key: cord-0936945-9kxvri56 authors: Rehman, Muhammad Fayyaz ur; Fariha, Chaudhary; Anwar, Aqsa; Shahzad, Naveed; Ahmad, Munir; Mukhtar, Salma; Haque, Muhammad Farhan Ul title: Novel coronavirus disease (COVID-19) pandemic: A recent mini review date: 2020-12-31 journal: Comput Struct Biotechnol J DOI: 10.1016/j.csbj.2020.12.033 sha: ae55d0f0c23dcb054b38e52e28424cea12ffccbf doc_id: 936945 cord_uid: 9kxvri56 The COVID-19, caused by a novel coronavirus, was declared as a global pandemic by WHO more than five months ago, and we are still experiencing a state of global emergency. More than 74.30 million confirmed cases of the COVID-19 have been reported globally so far, with an average fatality rate of almost 3.0%. Seven different types of coronaviruses had been detected from humans; three of them have resulted in severe outbreaks, i.e., MERS-CoV, SARS-CoV, and SARS-CoV-2. Phylogenetic analysis of the genomes suggests the possible occurrence of recombination between SARS-like-CoVs from pangolin and bat might have led to the origin of SARS-CoV-2 and the COVID-19 outbreak. Coronaviruses are positive-sense, single-stranded RNA viruses and harbour a genome (30 kb) consisting of two terminal untranslated regions and twelve putative functional open reading frames (ORFs), encoding for non-structural and structural proteins. There are sixteen putative non-structural proteins, including proteases, RNA-dependent RNA polymerase, helicase, other proteins involved in the transcription and replication of SARS-CoV-2, and four structural proteins, including spike protein (S), envelope (E), membrane (M), and nucleocapsid (N). SARS-CoV-2 infection, with a heavy viral load in the body, destroys the human lungs through cytokine storm, especially in elderly persons and people with immunosuppressed disorders. A number of drugs have been repurposed and employed, but still, no specific antiviral medicine has been approved by the FDA to treat this disease. This review provides a current status of the COVID-19, epidemiology, an overview of phylogeny, mode of action, diagnosis, and possible treatment methods and vaccines. Introduction 71 million confirmed COVID-19 cases with a death toll of above 1.67 million 72 (https://covid19.who.int/ accessed on December 19, 2020). 73 Without any proper treatment and vaccine for COVID-19, we are currently experiencing a 74 worldwide emergency affecting all societies, and it has sent billions of people into lockdown. 75 Around the world, desperate efforts are underway to curtail this pandemic while it has resulted in 76 the collapsing of health systems and has triggered lasting geopolitical and economic changes. To 87 Human coronaviruses (HCoVs) were first reported in the mid-1960s when two species were 88 isolated from persons with the common cold: HCoV-229E [12] and HCoV-OC43 [13] . Since then, 89 seven different types of CoVs had been detected from humans, three of them happened to be highly . 105 A few months ago, a novel CoV emerged and caused a serious disaster across the whole world. 106 During the last two months of 2019, several cases of 'viral pneumonia' in Wuhan, People's 107 Republic of China, were reported [17, 18] . The cause of this infectious disease was identified as a 108 natural virus of an animal origin with spillover infection potential [19] . It was traced that the 109 geographical source of this virus was Huanan South China Seafood Market, but the actual animal 110 source of this CoV was not known. It is now thought that this virus came from bats as their primary Since the first confirmed diagnosis of SARS-CoV-2 in China, more than 74.30 million people 121 have been affected, from which more than 1.67 million lives have been claimed 122 (https://covid19.who.int/, assessed on December 19, 2020 ). Although more than 52 million people 123 have defeated COVID-19 and recovered from the disease, yet the battle between SARS-CoV-2 124 and humans is continued, and still, no specific therapeutics are available. The United States of 125 America (USA) shares 22.7% of total infection cases, followed by India and Brazil, sharing 13.5% 126 and 9.6% of cases, respectively (https://covid19.who.int/, assessed on December 19, 2020) ( Figure 127 1). Although a decrease in death rate is observed (September 10, 3.22; July 20, 6.65%; April 10, 128 22.36% and Feb 2, 41.80%), there is no substantial reduction in active COVID-19 cases 129 (>700,000daily cases on December 19, 2020). The cumulative incidences for COVID-19 vary by 130 a multitude of factors, including comorbidities, age, gender, health and living conditions [21, 22] . In the USA, the situation is still aggravating, where COVID-19 death toll is over 300, 000 and the 139 rate is still rising as 95 deaths per 100,000 since January 2020, across the country 140 (https: //www.cdc.gov/coronavirus/2019 //www.cdc.gov/coronavirus/ -ncov, accessed December 20, 2020 Several genome sequences of SARS-CoV-2 retrieved from the COVID-19 patients have been 183 reported by researchers from various countries. According to the NCBI database, more than 28,000 (full length) SARS-CoV-2 genome sequences from human hosts and more than 113,000 Sequence 185 Read Archive (SRA) high throughput sequence submissions through multiple cloud providers 186 and NCBI servers (December 20, 2020). The single-stranded positive-sense RNA genome of 187 SARS-CoV-2 is around ~30 kb that starts with a 5′-cap structure and ends with a 3′-poly-A tail. The initial attachment of the virus to the host cell is mediated by S protein, which has two subunits, 203 S1 (specific receptor binding domain known as RBD) and S2 (CoV S2 glycoprotein). S protein, 204 through its specific RBD, binds to its receptor on the host cell [47] . Wan et al. [48] reported that 205 SARS-CoV-2 is optimized to bind on angiotensin-converting enzyme II (ACE2) human receptors. RBD in the S protein is the most variable part, and it differs for each type of CoV. After binding 207 to the receptor, the host protease cleaves the S protein, which causes the release of the spike fusion sore throat to high fever, GI distress, diarrhea, nausea, myalgia, dyspnea, lymphopenia, difficulty 254 in breathing and pneumonia [67] [68] [69] [70] . Unfortunately, COVID-19 symptoms, at the initial stage 255 cannot make the basis for diagnosis as they mimic many respiratory and common infections (Table 256 1). Moreover, SARS-CoV-2 infected persons might also be asymptomatic carriers. COVID-19 may progress with cytokine storm leading to acute pneumonia, acute respiratory 258 distress syndrome (ARDS) (Figure 4) Treatment of severe COVID-19 patients using convalescent plasma or immunoglobulins from the 370 recovered patients has also been found successful against 149] . Corticosteroids can help in alleviating lung inflammation, but their uses may lead to other 372 complications like hyperglycemia, avascular necrosis, and psychosis [150] . The use of 373 dexamethasone has been found safer to lower down the mortality rate in COVID-19 patients [151] . is a SARS-CoV-2 like particle. They proposed that this virus-like particle would force the immune 412 system of humans to produce antibodies against SARS-CoV-2. 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Institute of Chemistry Authors Statement: 935 MFUH and SM: conceptualisation, acquisition of data MFR: organized, drafted and revised the manuscript enzyme halts genomic replication and stops viral dissemination (2) Several drugs have been 888 proposed against helicase but none of them is approved yet (3) Ivermectin dissociates IMP α/β1 889 (importins) heterodimer, which is responsible for nuclear transport of viral protein cargos, so viral 890 proteins cannot enter into the nucleus to continue vital processes like replication (4) Lopinavir,