On the 24 th November 2021 the sequence of a new SARS CoV-2 viral isolate Omicron-B.1.1.529 was announced, containing far more mutations in Spike (S) than previously reported variants. Neutralization titres of Omicron by sera from vaccinees and convalescent subjects infected with early pandemic as well as Alpha, Beta, Gamma, Delta are substantially reduced or fail to neutralize. Titres against Omicron are boosted by third vaccine doses and are high in cases both vaccinated and infected by Delta. Mutations in Omicron knock out or substantially reduce neutralization by most of a large panel of potent monoclonal antibodies and antibodies under commercial development. Omicron S has structural changes from earlier viruses, combining mutations conferring tight binding to ACE2 to unleash evolution driven by immune escape, leading to a large number of mutations in the ACE2 binding site which rebalance receptor affinity to that of early pandemic viruses.

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Hepatitis C virus (HCV) is the major causative pathogen associated with liver cirrhosis and hepatocellular carcinoma. The virus has a positive-sense RNA genome encoding a single polyprotein with the virion components located in the N-terminal portion. During biosynthesis of the polyprotein, an internal signal sequence between the core protein and the envelope protein E1 targets the nascent polypeptide to the endoplasmic reticulum (ER) membrane for translocation of E1 into the ER. Following membrane insertion, the signal sequence is cleaved from E1 by signal peptidase. Here we provide evidence that after cleavage by signal peptidase, the signal peptide is further processed by the intramembrane-cleaving protease SPP that promotes the release of core protein from the ER membrane. Core protein is then free for subsequent trafficking to lipid droplets. This study represents an example of a potential role for intramembrane proteolysis in the maturation of a viral protein.

Cheung, M. C. M. et al. (2016) Outcomes after successful direct-acting antiviral therapy for patients with chronic hepatitis C and decompensated cirrhosis. Journal of Hepatology, 65(4), pp. 741-747. (doi:10.1016Hepatology, 65(4), pp. 741-747. (doi:10. /j.jhep.2016 This is the author's final accepted version.There may be differences between this version and the published version. You are advised to consult the publisher's version if you wish to cite from it.http://eprints.gla.ac.uk/123893/ There was no significant difference in liver cancer incidence (10/406 (2.5%) in months 6-15 and 17/406 (4%) in months 0-6 for treated patients vs 11/261 (4%) in untreated patients).2

Our previous DNA sequence comparisons of 3' terminal portions from equivalent herpes simplex virus type 1 (HSV-1) and HSV-2 genes identified a conserved sequence (consensus YGTGTTYY; Y = pyrimidine) located approximately 30bp downstream from the AATAAA signal. We report here that this signal is located downstream from 67% of the mammalian mRNA 3' termini examined. Using constructions with the bacterial chloramphenicol acetyl transferase (CAT) gene linked to an HSV 'terminator' fragment, we show that deletions in the 'terminator' reduce CAT activities and the levels of CAT mRNA 3' termini. Specifically: (1) deletions of downstream sequences which extend up to the consensus YGTGTTYY signal reduce CAT levels to values 35% of those obtained with undeleted plasmids, (2) a deletion of a further 14bp, which removes the YGTGTTYY consensus but not the poly A site, reduces CAT activities to 1%-4%. The levels of CAT mRNA 3' termini reflect the reductions in CAT activities however, levels of mRNA 5' termini are unaffected by these deletions. The RNA produced in the absence of the YGTGTTYY signal is present in the cytoplasm although no CAT activity is detectable.

Hepatitis C virus core protein forms the viral capsid and is targeted to lipid droplets (LDs) by its domain 2 (D2). By using a comparative analysis of two hepatitis C virus genomes (JFH1 and Jc1) differing in their level of virus production in cultured human hepatoma cells, we demonstrate that the core of the genotype 2a isolate J6 that is present in Jc1 mediates efficient assembly and release of infectious virions. Mapping studies identified a single amino acid residue in D2 as a major determinant for enhanced assembly and release of infectious Jc1 particles. Confocal microscopy analyses demonstrate that core protein in JFH1-replicating cells co-localizes perfectly with LDs and induces their accumulation in the perinuclear area, whereas no such accumulation of LDs and only a partial co-localization of core and LDs were found with the Jc1 genome. By using a fluorescence recovery after photobleaching assay, we found that green fluorescent protein-tagged D2 variants are mobile on LDs and that J6-and JFH1-D2 differ in their mobility. Taken together, our results demonstrate that the binding strength of the D2 domain of core for LDs is crucial for determining the efficiency of virus assembly. HCV3 infection is a major cause of chronic hepatitis, liver cirrhosis, and hepatocellular carcinoma. About 170 million individuals worldwide are currently infected with HCV (1). A protective vaccine does not exist to date, and the therapeutic options are still limited (2). HCV has been classified in the Hepacivirinae genus within the family Flaviviridae (3). The viral genome is a 9.6-kb plus-strand RNA, which encodes a polyprotein of about 3,000 amino acids in a single open reading frame flanked at the 5Ј and 3Ј ends by nontranslated regions (NTRs). The NTRs are required for RNA translation and replication (reviewed in Refs. 4 and 5). An internal ribosome entry site resides in the 5Ј NTR, which allows expression of the polyprotein. It is co-and post-translationally processed by cellular and viral proteases to yield the mature structural and nonstructural (NS) proteins. The structural proteins include the core protein, which forms the viral capsid, and the envelope glycoproteins E1 and E2. They are separated from the NS proteins by p7, which is assumed to be a viroporin. The NS proteins include the NS2-3 autoprotease, the NS3 serine protease, a nucleotide triphosphatase/RNA helicase located in the C-terminal two-thirds of NS3, the NS4A serine-protease cofactor, NS4B, which induces membrane alterations, the RNA binding protein NS5A, and the NS5B RNA-dependent RNA polymerase (reviewed in Refs. 4 -6).The HCV core protein is a highly basic, RNA-binding protein. It is 191 aa in length and consists of three distinct domains: an N-terminal hydrophilic domain 1 (D1) formed by the first 117 aa; a hydrophobic D2 directly C-terminal of D1 and reaching to about aa 169; and a highly hydrophobic domain 3 (D3) spanning the C-terminal 20 aa, which serves as the signal peptide of the C-terminal E1 protein (7,8). This immature form of core protein...

The core protein of hepatitis C virus (HCV) is believed to form the capsid shell of virus particles. Maturation of the protein is achieved through cleavage by host cell proteases to give a product of 21 000 MW, which is found in tissue culture systems and sera from infected individuals. However, efficient propagation of the virus is not possible at present in tissue culture. Hence, studies have focused on the properties of the core protein and its possible role in pathologies associated with HCV infection. This review describes key features of the polypeptide and the status of current knowledge on its ability to influence several cellular processes.

In infected cells, hepatitis C virus (HCV) core protein is targeted to lipid droplets, which serve as intracellular storage organelles. Using a tissue culture system to generate infectious HCV, we have shown that the coating of lipid droplets by the core protein occurs in a time-dependent manner and coincides with higher rates of virus production. At earlier times, the protein was located at punctate sites in close proximity to the edge of lipid droplets. Investigations by using Z-stack analysis have shown that many lipid droplets contained a single punctate site that could represent positions where core transfers from the endoplasmic reticulum membrane to droplets. The effects of lipid droplet association on virus production were studied by introducing mutations into the domain D2, the C-terminal region of the core protein necessary for droplet attachment. Alteration of a phenylalanine residue that was crucial for lipid droplet association generated an unstable form of the protein that could only be detected in the presence of a proteasome inhibitor. Moreover, converting two proline residues in D2 to alanines blocked coating of lipid droplets by core, although the protein was directed to punctate sites that were indistinguishable from those observed at early times for wild-type core protein. Neither of these virus mutants gave rise to virus progeny. By contrast, mutation at a cysteine residue positioned 2 aa upstream of the phenylalanine residue did not affect lipid droplet localization and produced wild-type levels of infectious progeny. Taken together, our findings indicate that lipid droplet association by core is connected to virus production. INTRODUCTIONChronic infection by hepatitis C virus (HCV) affects about 170 million individuals worldwide and is a major cause of liver disease (Hoofnagle, 2002). HCV is an enveloped virus belonging to the genus Hepacivirus within the family Flaviviridae (Murphy et al., 1995). The viral genome is a single-stranded, positive-sense RNA molecule approximately 9.6 kb in length that encodes a polyprotein of some 3000 aa. The polyprotein is cleaved both co-and post-translationally at the endoplasmic reticulum (ER) membrane by cellular and viral proteases to yield the mature viral proteins (Bartenschlager & Lohmann, 2000;Penin et al., 2004). The structural proteins are located at the N-terminal end of the polyprotein and consist of the core protein, which forms the viral capsid, and two envelope glycoproteins, E1 and E2. The glycoproteins are released from the polyprotein by signal peptidase (SP) cleavage, whereas maturation of the core protein requires proteolysis by both SP and signal peptide peptidase (SPP) (Hussy et al., 1996;McLauchlan et al., 2002).The mature form of core is a dimeric, a-helical protein that is separable into two domains, D1 and D2 (McLauchlan, 2000;Boulant et al., 2005Boulant et al., , 2006. D1 consists of the Nterminal 117 aa, while D2 begins at amino acid residue 118 and ends between amino acids 171 and 182. D2 is required for correct folding of D1 a...