Table 1.

Genes encoded by SARS-CoV-2 and their known or predicted functions.

Sl. No.	ORF/Protein Name	Type of protein	Gene size (in bp)	Role of the protein in viral replication and assembly	Role of the protein in host-poathogen interactions	The features that are unique to SARS-CoV-2 if any	Reference
1	ORF1a (codes for 16 nsps)	Non-structural	13218	Associated with gene expression/regulation, proteases involved in cleaving viral polyproteins, membrane rearrangement, RNA polymerase activities, proteins involved in viral replication (helicases, methyltransferases, exonucleases, etc.)	Involved in repression of host gene expression, disruption of host cell responses, dysregulation of autophagy.	NA	(52)
2	S (Spike protein)	Structural	3822	Helps in entry to host cells	Binds with ACE2 to gain entry into human cells. One of the most immunogenic viral antigens.	A furin cleavage site. A key protein being targeted for vaccine development. It carries several non-synonymous mutations in the RBD region and some in the hinge region. Collectively several mutations are predicted to enhnace binding of S protein with hACE2.	(53–55)
3	E (Envelope protein)	Structural	228	Participates in viral assembly, budding, envelope formation and pathogenesis	Interacts with several host cell proteins such as PALS1 disrupting tight junctions of epithelial cells and promotes viral spread. Also affects host cellular activities by interfering with endoplasmic reticulum (ER), Golgi and ER-Golgi intermediate compartment	Carries several non-synonymouos mutations which could play a role in enhanced viral pathogenesis; e.g., The changes resulted in Ser (56), Phe (57), Arg (58) and the C-terminal end (DLLV:72-75) are speculated to improve E protein interaction with tight junction-associated PALS1 which could play a critical role in SARS-CoV-2 pathogenesis and viral spread	(59–62)
4	M (Membrane protein)	Structural	669	Role in cell attachment and entry, viral particle assembly, and budding	Interacts with host cell proteins. Inhibits the production of type I interferon by blocking the formation of TRAF3.TANK,TBK1/IKKepsilon complex	Carries several non-synonymouos mutations which could play a role in viral pathogenesis.	(63)
	N (Nucleo-capsid)	Structural	1260	Protectis the genomic RNA of the virus, interacts with the M protein durin virion assembly and helps in viral transcription and assembly and budding.	Highly immunogenic, recognized as antigen in hosts. Associates with the host ER-Gologi complex. Modulates host cell cycle by regulating cyclin and cyclin-dependent kinase activities resulting in cell cycle arrest in S phase. Interacts with host translation elongation factor 1α (EF1α), suppressing host mRNA translation. Intereferes with interferon type I production and signaling. Antogonizes host anitviral RNAi responses.	Carries multiple non-synonymous mutataions. Some of these mutations might create a unique potential RNA binding pocket.	(64–66)
5	ORF6	Accessory	186	Role in  viral pathogenesis.	Localizes at the nuclear pore complex and inhibits nuclear translocation of STAT1, antagonizing IFN-I signaling. Interacts with host cell proteins.	Not known yet	(67, 68)
6	ORF7a	Accessory	366	Not known yet, although it is under selective pressure with a possible role in host-switiching.	Interacts with host cell proteins and speculated to facilitate viral growth and replication. It is primarily localized to Gologi apparatus and also found on host cell surface. It interacts with Bcl-XL protein and induces apoptosis via caspase-dependent pathway. Inhibits antiviral mechanisms by inhibiting glycosylation of host protein BST-2 (also known as CD317)	Not known yet	(69, 70)
7	ORF7b	Accessory	132	Not known yet	Interacts with host cell proteins and speculated to facilitate viral growth and replication. Localized yo Gologi apparatus. Possseses leucine zipper motif with a potential to interfere with the functin of host cellular proteins which employ similar motifs.	Not known yet	(71)
8	ORF8	Accessory	366	Not known yet	It has ER-localization signal. Within the lumen of ER, it interacts with a vareity of host proteins and involved in inactivation of IFN-I signalling. It is presumably secreted out of host cells. ORF8 antibodies are one of the principal markers of SARS-CoV-2 infection.	SARS-CoV-2 has single ORF8 protein while SARS-CoV has ORF 8a and ORF 8b. It shares less than 20% similarity with SARS-CoV ORF8 sequences. Downregulates MHC-I in cells.	(72, 73)