coronavirus - An overview about basic

INTRODUCTION

 Coronaviruses are a group of related RNA viruses that cause diseases in mammals and birds. In humans, these viruses cause respiratory tract infections that can range from mild to lethal. Mild illnesses include some cases of the common cold (which is caused also by certain other viruses, predominantly rhinoviruses), while more lethal varieties can cause SARS, MERS, and COVID-19. 

Symptoms in other species vary: in chickens, they cause an upper respiratory tract disease, while in cows and pigs they cause diarrhea. 

There are as yet no vaccines or antiviral drugs to prevent or treat human coronavirus infections.

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CORONAVIRUS GENETICS 

The typical generic coronavirus genome is a single strand of RNA, 32 kilobases long, and is the largest known RNA virus genome. 

Coronaviruses have the highest known frequency of recombination of any positive-strand RNA virus, promiscuously combining genetic information from different sources when a host is infected with multiple coronaviruses. 

These viruses mutate and change at a high rate, which can create havoc for both diagnostic detection as well as therapy (and vaccine) regimens.

 Coronaviruses have an unusual replication process, which involves a 2-step replication mechanism. 
Many RNA virus genomes contain a single open reading frame (ORF) which is then translated as a single polyprotein that is then catalytically cleaved into smaller functional viral proteins, but coronaviruses can contain up to 10 separate ORFs. 

Most ribosomes translate the biggest one of these ORFs, called replicase, which alone is twice the size of many other RNA viral genomes. 

The replicase gene encodes a series of enzymes that use the rest of the genome as a template to produce a set of smaller, overlapping messenger RNA molecules, which are then translated into the structural proteins

VIRUS CLASSIFICATION 

Realm: Riboviria

Kingdom:Orthornavirae

Phylum:Pisuviricota

Class:Pisoniviricetes

Order:Nidovirales

Family:Coronaviridae

Subfamily:Orthocoronavirinae

STRUCTURE

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Photo credit : nature.com

LIFE CYCLE

Photo credit : https://doi.org/10.1016/j.jare.2020.03.005

TYPES

• Common human coronaviruses
• 229E (alpha coronavirus)
• NL63 (alpha coronavirus)
• OC43 (beta coronavirus)
• HKU1 (beta coronavirus)

• Other human coronaviruses
• 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 causes coronavirus disease 2019, or COVID-19)

SYMPTOMS 

• Most common symptoms:
• fever
• dry cough
• tiredness

• Less common symptoms:
• aches and pains
• sore throat
• diarrhoea
• conjunctivitis
• headache
• loss of taste or smell
• a rash on skin, or discolouration of fingers or toes

• Serious symptoms:
• difficulty breathing or shortness of breath
• chest pain or pressure
• loss of speech or movement

DIAGNOSIS :

SPECIMEN COLLECTION:

Test : NAAT (Nucleic acid amplification tests) 

Type of sample:

•  Lower respiratory tract 
• sputum 
• aspirate 
• lavage 

• Upper respiratory tract 
•  nasopharyngeal and 
• oropharyngeal swabs 
• nasopharyngeal wash/nasopharyngeal aspirate 

Consider stools, whole blood, urine, and if diseased, material from autopsy

Timing:Collect on presentation. 

Possibly repeated sampling to monitor clearance. 

Further research needed to determine effectiveness 

and reliability of repeated sampling. 

Test : Serology

Type of sample: Serum for serological testing once validated and available 

Timing: Paired samples are necessary for confirmation with the initial sample collected in the first week of illness and the second ideally collected 2-4 weeks later (optimal timing for convalescent sample needs to be established). 

The above 2 samples taken from patient

Test: NAAT 

Type of sample: Nasopharyngeal and 

oropharyngeal swabs 

Timing: Within incubation period of last documented contact.

Test: Serology 

Type of sample : Serum for serological testing

Timing: Baseline serum taken as early as possible within incubation period of contact and convalescent serum taken 2-4 weeks after last contact (optimal timing for convalescent sample needs to be established).

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LABORATORY TESTING

• Nucleic acid amplification tests (NAAT) for COVID-19 virus 

Routine confirmation of cases of COVID-19 is 

based on detection of unique sequences of virus 

RNA by NAAT such as real-time reverse-

transcription polymerase chain reaction (rRT-PCR) 

with confirmation by nucleic acid sequencing when 

necessary. The viral genes targeted so far include the N, E, S and RdRP genes. 

• Serological testing 

Serological surveys can aid investigation of an 

ongoing outbreak and retrospective assessment of 

the attack rate or extent of an outbreak.

• Viral sequencing 

In addition to providing confirmation of the 

presence of the virus, regular sequencing of a 

percentage of specimens from clinical cases can be 

useful to monitor for viral genome mutations that might affect the performance of medical countermeasures, including diagnostic tests.

• Viral culture 

Virus isolation is not recommended. 

TREATMENT

To date, there are no specific vaccines or medicines for COVID-19. 

• Self-care

If you feel sick you should rest, drink plenty of fluid, and eat nutritious food. Stay in a separate room from other family members, and use a dedicated bathroom if possible. Clean and disinfect frequently touched surfaces.

• Medical treatments

If you have mild symptoms and are otherwise healthy, self-isolate and contact your medical provider or a COVID-19 information line for advice.

PREVENTION

• Clean your hands often. Use soap and water, or an alcohol-based hand rub.
• Maintain a safe distance from anyone who is coughing or sneezing.
• Don’t touch your eyes, nose or mouth.
• Cover your nose and mouth with your bent elbow or a tissue when you cough or sneeze.
• Stay home if you feel unwell.
• If you have a fever, cough and difficulty breathing, seek medical attention. Call in advance.
• Follow the directions of your local health authority. 

REFERENCES:

WIKIPEDIA 

WHO novel corona virus websitehttps://www.who.int/emergencies/diseases/novel-coronavirus-2019 

www.cdc.gov.in

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