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. 2013 Nov 14;49(10):899–908. doi: 10.1111/j.1348-0421.2005.tb03681.x

In Silico Analysis of ORF1ab in Coronavirus HKU1 Genome Reveals a Unique Putative Cleavage Site of Coronavirus HKU1 3C‐Like Protease

Patrick CY Woo 1,2,3,1, Yi Huang 1,1, Susanna KP Lau 1,2,3, Hoi‐wah Tsoi 1, Kwok‐yung Yuen 1,2,3,✉
PMCID: PMC7168382  PMID: 16237267

Abstract

Recently we have described the discovery and complete genome sequence of a novel coronavirus associated with pneumonia, coronavirus HKU1 (CoV‐HKU1). In this study, a detailed in silico analysis of the ORF1ab, encoding the 7,182‐amino acid replicase polyprotein in the CoV‐HKU1 genome showed that the replicase polyprotein of CoV‐HKU1 is cleaved by its papain‐like proteases and 3C‐like protease (3CLpro) into 16 polypeptides homologous to the corresponding polypeptides in other coronaviruses. Surprisingly, analysis of the putative cleavage sites of the 3CLpro revealed a unique putative cleavage site. In all known coronaviruses, the P1 positions at the cleavage sites of the 3CLpro are occupied by glutamine. This is also observed in CoV‐HKU1, except for one site at the junction between nsp10 (helicase) and nsp11 (member of exonuclease family), where the P1 position is occupied by histidine. This amino acid substitution is due to a single nucleotide mutation in the CoV‐HKU1 genome, CAG/A to CAT. This probably represents a novel cleavage site because the same mutation was consistently observed in CoV‐HKU1 sequences from multiple specimens of different patients; the P2 and P1′‐P12′ positions of this cleavage site are consistent between CoV‐HKU1 and other coronaviruses; and as the helicase is one of the most conserved proteins in coronaviruses, cleavage between nsp10 and nsp11 should be an essential step for the generation of the mature functional helicase. Experiments, including purification and C‐terminal amino acid sequencing of the CoV‐HKU1 helicase and trans‐cleavage assays of the CoV‐HKU1 3CLpro will confirm the presence of this novel cleavage site.

Keywords: coronavirus HKU1, ORF1ab, 3C‐like protease

Abbreviations

Appr>p

ADP‐ribose 1″,2″‐cyclic phosphate

Appr‐1″p

ADP‐ribose 1 ″‐phosphate

ADRP

ADP‐ribose 1″‐phosphatase

BCoV

bovine coronavirus

3CLpro

3C‐like protease

CoV‐HKU1

coronavirus HKU1

CPDase

cyclic nucleotide phosphodiesterase

E

envelope

ExoN

3′‐to‐5′ exonuclease

HCoV‐229E

human coronavirus 229E

HCoV‐NL63

human coronavirus NL63

HCoV‐OC43

human coronavirus OC43

IBV

infectious bronchitis virus

M

membrane

MHV

murine hepatitis virus

N

nucleocapsid

2′‐O‐MT

S‐adenosylmethionine‐dependent ribose 2′‐O‐methyltransferase

ORF

open reading frame

PLpro

papain‐like proteases

pol

RNA‐dependent RNA polymerase

RT‐PCR

reverse transcriptase polymerase chain reaction

S

spike

SARS

Severe Acute Respiratory Syndrome

SARS‐CoV

SARS coronavirus

XendoU

poly(U)‐specific endoribonuclease.

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