by Kamal Pratap Singh, Managing Editor, Biotech Express
E-mail- kamal9871@gmail.com
Coronaviruses (CoVs): Introduction
Coronaviruses (CoV) are member of a group of related viruses that cause diseases in mammals and birds. There are many diverse groups of viruses and each group contains further more different viruses (see complete phylogeny here). Novel CoV-2019’s story is not very old, a new group of viruses with the name of coronaviruses have been recognized by an informal group of virologists who have sent their conclusions to Nature and consequently in 1975 the International Committee on the Taxonomy of Viruses (ICTV) approved the creation of a new family, Coronaviridae, with one genus, Coronavirus (Tyrrell et al., 1975).
Find out more relevant info about Coronaviruses: https://www.who.int/health-topics/coronavirus#tab=tab_1
CoVs: Classification
Coronaviruses (CoVs) are the largest group of viruses belonging to the Nidovirales order, which includes 4 families Coronaviridae, Arteriviridae, Mesoniviridae, and Roniviridae. The Coronavirinae Suborder is further subdivided into Coronaviridae family, two subfamilies Letovirinae and Orthocoronavirinae four genera the alpha, beta, gamma, and delta coronaviruses and further into 24 subgenera and 39 species (more on ICTV). One of the oldest review on coronaviruses which explained about them in detail was published in 1983.
With introduction of SARS-CoV2, coronaviruses which affects Human are now of 7 types:
- 229E (alpha coronavirus)
- NL63 (alpha coronavirus)
- OC43 (beta coronavirus)
- HKU1 (beta coronavirus)
- MERS-CoV (the beta coronavirus that causes Middle East Respiratory Syndrome, or MERS)
- SARS-CoV (the beta coronavirus that causes severe acute respiratory syndrome, or SARS)
- SARS-CoV-2 (the novel coronavirus that is causing coronavirus disease 2019 or COVID19, it is attached to beta coronavirus species as we will see in next headings )
Image: Phylogenetic analysis of RNA-dependent RNA polymerases (Pol) of coronaviruses with complete genome sequences available. (Image source: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3185738/)
People around the world commonly get infected with human coronaviruses 229E, NL63, OC43, and HKU1. Sometimes coronaviruses that infect animals can evolve and make people sick and become a new human coronavirus. Three recent examples of this are SARS2 CoV2019, SARS-CoV, and MERS-CoV (https://www.cdc.gov/coronavirus/types.html).
Find out more relevant info: https://www.sciencedirect.com/topics/neuroscience/coronavirus
Recognizing Coronavirus: Identification and naming of novel CoV
CoVs have a crown-like appearance due to the presence of spike glycoproteins on the envelope under an electron microscope (coronam is the Latin term for crown). The Coronaviridae Study Group (CSG) of the International Committee on Taxonomy of Viruses assessed the placement of the human pathogen which was tentatively named 2019-nCoV (Reference), within the Coronaviridae. The CSG recognizes this virus as forming a sister clade to the human and bat severe acute respiratory syndrome coronaviruses (SARS-CoVs) and designates it as SARS-CoV-2. They further proposed to use the following naming convention for individual isolates: SARS-CoV-2/host/location/isolate/date.
Find out more relevant info: https://www.nature.com/articles/s41564-020-0695-z
CoVs Structure: What they look like?
All viruses in the Nidovirales order are enveloped, coronavirus virions are spherical in shape. The coronaviral genome encodes four major structural proteins: the spike (S) protein, nucleocapsid (N) protein, membrane (M) protein, and the envelope (E) protein and many non-structural proteins. Little information is available toward the complete proteome of SARS-CoV2, the main proteins that are usaual in CoVs or have been studied in SARS-CoV-2 are:
The S protein is ~150 kDa. It utilizes peptide terminal signal sequence to gain access to the Endoplasmic Reticulum and is heavily N-linked glycosylated. Homotrimers of the virus encoded S protein make up the distinctive spike structure on the surface of the virus. The trimeric S glycoprotein is a class I fusion protein and mediates attachment to the host receptor.
The N protein constitutes the only protein present in the nucleocapsid. It is composed of two separate domains, an N-terminal domain (NTD) and a C-terminal domain (CTD), both capable of binding RNA in vitro, but each domain uses different mechanisms to bind RNA. It has been suggested that optimal RNA binding requires contributions from both domains (Reference). N protein is also heavily phosphorylated and phosphorylation has been suggested to trigger a structural change enhancing the affinity for viral versus non-viral RNA.
The M protein is the most abundant structural protein in the virion. It is a small (~25–30 kDa) protein with three transmembrane domains and is thought to give the virion its shape. It has a small N-terminal glycosylated ectodomain and a much larger C-terminal endodomain that extends 6–8 nm into the viral particle. Despite being co-translationally inserted in the ER membrane, most M proteins do not contain a signal sequence.
The E protein (~8–12 kDa) is found in small quantities within the virion. The E protein has an N-terminal ectodomain and a C-terminal endodomain and has ion channel activity. The E protein facilitates assembly and release of the virus, but also has other functions. For instance, the ion channel activity in SARS-CoV E protein is not required for viral replication but is required for pathogenesis.
A fifth structural protein, the hemagglutinin-esterase (HE), is present in subset of β-coronaviruses. The protein acts as a hemagglutinin, binds sialic acids on surface glycoproteins, and contains acetyl-esterase activity. These activities are thought to enhance S protein-mediated cell entry and virus spread through the mucosa (Reference).
Find out more relevant info: https://www.uniprot.org/proteomes/UP000000354
Genome: What does it contain for inheritance?
The Genome of SARS – CoV2 is 30kb long single stranded positive sense RNA which is non-segmented. Positive sense RNA gives mRNA which would incorporate in host polymerase and make protein as quickly as possible. Professor Leo Poon from Hong Kong University was one of the first scientists to decode the genome of novel coronavirus.
The main aim of a virus is to enter the host cell, to acquire its genetic machinery and to make progenies which if grows in a suitable atmosphere may reach to billions or even trillions within a fraction of time and thus it carries minimum genes to carry forward their lifecycle.
Analysis of complete SARS – CoV2 genome submitted by Indian Scientists revealed that it has total 29854 bp in a linear RNA. It has several open reading frames (ORFs) and genes which are in following order orf1ab -- Gene S — orf3a – Gene E — Gene M — orf6 — orf7a — orf8 — GeneN — orf10. Orf1ab is the longest gene in SARS COV2 which spread upto 21.5 kbp.
According to a recent study (Reference) SARS – CoV2 was found closely related (with 88% identity) to two bat-derived SARS-like coronaviruses, bat-SL-CoVZC45 and bat-SL-CoVZXC21, collected in 2018 in Zhoushan, eastern China, but were more distant from SARS-CoV (about 79%) and MERS-CoV (about 50%). Phylogenetic analysis revealed that SARS- CoV2 fell within the subgenus Sarbecovirus of the genus Betacoronavirus.
Find out more relevant info: https://www.ncbi.nlm.nih.gov/protein/?term=Severe+acute+respiratory+syndrome+coronavirus+2%5Borganism%5D+AND+protein_structure_direct%5BFilt%5D
CoV: Transmission
SARS- CoV2 transmits from person to person although according to some theories it came from bat or pangolin which was eaten by a human in Wuhan, China. Between people it can transfer through close contact, aerosol respiratory droplets (coughing or sneezing) and by touch either through body surface of infected surfaces which have virus particles. These circulating virus particles enter the body through the mouth, eyes or nose.
The initial attachment is initiated by interactions between the S protein (S1 region) and its receptor. ACE2 receptor has been proposed as entry receptor for SARS2.
Find out more relevant info: https://www.healthline.com/health/coronavirus-transmission
CoV: How it harms its Host?
The incubation period for COVID-19 in human (i.e. the time between exposure to the virus and onset of symptoms) is currently estimated to between one and 14 days. The early symptoms are usually cough, fever and shortness of breath, and look a lot like the flu or common cold. Other like general weakness, fatigue and muscular pain and in the most severe cases, severe pneumonia, acute respiratory distress syndrome, sepsis and septic shock, all potentially leads to death. Reports show that clinical deterioration can occur rapidly, often during the second week of disease. Recently, anosmia – loss of the sense of smell – (and in some cases the loss of the sense of taste) have been reported as a symptom of a COVID-19 infection.
Find out more relevant info: https://www.ecdc.europa.eu/en/covid-19/questions-answers
CoVs: How they multiplies?
Following receptor binding, the virus must next gain access to the host cell cytosol. This is generally accomplished by acid dependent proteolytic cleavage of S protein by a cathepsin, TMPRRS2 or another protease, followed by fusion of the viral and cellular membranes. The next step in the coronavirus lifecycle is the translation of the replicase gene from the virion genomic RNA. The replicase gene encodes two large ORFs, rep1a and rep1b, which express two co-terminal polyproteins, pp1a and pp1ab. Polyproteins pp1a and pp1ab contain the non-structural proteins (nsps) 1–11 and 1–16, respectively. These polyproteins are subsequently cleaved into the individual nsps. Coronaviruses encode either two or three proteases that cleave the replicase polyproteins. Many of the nsps assemble into the replicase–transcriptase complex (RTC) to create an environment suitable for RNA synthesis, and ultimately are responsible for RNA replication and transcription of the sub-genomic RNAs.
The nsps also contain other enzyme domains and functions, including those important for RNA replication, for example nsp12 encodes the RNAdependent RNA polymerase (RdRp) domain; nsp13 encodes the RNA helicase domain and RNA 5′-triphosphatase activity; nsp14 encodes the exoribonuclease (ExoN) involved in replication fi delity and N7-methyltransferase activity; and nsp16 encodes 2′-O-methyltransferase activity. In addition to the replication functions other activities, such as blocking innate immune responses (nsp1; nsp16-2′-O-methyl transferase; nsp3-deubiquitinase) have been identified for some of the nsps, while others have largely unknown functions.
Viral RNA synthesis produces both genomic and sub-genomic RNAs. Sub-genomic RNAs serve as mRNAs for the structural and accessory genes. Following replication and sub-genomic RNA synthesis, the viral structural proteins, S, E, and M are translated and inserted into the endoplasmic reticulum (ER). These proteins move along the secretory pathway into the endoplasmic reticulum–Golgi intermediate compartment (ERGIC). There, viral genomes encapsidated by N protein bud into membranes of the ERGIC containing viral structural proteins, forming mature virions. Following assembly, virions are transported to the cell surface in vesicles and released by exocytosis (Reference).
https://www.biorxiv.org/content/10.1101/2020.03.22.002386v3.full.pdf
Coronavirus Tests:
When start feeling ill with COVID-19 symptoms (such as fever, cough, difficulty breathing, muscle pain or general weakness), it is recommended that you contact your local healthcare services online or by telephone ( Govt. of India helpline no. is 1075 ). ECDC has suggested prioritize testing in the following groups:
- hospitalised patients with severe respiratory infections;
- symptomatic healthcare staff including those with mild symptoms;
- cases with acute respiratory infections in hospital or long-term care facilities;
- patients with acute respiratory infections or influenza-like illness in certain outpatient clinics or hospitals;
- elderly people with underlying chronic medical conditions such as lung disease, cancer, heart failure, cerebrovascular disease, renal disease, liver disease, diabetes, and immunocompromising conditions.
The test which performed to detect Virus is Real time Polymerase Chain Reaction (RT-PCR), a molecular test that analyze RNA of virus. Many companies are providing diagnostic kits to test COVID19 and the protocol can be found here. In India, ICMR – National Institute of Virology, Pune has been recognized as WHO reference laboratories providing confirmatory testing for COVID-19.
Prevention is always better than cure: How to prevent COVID19?
The virus enters our body via eyes, nose and/or mouth, so it is important to avoid touching your face with unwashed hands. Washing of hands with soap and water for at least 20 seconds, or cleaning hands thoroughly with alcohol-based solutions, gels or tissues is recommended in all settings. It is also recommended to stay 1 metre or more away from people infected with COVID-19 who are showing symptoms, to reduce the risk of infection through respiratory droplets.
Vaccine is for Viruses?
As this is a new virus, no vaccine is currently available. Although work on a vaccine has already started by several research groups and pharmaceutical companies worldwide, it may be months to more than a year before a vaccine has been tested and is ready for use in humans.
Healthcare providers are mostly using a symptomatic approach, meaning they treat the symptoms rather than target the virus, and provide supportive care (e.g. oxygen therapy, fluid management) for infected persons, which can be highly effective.
Origin of Human CoV Pandemic
In 2003 a SARS study group at Queen Mary Hospital, University of Hong Kong analysed case notes and microbiological findings for 50 patients with severe acute respiratory syndrome. They interpreted that a coronavirus which was isolated from patients with SARS might be the primary agent associated with this disease. https://www.ncbi.nlm.nih.gov/pubmed/12711465
SCoV-like viruses were isolated from Himalayan palm civets found in a live-animal market in Guangdong, China. Evidence of virus infection was also detected in other animals (including a raccoon dog, Nyctereutes procyonoides) and in humans working at the same market. All the animal isolates retain a 29-nucleotide sequence that is not found in most human isolates. https://www.ncbi.nlm.nih.gov/pubmed/12958366
Origin of novel Human CoV Pandemic
There have been many skeptical theories floating around. According to one, as written by vox (https://www.vox.com/2020/3/4/21156607/how-did-the-coronavirus-get-started-china-wuhan-lab) the virus was engineered in the lab by humans as a bioweapon or the virus being studied in the lab “escaped” or “leaked” because of poor safety protocol.
According to Chinese scientists and officials, the source of the SARS2 coronavirus is believed to be a “wet market” in Wuhan which sold both dead and live animals including fish and birds. They (including Lit Man Leo Poon himself) have issues a statement in The Lancet as “We stand together to strongly condemn conspiracy theories suggesting that COVID-19 does not have a natural origin, Conspiracy theories do nothing but create fear, rumours, and prejudice that jeopardise our global collaboration in the fight against this virus”.
https://www.thelancet.com/journals/lancet/article/PIIS0140-6736(20)30418-9/fulltext
Source of the Current CoV Outbreak
Officials from the Chinese Center for Disease Control and Prevention said they have successfully isolated the virus in samples taken from a seafood and wildlife market in Wuhan believed to be the source of the outbreak. Nearly three dozen of the samples taken from the market contained the nucleic acid of the coronavirus, and 31 of those samples were collected from the section of the market dedicated to the sale of wild animals, the Chinese CDC said.
The coronavirus that caused the 2003 SARS outbreak was traced to the civet cat, a wild animal considered a delicacy in parts of South China. (https://edition.cnn.com/2020/01/27/world/coronavirus-china-bans-wildlife-trade-trnd/index.html)
Author Note: COVID is caused by novel virus which still needs more research therefore this article suggests readers to explore given resources. Any Suggestions/corrections are welcome.
The article has been highly plagiarised and due references are given.
