ArticlePDF Available

Genes of SARS-CoV-2 and emerging variants

April 2021
Microbiology Australia 42(1)

DOI:10.1071/MA21004

Authors:

Sudip Dhakal

The Commonwealth Scientific and Industrial Research Organisation

Ian G Macreadie

RMIT University

The pandemic caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) is distinctly different from outbreaks caused by other coronaviruses: SARS-CoV and Middle East respiratory syndrome coronavirus (MERS-CoV). The differences in the rapid transmission and severity of human coronaviruses are due to the genetic composition of the virus. SARS-CoV-2 contains genes encoding non-structural proteins (NSPs), structural proteins, and accessory proteins. The NSPs are mainly involved in replication of the virus within the host and inhibition of the host defence system. Structural proteins are involved in viral entry and attachment to host cells, preservation of the core virion and elicit the majority of the immune response. The functions of the accessory proteins are largely unknown. Most focus has been given to structural proteins, especially the spike protein as the strongest vaccine candidate. However, the recent emergence of spike variants and their ability to rapidly transmit and escape neutralisation by vaccine-induced antibodies has threatened the global community. Meanwhile, recent studies of accessory proteins reveal their importance in viral pathogenesis. Hence, proper understanding of the functions of all unknown viral proteins is crucial to devise alternate antiviral strategies.

Emerging SARS-CoV-2 variants of concern and their effect on viral pathogenesis.

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Genes of SARS-CoV-2 and emerging variants

Sudip Dhakal

and Ian Macreadie

A,B

School of Science, RMIT University, Bundoora, Vic. 3083, Australia.

Tel.: +61 402 564 308; Email: ian.macreadie@rmit.edu.au

Abstract. The pandemic caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) is distinctly different

from outbreaks caused by other coronaviruses: SARS-CoV and Middle East respiratory syndrome coronavirus (MERS-CoV).

The differences in the rapid transmission and severity of human coronaviruses are due to the genetic composition of the

virus. SARS-CoV-2 contains genes encoding non-structural proteins (NSPs), structural proteins, and accessory proteins.

The NSPs are mainly involved in replication of the virus within the host and inhibition of the host defence system. Structural

proteins are involved in viral entry and attachment to host cells, preservation of the core virion and elicit the majority of the

immune response. The functions of the accessory proteins are largely unknown. Most focus has been given to structural

proteins, especially the spike protein as the strongest vaccine candidate. However, the recent emergence of spike variants

and their ability to rapidly transmit and escape neutralisation by vaccine-induced antibodies has threatened the global

community. Meanwhile, recent studies of accessory proteins reveal their importance in viral pathogenesis. Hence, proper

understanding of the functions of all unknown viral proteins is crucial to devise alternate antiviral strategies.

Received 15 February 2021, accepted 24 February 2021, published online 9 April 2021

Introduction

The COVID-19 pandemic, caused by the member of Coronaviridae

family, Orthocoronavirinae subfamily, Betacoronavirus genus and

subgenus Sarbecovirus, has severely affected human lifestyles all

around the globe

. Owing to its high similarity to the severe acute

respiratory syndrome coronavirus (SARS-CoV), the virus was

named SARS-CoV-2. Disease caused by the virus varies from

asymptomatic to severe and frequently fatal pneumonia. Inadequate

measures to control the virus, combined with its high infectivity,

have had serious consequences for public health worldwide.

Genes of SARS-CoV-2

Coronaviruses are small, 80-220 nm diameter, enveloped, positive

sense, single-stranded RNA viruses that replicate within the

cytoplasm of host cells using the host endoplasmic reticulum and

Golgi network for processing of the proteins and assembly of the

virus

2,3

. The 30 kb genome sequence of the SARS-CoV-2 virus has

15 open reading frames (ORF) that encode nearly 29 proteins

(Figure 1)

2,4

. At the 50end of the viral genome are ORF1a and

ORF1b, encoding polyproteins that are proteolytically processed

into 16 non-structural proteins (NSP1 to NSP16). The non-structural

proteins play vital roles in creating a suitable environment for viral

invasion and replication by hijacking the host protein synthesis

machinery, inhibiting host mRNA expression and antiviral

defences

. Detailed descriptions of the functions of the majority of

the SARS-CoV-2 proteins are reviewed elsewhere

.Atthe3

0end are

13 ORFs that encode four structural proteins (spike protein (S),

envelope protein (E), nucleocapsid protein (N) and membrane

protein (M)) and nine accessory proteins. Among the structural

proteins, the trimeric S protein (composed of two subunits S1 and

S2) is crucial for allowing viral attachment. It interacts with the host

cell angiotensin converting enzyme 2 (ACE2) receptor via a receptor

binding domain (RBD) present in the S1 subunit allowing the viral

attachment to host cells and aiding in the fusion of the membrane via

S2 subunit

. Importantly the S protein is also the major viral protein

eliciting both humoral and cell-mediated immune responses, making

it an excellent vaccine candidate

. However, mutations in the S

protein pose a signiﬁcant threat by possible generation of mutant

strains with the potential to escape antibody neutralisation, thus

rendering the current vaccine strategy less effective

7–10

Emerging variants of concern

Several lineages of variants have emerged since the ﬁrst case in

Wuhan, China in December 2019, posing greater risks to the global

community due to speciﬁc mutations in their spike proteins, causing

the strains to become more virulent and resistant to neutralising

antibodies

. The most striking ones are those with mutations at the

MICROBIOLOGY AUSTRALIA, 2021

https://doi.org/10.1071/MA21004

In Focus

The Authors 2021 Open Access CC BY, published (by CSIRO Publishing) on behalf of the ASM A

receptor binding domains, which not only alter the interaction of the

spike proteins with the ACE2 receptor but also reduce afﬁnity

towards human neutralising antibodies (refer to Table 1). Examples of

such variants are the UK variant (B.1.1.7), South African variant

(B.1.351) and the Brazilian variant (P.1), that are currently emerging

as increased threats worldwide.

Future directions

Among the various mutations in new variants of SARS-CoV-2, the

spike mutations K417N, E484K, N501Y, N501T and D614G appear

crucial for determining critical alterations in viral behaviour. Muta-

tions that occur in the RBDs of spike proteins cause serious concerns

as current vaccination strategies are based on the original spike

protein. Currently, there are no antiviral agents that can effectively

inhibit SARS-CoV-2 replication in humans

. Considering these

limitations, it is of utmost importance to explore new ways towards

ﬁnding strategies to reduce viral proliferation. Some NSPs, non-

spike structural proteins and accessory proteins could be investigat-

ed as these proteins are involved in important steps of viral repli-

cation and pathogenesis such as viral protein synthesis, hijacking

host protein synthesis machinery and inhibiting intracellular host

defence mechanisms

. Some such protein targets are NSP1 (inhibits

host mRNA translation), NSP3 (papain like protease that releases

NSP1, NSP2 and NSP3 from viral polyprotein), NSP5 (main pro-

tease that cleaves viral polyproteins into individual functional

proteins), NSP6 (prevents host autophagosome-lysosome fusion)

and N-protein (preserves viral RNA from interfering RNAs from

host).

The functions of the accessory proteins of SARS-CoV-2 are

largely unknown and further investigations uncovering their role

may shed light on the unanswered questions of rapid spread and

differences in disease severity of SARS-CoV-2. Several accessory

proteins are been investigated for their role during viral invasion. In

a recent study comparison of the proteins encoded by SARS-CoV-2

with the proteins of SARS-CoV revealed the presence of novel

ORF8 and ORF10 proteins in SARS-CoV-2. Structural analysis of

ORF8 protein supported the claim that the protein can form unique

large-scale assemblies that are not present in SARS-CoV, potentially

inhibiting the host defence system

. Additionally, association of

ORF8 deletion variant (D382 variant) with milder disease outcome

strongly supports the importance of ORF8 protein as a therapeutic

target against SARS-CoV-2

. Meanwhile, ORF10 is the only

protein that is not present in other human coronaviruses and is yet

to be studied. Nucleotide sequences similar to ORF10 were found in

SARS-CoV but with a nonsense mutation, causing early termination

of protein synthesis

. Further analysis of the predicted structure of

the ORF10 protein showed a signal peptide and a hydrophobic

Figure 1. Schematic diagram showing genome of SARS-CoV-2. Green coloured genes encode polyproteins that are proteolytically cleaved into non-

structural proteins (NSP), red coloured genes encoding structural proteins and blue coloured genes encoding accessory proteins.

Table 1. Emerging SARS-CoV-2 variants of concern and their effect on viral pathogenesis.

Emerging variants Lineage Spike protein mutation Viral pathogenesis of variant Reference

South African variant 20H/501Y.V2 or

B.1.351

L18F, D80A, D215G, R246I, K417N, E484K, N501Y,

D614G, A701V

Increased infectivity and escape from

human neutralising antibodies

9,10

Potential deletion at L242_L244 or mutation L242H

Italian variant MB61 K182N, Q493K, N501T, D614G Alteration in ACE2 binding and escape

from vaccine induced or natural

neutralising antibodies

L242 deletion

UK variant 20I/501Y.V1, VOC

202012/01, or

B.1.1.7

N501Y, A570D, P681H, T716I, S982A, D1118H Increased transmissibility, disease

severity

8,13

Y144 deletion, H69_V70 deletion

Brazilian variant P.1 or 20J/501Y.V3) L18F, T20N, P26S, D138Y, R190S, K417T, E484K, N501Y,

H655Y, T1027I

Alteration in ACE2 interaction and

human antibody; increased resistance

to neutralising antibodies

8,14

In Focus

BMICROBIOLOGY AUSTRALIA *2021

b-sheet region beyond the cleavage site, suggesting a possible

hydrophobic interaction and membrane localisation, maybe as trans-

port protein. These ﬁndings suggest ORF10 protein’s possible role in

viral invasion, which needs to be explored further

Other accessory proteins differ in their effect and activity despite

a high similarity in protein sequence alignment. A recent study

comparing the ability of ORF3a proteins of SARS-CoV-2 and

SARS-CoV to induce apoptosis showed reduced induction of cell

death by SARS-CoV-2 protein

. These differences in the viral

proteins could explain the differences in the severity of the

SARS-CoV-2 and SARS-CoV. Further research and new insights

in the potential role of accessory proteins during viral invasion could

indicate novel ways to reduce the infectivity, rapid spread and boost

host immune system. Such studies will not only lead to therapeutic

strategies against SARS-CoV-2 virus, but also be useful for similar

viral infections including SARS-CoV and MERS-CoV infections.

Conﬂicts of interest

Ian Macreadie is the Editor-in-Chief of Microbiology Australia but

was blinded from the peer-review process for this paper.

Acknowledgements

This research did not receive any speciﬁc funding.

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Biographies

Sudip Dhakal is a PhD candidate at

School of Science, RMIT University

under Biosciences discipline, whose

research focuses on overcoming reduced

proteostasis in Alzheimer’s disease.

Ian Macreadie is an Honorary Professor

at RMIT University and Editor-in-Chief

of Microbiology Australia. His research

and expertise are in diverse ﬁelds of bios-

ciences ranging from industrial microbi-

ology to biomedical research.

In Focus

MICROBIOLOGY AUSTRALIA *2021 C

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