SARS-CoV-2: Introduction, Classification, Variant, Pathogenicity, Lab Diagnosis, Treatment, and Prevention

Introduction of SARS-CoV-2

SARS-CoV-2 is a positive-sense single-stranded RNA virus that causes coronavirus disease 2019 ( COVID -19). SARS-CoV-2 stands for severe acute respiratory syndrome coronavirus 2. On March 11, 2020, the World Health Organization (WHO) characterized COVID-19 as a pandemic. On March 11, 2020, the World Health Organization (WHO) characterized COVID-19 as a pandemic.

Classification of SARS-CoV-2

Virus classification
(unranked): Virus
Realm: Riboviria
Kingdom: Orthornavirae
Phylum: Pisuviricota
Class: Pisoniviricetes
Order: Nidovirales
Family: Coronaviridae
Genus: Betacoronavirus
Subgenus: Sarbecovirus
Species: Severe acute respiratory syndrome-related coronavirus
Virus: Severe acute respiratory syndrome coronavirus 2

Variants of SARS-CoV-2

WHO Label	PANGOLIN Lineage	First Outbreak	Earliest Sample	Designated VOC	Notable Mutation
Alpha	B.1.1.7	UK	20 Sep 2020	18 Dec 2020	69–70del, N501Y, P681H
Beta	B.1.351	South Africa	May 2020	14 Jan 2021	K417N, E484K, N501Y
Gamma	P.1 (B.1.1.28.1)	Brazil	Nov 2020	15 Jan 2021	K417T, E484K, N501Y
Delta	B.1.617.2	India	Oct 2020	6 May 2021	L452R, T478K, P681R
Omicron	B.1.1.529	South Africa	9 Nov 2021	26 Nov 2021	P681H, N440K, N501Y, S477N, many others

Pathogenicity of SARS-CoV-2

SARS-CoV-2 causes COVID-19.

Incubation period for COVID-19

The incubation period is the time between exposure to a virus and the onset of symptoms.
With COVID-19, symptoms may show 2-14 days after exposure. CDC indicates that people are most contagious when they are the most symptomatic. Several studies show that people may be contagious before developing symptoms.

Symptoms of COVID-19

COVID-19 can cause mild to severe symptoms. The most common symptoms include:

• Fever
• Cough
• Shortness of breath
• Other symptoms may include:
• Sore throat
• Runny or stuffy nose
• Body aches
• Headache
• Chills
• Fatigue
• Gastrointestinal: diarrhea, nausea
• Loss of smell and taste

Laboratory Diagnosis of SARS-CoV-2

Specimens: It depends on the nature of the tests. For antigen, RT-PCR, and viral culture nasopharyngeal swabs, oropharyngeal swabs, and bronchoalveolar lavage (BAL) were used. In the case of antibody detection, blood is preferred.

Immunological assay: It is applied for antibody and antigen detection.SARS-CoV-2 antigen test: It works on the principle of immunochromatography. It is a very fast assay than the remaining RT-PCR and virus culture. The report can be generated within an hour. The SARS-CoV-2 Antigen Test is a screening test on asymptomatic persons to detect or exclude COVID-19 or to determine whether a person who previously was diagnosed with COVID-19 remains infectious. SARS-CoV-2 Antibodies test: SARS-CoV-2 Antibodies test is usually an indicator of passive infection since IgM could be detected 7 days post-symptom onset whereas for 14 days after illness that tells our previous infection with SARS-CoV-2. It is tested at the point of care (outside laboratories) or in higher throughput formats in laboratories. The beneficial points of the assay are easy to perform, has quick results (within 30 minutes), and is cheap than nucleic acid amplification testing (NAAT), e.g., RT-PCR assays.

Nucleic acid testing assay: Real-Time RT-PCR test detects active as well as inactive SARS-CoV-2 infection and therefore there is the significance of cycle threshold (Ct) values. A Ct less than 25 indicates a high viral load, Ct 25-30 medium viral load, and Ct greater than 30 low viral loads. This assay is highly sensitive and specific and it is also a gold standard test for diagnosing COVID-19.

Virus Culture: Virus culture is cumbersome and time is taken the method of diagnosis for SARS-CoV-2 since it also comes under high-risk group organisms. It needs an advanced setup of laboratory.

Treatment

There is no selective antiviral drug for the treatment of COVID-19 but optimal supportive care includes oxygen for severely ill patients and those who are at risk for severe disease and more advanced respiratory support such as ventilation for patients who are critically ill. Dexamethasone is a corticosteroid that can assist reduce the time length on a ventilator patient and save the lives of patients with severe and critical illnesses.

Prevention

COVID-19 spread can be minimized using the following points-

• Maintain a safe distance from others (at least 1 mere).
• Wear a mask in public, particularly indoors or when physical distancing is impossible.
• Choose open and well-ventilated spaces over closed ones.
• Hand cleaning should be followed on regular basis using soap and water, or an alcohol-based hand rub.
• Get vaccinated.
• Do not forget to cover your nose and mouth with your bent elbow or a tissue when you cough or sneeze.
• Take rest at home if you feel unwell.

Keynotes on SARS-CoV-2

• Omicron BA.2 subvariant is emerging and it is responsible for 51% of all positive Covid cases for the week ending March 19 in the USA.
• The sensitivity of antigen tests varies but is generally lower than most NAATs.
• Antigen test happens positive typically 1−3 days prior to the onset of symptoms and during the first 5−7 days after the onset of symptoms and is thus known as an early marker of lab diagnosis.
• The “gold standard” for clinical diagnostic detection of SARS-CoV-2 is nucleic-acid amplification tests(NAATs), such as reverse transcription PCR ( RT-PCR).

Bibliography

1. http://www.cdc.gov
2. http://www.osha.gov
3. http://www.who.int/en/
4. http://www.cdc.gov/NIOSH/
5. https://tools.niehs.nih.gov/wetp/index.cfm?id=2554
6. https://www.cnbc.com/2022/03/23/covid-omicron-bapoint2-subvariant-will-soon-dominate-in-us-but-fauci-doesnt-expect-another-surge.html