Coronavirus Genomics and Bioinformatics Analysis

Basic information about coronavirus:

Coronaviruses are a family of viruses that can cause illnesses such as the common cold, severe acute respiratory syndrome (SARS) and Middle East respiratory syndrome (MERS). In 2019, a new coronavirus was identified as the cause of a disease outbreak that originated in China.

Figure:CoronaVirus

The virus is now known as the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The disease it causes is called coronavirus disease 2019 (COVID-19). In March 2020, the World Health Organization (WHO) declared the COVID-19 outbreak a pandemic.

Human Coronavirus Types

Coronaviruses are named for the crown-like spikes on their surface. There are four main sub-groupings of coronaviruses, known as alpha, beta, gamma, and delta.

Human coronaviruses were first identified in the mid-1960s. The seven coronaviruses that can infect people are:

Common human coronaviruses

1. 229E (alpha coronavirus)
2. NL63 (alpha coronavirus)
3. OC43 (beta coronavirus)
4. HKU1 (beta coronavirus)

Other human coronaviruses

5. MERS-CoV (the beta coronavirus that causes Middle East Respiratory Syndrome, or MERS)
6. SARS-CoV (the beta coronavirus that causes severe acute respiratory syndrome, or SARS)
7. SARS-CoV-2 (the novel coronavirus that causes coronavirus disease 2019, or COVID-19)

 Symptoms

Signs and symptoms of coronavirus disease 2019 (COVID-19) may appear two to 14 days after exposure. This time after exposure and before having symptoms is called the incubation period. Common signs and symptoms can include:

• Fever
• Cough
• Shortness of breath or difficulty breathing

Other symptoms can include:

• Tiredness
• Aches
• Chills
• Sore throat
• Loss of smell
• Loss of taste
• Headache
• Diarrhea
• Severe vomiting 

Bioinformatics Analysis:

The drastic increase in the number of coronaviruses discovered and coronavirus

genomes being sequenced have given us an unprecedented opportunity to perform genomics

and bioinformatics analysis on this family of viruses. Coronaviruses possess the largest

genomes (26.4 to 31.7 kb) among all known RNA viruses, with G + C contents varying from

32% to 43%. Variable numbers of small ORFs are present between the various conserved

genes (ORF1ab, spike, envelope, membrane and nucleocapsid) and downstream to nucleocapsid gene in different coronavirus lineages. Phylogenetically, three genera,

Alphacoronavirus, Betacoronavirus and Gammacoronavirus, with Betacoronavirus consisting of subgroups A, B, C and D, exist. A fourth genus, Deltacoronavirus, which includes bulbul coronavirus HKU11, thrush coronavirus HKU12 and munia coronavirus HKU13, is emerging. Molecular clock analysis using various gene loci revealed that the time of most recent common ancestor of human/civet SARS related coronavirus to be 1999-2002,

with estimated substitution rate of 410-4 to 210-2 substitutions per site per year.

Recombination in coronaviruses was most notable between different strains of murine hepatitis virus (MHV), between different strains of infectious bronchitis virus, betweenMHV and bovine coronavirus, between feline coronavirus (FCoV) type I and canine coronavirus generating FCoV type II, and between the three genotypes of human coronavirus HKU1 (HCoV-HKU1). Codon usage bias in coronaviruses were observed, with HCoV-HKU1 showing the most extreme bias, and cytosine deamination and selection of CpG suppressed clones are the two major independent biological forces that shape such codon usage bias in coronaviruses.[for more information about this research paper:https://www.mdpi.com/1999-4915/2/8/1804]