow). The patient tested positive for SARS-CoV-2 RNA.

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