With input from Dr Monica Vasudev

1079:  Update on Covid-19

IMA-CMAAO Webinar on “Understanding the molecular biology of coronavirus proteins”

5^th September, 2020, 4-5pm

Participants: Dr KK Aggarwal, President CMAAO, Dr RV Asokan, Hony Secretary General IMA, Dr Ramesh K Datta, Hony Finance Secretary IMA, Dr Jayakrishnan Alapet, Dr S Sharma

Faculty: Dr Pavithra Venkatagopalan, PhD Coronavirus studies, Director, Care Health Diagnostic Center, Chennai

Key points from the discussion

• Life has three main domains: Bacteria and Archaea, which are single-celled; everything else - from yeast to humans - comes under Eukarya.
• Viruses have their own domain. A virus is neither living nor dead; it is an obligate intracellular parasite.
• All cells in the domain of life carry DNA (genetic information), which make mRNA (instructions for forming a protein from a gene) via transcription. This information is translated to form proteins.
• DNA viruses can be either double- or single-stranded; double-stranded can be enveloped or unenveloped.
• RNA viruses (coronaviruses) have no DNA in their entire life cycle.
• Coronaviruses are classified under order Nidovirales and family Coronaviridae. The viruses under this order typically infect humans and animals, so they are typically considered zoonotic viruses. Bats are a common reservoir (Nipah, rabies, etc.)
• They mainly cause respiratory and enteric infections. About 30% of all common colds are caused by Coronaviruses.
• Coronaviruses are divided into three classes: alpha, beta (COVID) and gamma. Genetic sequencing has been identified - COVID-19 virus as being very close to bat coronaviruses.
• The virus has four structural proteins (spike, membrane, envelope and nucleocapsid) and one RNA (viral genome).
• The S protein has two domains (N terminal and C terminal); the N terminal is the exposed part and binds to the ACE2 receptors. The C terminal causes change in the viral envelope structure so that it fuses with the cellular envelope, thereby releasing virus RNA into the cell.
• After infection occurs, the S protein downregulates the expression of ACE2 receptors and promotes lung injury, resulting in respiratory distress.
• The virus lifecycle is entirely in the cytoplasm. The viral genome resembles cell mRNA so the cell recognizes it as its own and starts making mRNA. RdRP (RNA-dependent RNA-polymerase) will make more copies of the genome. And, the cellular translation machinery will make all the viral proteins.
• RdRP is the target for antivirals (remdesivir).
• The coronavirus is a single stranded, positive sense ~30kb RNA genome virus.
• Functions of coronavirus proteins: The function of ORF 1ab-15 nonstructural protein is virus replication, proof reading and suppression of cellular immunity. The spike protein enables receptor binding and entry into the cell and initiates infection. ORF3 causes virus release, envelope protein is responsible for virus assembly, and the membrane protein (most abundant of the viral protein) forms and stabilizes the viral envelope. ORF 6, 7a, 7b, 8a, 8b, 9b suppress cellular immunity and help virus release.  The Nsp 3 protein counteracts host innate immunity, while Nsp 4, 6 and Nsp 7-10 are involved in the replication of the genome. Nsp 16 is involved in proof reading. N proteins increase interferon resistance to cell.
• RT PCR detects ORF 1ab and E proteins to see if full genome replication is taking place.
• Proteins are synthesized in the endoplasmic reticulum and the assembly takes place in ERGIC (ER-Golgi intermediate compartment) and then the virus is released from the cell.
• Testing is relevant as we want to see active virus replication. It checks the entire genome. Whatever gene you test, they should be spaced apart.
• Most labs have cut off value of 40 cycles; New York Public health system says this has to be higher as otherwise asymptomatic cases can be missed.
• Worsening infection does not mean lower Ct value.

Dr KK Aggarwal

President CMAAO, HCFI and Past National President IMA