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Journal articles on the topic 'ORF8 accessory gene'

Author: Grafiati

Published: 4 June 2025

Last updated: 1 August 2025

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1

Pereira, Filipe. "Evolutionary dynamics of the SARS-CoV-2 ORF8 accessory gene." Infection, Genetics and Evolution 85 (November 2020): 104525. http://dx.doi.org/10.1016/j.meegid.2020.104525.

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2

Tabibzadeh, Alireza, Mohammad Hadi Karbalaie Niya, Hossein Keyvani, et al. "A survey of ORF8 sequence and immunoinformatics features during alpha, delta, and wild type peaks of the SARS-CoV-2 pandemic in Iran." Malawi Medical Journal 35, no. 2 (2023): 101–5. http://dx.doi.org/10.4314/mmj.v35i2.5.

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BackgroundThe Coronavirus disease 2019 (COVID-19) pandemic influences all around the world. The SARS-CoV-2 ORF8 accessory gene represents multiple functions in virus-host interaction. The current study aimed to compare the ORF8 substitutions and epitope features of these substitutions in the various SARS-CoV-2 outbreaks including delta, alpha, and wild type variants in Iran from 2020 to 2022. In addition, we evaluate B cell, HLA I and II epitopes, by in-silico approach to ORF8 binding site prediction.MethodsThe samples were collected from patients diagnosed with SARS-CoV-2 infection via a real

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3

Wang, Ning, Chuming Luo, Haizhou Liu, et al. "Characterization of a New Member of Alphacoronavirus with Unique Genomic Features in Rhinolophus Bats." Viruses 11, no. 4 (2019): 379. http://dx.doi.org/10.3390/v11040379.

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Bats have been identified as a natural reservoir of a variety of coronaviruses (CoVs). Several of them have caused diseases in humans and domestic animals by interspecies transmission. Considering the diversity of bat coronaviruses, bat species and populations, we expect to discover more bat CoVs through virus surveillance. In this study, we described a new member of alphaCoV (BtCoV/Rh/YN2012) in bats with unique genome features. Unique accessory genes, ORF4a and ORF4b were found between the spike gene and the envelope gene, while ORF8 gene was found downstream of the nucleocapsid gene. All th

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4

Wang, Ning, Chuming Luo, Haizhou Liu, et al. "Characterization of a New Member of Alphacoronavirus with Unique Genomic Features in Rhinolophus Bats." Viruses 11, no. 4 (2019): 379. https://doi.org/10.5281/zenodo.13508473.

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(Uploaded by Plazi for the Bat Literature Project) Bats have been identified as a natural reservoir of a variety of coronaviruses (CoVs). Several of them have caused diseases in humans and domestic animals by interspecies transmission. Considering the diversity of bat coronaviruses, bat species and populations, we expect to discover more bat CoVs through virus surveillance. In this study, we described a new member of alphaCoV (BtCoV/Rh/YN2012) in bats with unique genome features. Unique accessory genes, ORF4a and ORF4b were found between the spike gene and the envelope gene, while ORF8 gene wa

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5

Wang, Ning, Chuming Luo, Haizhou Liu, et al. "Characterization of a New Member of Alphacoronavirus with Unique Genomic Features in Rhinolophus Bats." Viruses 11, no. 4 (2019): 379. https://doi.org/10.5281/zenodo.13508473.

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Abstract:

(Uploaded by Plazi for the Bat Literature Project) Bats have been identified as a natural reservoir of a variety of coronaviruses (CoVs). Several of them have caused diseases in humans and domestic animals by interspecies transmission. Considering the diversity of bat coronaviruses, bat species and populations, we expect to discover more bat CoVs through virus surveillance. In this study, we described a new member of alphaCoV (BtCoV/Rh/YN2012) in bats with unique genome features. Unique accessory genes, ORF4a and ORF4b were found between the spike gene and the envelope gene, while ORF8 gene wa

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6

Wang, Ning, Chuming Luo, Haizhou Liu, et al. "Characterization of a New Member of Alphacoronavirus with Unique Genomic Features in Rhinolophus Bats." Viruses 11, no. 4 (2019): 379. https://doi.org/10.5281/zenodo.13508473.

Full text

Abstract:

(Uploaded by Plazi for the Bat Literature Project) Bats have been identified as a natural reservoir of a variety of coronaviruses (CoVs). Several of them have caused diseases in humans and domestic animals by interspecies transmission. Considering the diversity of bat coronaviruses, bat species and populations, we expect to discover more bat CoVs through virus surveillance. In this study, we described a new member of alphaCoV (BtCoV/Rh/YN2012) in bats with unique genome features. Unique accessory genes, ORF4a and ORF4b were found between the spike gene and the envelope gene, while ORF8 gene wa

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7

Wang, Ning, Chuming Luo, Haizhou Liu, et al. "Characterization of a New Member of Alphacoronavirus with Unique Genomic Features in Rhinolophus Bats." Viruses 11, no. 4 (2019): 379. https://doi.org/10.5281/zenodo.13508473.

Full text

Abstract:

(Uploaded by Plazi for the Bat Literature Project) Bats have been identified as a natural reservoir of a variety of coronaviruses (CoVs). Several of them have caused diseases in humans and domestic animals by interspecies transmission. Considering the diversity of bat coronaviruses, bat species and populations, we expect to discover more bat CoVs through virus surveillance. In this study, we described a new member of alphaCoV (BtCoV/Rh/YN2012) in bats with unique genome features. Unique accessory genes, ORF4a and ORF4b were found between the spike gene and the envelope gene, while ORF8 gene wa

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8

Lo, Van Thi, Sun Woo Yoon, Yong Gun Choi, Dae Gwin Jeong, and Hye Kwon Kim. "Genomic Comparisons of Alphacoronaviruses and Betacoronaviruses from Korean Bats." Viruses 14, no. 7 (2022): 1389. http://dx.doi.org/10.3390/v14071389.

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Coronaviruses are well known as a diverse family of viruses that affect a wide range of hosts. Since the outbreak of severe acute respiratory syndrome, a variety of bat-associated coronaviruses have been identified in many countries. However, they do not represent all the specific geographic locations of their hosts. In this study, full-length genomes representing newly identified bat coronaviruses in South Korea were obtained using an RNA sequencing approach. The analysis, based on genome structure, conserved replicase domains, spike gene, and nucleocapsid genes revealed that bat Alphacoronav

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9

Lo, Van Thi, Sun Woo Yoon, Yong Gun Choi, Dae Gwin Jeong, and Hye Kwon Kim. "Genomic Comparisons of Alphacoronaviruses and Betacoronaviruses from Korean Bats." Viruses 14, no. 7 (2022): 1389. https://doi.org/10.5281/zenodo.13445916.

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(Uploaded by Plazi for the Bat Literature Project) Coronaviruses are well known as a diverse family of viruses that affect a wide range of hosts. Since the outbreak of severe acute respiratory syndrome, a variety of bat-associated coronaviruses have been identified in many countries. However, they do not represent all the specific geographic locations of their hosts. In this study, full-length genomes representing newly identified bat coronaviruses in South Korea were obtained using an RNA sequencing approach. The analysis, based on genome structure, conserved replicase domains, spike gene, an

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10

Lo, Van Thi, Sun Woo Yoon, Yong Gun Choi, Dae Gwin Jeong, and Hye Kwon Kim. "Genomic Comparisons of Alphacoronaviruses and Betacoronaviruses from Korean Bats." Viruses 14, no. 7 (2022): 1389. https://doi.org/10.5281/zenodo.13445916.

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Abstract:

(Uploaded by Plazi for the Bat Literature Project) Coronaviruses are well known as a diverse family of viruses that affect a wide range of hosts. Since the outbreak of severe acute respiratory syndrome, a variety of bat-associated coronaviruses have been identified in many countries. However, they do not represent all the specific geographic locations of their hosts. In this study, full-length genomes representing newly identified bat coronaviruses in South Korea were obtained using an RNA sequencing approach. The analysis, based on genome structure, conserved replicase domains, spike gene, an

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11

Lo, Van Thi, Sun Woo Yoon, Yong Gun Choi, Dae Gwin Jeong, and Hye Kwon Kim. "Genomic Comparisons of Alphacoronaviruses and Betacoronaviruses from Korean Bats." Viruses 14, no. 7 (2022): 1389. https://doi.org/10.5281/zenodo.13445916.

Full text

Abstract:

(Uploaded by Plazi for the Bat Literature Project) Coronaviruses are well known as a diverse family of viruses that affect a wide range of hosts. Since the outbreak of severe acute respiratory syndrome, a variety of bat-associated coronaviruses have been identified in many countries. However, they do not represent all the specific geographic locations of their hosts. In this study, full-length genomes representing newly identified bat coronaviruses in South Korea were obtained using an RNA sequencing approach. The analysis, based on genome structure, conserved replicase domains, spike gene, an

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12

Lo, Van Thi, Sun Woo Yoon, Yong Gun Choi, Dae Gwin Jeong, and Hye Kwon Kim. "Genomic Comparisons of Alphacoronaviruses and Betacoronaviruses from Korean Bats." Viruses 14, no. 7 (2022): 1389. https://doi.org/10.5281/zenodo.13445916.

Full text

Abstract:

(Uploaded by Plazi for the Bat Literature Project) Coronaviruses are well known as a diverse family of viruses that affect a wide range of hosts. Since the outbreak of severe acute respiratory syndrome, a variety of bat-associated coronaviruses have been identified in many countries. However, they do not represent all the specific geographic locations of their hosts. In this study, full-length genomes representing newly identified bat coronaviruses in South Korea were obtained using an RNA sequencing approach. The analysis, based on genome structure, conserved replicase domains, spike gene, an

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13

Lo, Van Thi, Sun Woo Yoon, Yong Gun Choi, Dae Gwin Jeong, and Hye Kwon Kim. "Genomic Comparisons of Alphacoronaviruses and Betacoronaviruses from Korean Bats." Viruses 14, no. 7 (2022): 1389. https://doi.org/10.5281/zenodo.13445916.

Full text

Abstract:

(Uploaded by Plazi for the Bat Literature Project) Coronaviruses are well known as a diverse family of viruses that affect a wide range of hosts. Since the outbreak of severe acute respiratory syndrome, a variety of bat-associated coronaviruses have been identified in many countries. However, they do not represent all the specific geographic locations of their hosts. In this study, full-length genomes representing newly identified bat coronaviruses in South Korea were obtained using an RNA sequencing approach. The analysis, based on genome structure, conserved replicase domains, spike gene, an

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14

LaPierre, Lorie A., Donald L. Holzschu, Paul R. Bowser, and James W. Casey. "Sequence and Transcriptional Analyses of the Fish Retroviruses Walleye Epidermal Hyperplasia Virus Types 1 and 2: Evidence for a Gene Duplication." Journal of Virology 73, no. 11 (1999): 9393–403. http://dx.doi.org/10.1128/jvi.73.11.9393-9403.1999.

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ABSTRACT Walleye epidermal hyperplasia virus types 1 and 2 (WEHV1 and WEHV2, respectively) are associated with a hyperproliferative skin lesion on walleyes that appears and regresses seasonally. We have determined the complete nucleotide sequences and transcriptional profiles of these viruses. WEHV1 and WEHV2 are large, complex retroviruses of 12,999 and 13,125 kb in length, respectively, that are closely related to one another and to walleye dermal sarcoma virus (WDSV). These walleye retroviruses contain three open reading frames, orfA,orfB, and orfC, in addition togag, pol, and env. orfA and

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15

Zhang, Z., and D. Martineau. "Walleye Dermal Sarcoma Virus: OrfA N-Terminal End Inhibits the Activity of a Reporter Gene Directed by Eukaryotic Promoters and Has a Negative Effect on the Growth of Fish and Mammalian Cells." Journal of Virology 73, no. 10 (1999): 8884–89. http://dx.doi.org/10.1128/jvi.73.10.8884-8889.1999.

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ABSTRACT Walleye dermal sarcoma virus (WDSV) is a fish retrovirus causing a skin tumor termed walleye dermal sarcoma, which develops and regresses on a seasonal basis. The WDSV genome contains three short open reading frames designated orfA, orfB, andorfC in addition to the viral structural genes,gag, pol, and env. orfAand orfB transcripts are detected in tumors by reverse transcription-PCR. Recently, OrfA, whose amino acid sequence is similar to that of cyclins A and D, has been shown to complement a cyclin-deficient yeast strain. We report that expression of the accessory gene orfA inhibited

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16

Wu, Hui, Su Bu, Peter Newell, Qiang Chen, and Paula Fives-Taylor. "Two Gene Determinants Are Differentially Involved in the Biogenesis of Fap1 Precursors in Streptococcus parasanguis." Journal of Bacteriology 189, no. 4 (2006): 1390–98. http://dx.doi.org/10.1128/jb.00836-06.

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ABSTRACT Mature Fap1, a 200-kDa fimbria-associated adhesin, is required for fimbrial biogenesis and biofilm formation in Streptococcus parasanguis. Fap1-like proteins are found in the genomes of many streptococcal and staphylococcal species. Fap1 is a serine-rich glycoprotein modified by O-linked glycan moieties. In this study, we identified a seven-gene cluster including secY2, orf1, orf2, orf3, secA2, gtf1, and gtf2 that is localized immediately downstream of fap1. The lower G+C contents and the presence of a putative transposase element suggest that this gene cluster was horizontally transf

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17

Chen, Yi-Ywan M., and Robert A. Burne. "Identification and Characterization of the Nickel Uptake System for Urease Biogenesis in Streptococcus salivarius 57.I." Journal of Bacteriology 185, no. 23 (2003): 6773–79. http://dx.doi.org/10.1128/jb.185.23.6773-6779.2003.

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ABSTRACT Ureases are multisubunit enzymes requiring Ni2+ for activity. The low pH-inducible urease gene cluster in Streptococcus salivarius 57.I is organized as an operon, beginning with ureI, followed by ureABC (structural genes), and ureEFGD (accessory genes). Urease biogenesis also requires a high-affinity Ni2+ uptake system. By searching the partial genome sequence of a closely related organism, Streptococcus thermophilus LMG18311, three open reading frame (ORFs) homologous to those encoding proteins involved in cobalamin biosynthesis and cobalt transport (cbiMQO) were identified immediate

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18

Escamilla-Martínez, E. E., Y. M. Álvarez Cisneros, F. J. Fernández, M. Quirasco-Baruch, and E. Ponce-Alquicira. "Identification of Structural and Immunity Genes of a Class IIb Bacteriocin Encoded in the Enterocin A Operon of Enterococcus faecium Strain MXVK29." Journal of Food Protection 80, no. 11 (2017): 1851–56. http://dx.doi.org/10.4315/0362-028x.jfp-17-039.

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ABSTRACT The Enterococcus faecium strain MXVK29, isolated from fermented sausages, produces a bacteriocin with a molecular mass of 3.5 kDa that belongs to the class of enterocins II.1, according to the terminal amino acid sequence, and has been identified as enterocin A. This bacteriocin is active against selected strains of Listeria, Staphylococcus, Pediococcus, and Enterococcus. In this study, we identified the genes adjacent to the structural gene for this bacteriocin, such as the immunity gene (entI) and the inducer gene (entF). Accessory genes for this bacteriocin, such as entK, entR, and

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19

Si, Fusheng, Xiaoxia Hu, Chenyang Wang, et al. "Porcine Epidemic Diarrhea Virus (PEDV) ORF3 Enhances Viral Proliferation by Inhibiting Apoptosis of Infected Cells." Viruses 12, no. 2 (2020): 214. http://dx.doi.org/10.3390/v12020214.

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The genomes of coronaviruses carry accessory genes known to be associated with viral virulence. The single accessory gene of porcine epidemic diarrhea virus (PEDV), ORF3, is dispensable for virus replication in vitro, while viral mutants carrying ORF3 truncations exhibit an attenuated phenotype of which the underlying mechanism is unknown. Here, we studied the effect of ORF3 deletion on the proliferation of PEDV in Vero cells. To this end, four recombinant porcine epidemic diarrhea viruses (PEDVs) were rescued using targeted RNA recombination, three carrying the full-length ORF3 gene from diff

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20

Reynolds, Liam J., Muna F. Anjum, and Adam P. Roberts. "Detection of a Novel, and Likely Ancestral, Tn916-Like Element from a Human Saliva Metagenomic Library." Genes 11, no. 5 (2020): 548. http://dx.doi.org/10.3390/genes11050548.

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Tn916 is a conjugative transposon (CTn) and the first reported and most well characterised of the Tn916/Tn1545 family of CTns. Tn916-like elements have a characteristic modular structure and different members of this family have been identified based on similarities and variations in these modules. In addition to carrying genes encoding proteins required for their conjugation, Tn916-like elements also carry accessory, antimicrobial resistance genes; most commonly the tetracycline resistance gene, tet(M). Our study aimed to identify and characterise tetracycline resistance genes from the human

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21

Lorusso, Alessio, Nicola Decaro, Pepijn Schellen, et al. "Gain, Preservation, and Loss of a Group 1a Coronavirus Accessory Glycoprotein." Journal of Virology 82, no. 20 (2008): 10312–17. http://dx.doi.org/10.1128/jvi.01031-08.

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ABSTRACT Coronaviruses are positive-strand RNA viruses of extraordinary genetic complexity and diversity. In addition to a common set of genes for replicase and structural proteins, each coronavirus may carry multiple group-specific genes apparently acquired through relatively recent heterologous recombination events. Here we describe an accessory gene, ORF3, unique to canine coronavirus type I (CCoV-I) and characterize its product, glycoprotein gp3. Whereas ORF3 is conserved in CCoV-I, only remnants remain in CCoV-II and CCoV-II-derived porcine and feline coronaviruses. Our findings provide i

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22

Rakhely, Gabor, Annette Colbeau, Jerome Garin, Paulette M. Vignais, and Kornel L. Kovacs. "Unusual Organization of the Genes Coding for HydSL, the Stable [NiFe]Hydrogenase in the Photosynthetic BacteriumThiocapsa roseopersicina BBS." Journal of Bacteriology 180, no. 6 (1998): 1460–65. http://dx.doi.org/10.1128/jb.180.6.1460-1465.1998.

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ABSTRACT The characterization of a hyd gene cluster encoding the stable, bidirectional [NiFe]hydrogenase 1 enzyme in Thiocapsa roseopersicina BBS, a purple sulfur photosynthetic bacterium belonging to the family Chromatiaceae, is presented. The heterodimeric hydrogenase 1 had been purified to homogeneity and thoroughly characterized (K. L. Kovacs et al., J. Biol. Chem. 266:947–951, 1991; C. Bagyinka et al., J. Am. Chem. Soc. 115:3567–3585, 1993). As an unusual feature, a 1,979-bp intergenic sequence (IS) separates the structural geneshydS and hydL, which encode the small and the large subunits

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23

Kaewborisuth, Challika, Yodying Yingchutrakul, Sittiruk Roytrakul, and Anan Jongkaewwattana. "Porcine Epidemic Diarrhea Virus (PEDV) ORF3 Interactome Reveals Inhibition of Virus Replication by Cellular VPS36 Protein." Viruses 11, no. 4 (2019): 382. http://dx.doi.org/10.3390/v11040382.

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The accessory protein ORF3 of porcine epidemic diarrhea virus (PEDV) has been proposed to play a key role in virus replication. However, our understanding of its function regarding virus and host interaction is still limited. In this study, we employed immunoprecipitation and mass spectrometry to screen for cellular interacting partners of ORF3. Gene ontology analysis of the host interactome highlighted the involvement of ORF3 in endosomal and immune signaling pathways. Among the identified ORF3-interacting proteins, the vacuolar protein-sorting-associated protein 36 (VPS36) was assessed for i

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Zeng, Lei-Ping, Yu-Tao Gao, Xing-Yi Ge, et al. "Bat Severe Acute Respiratory Syndrome-Like Coronavirus WIV1 Encodes an Extra Accessory Protein, ORFX, Involved in Modulation of the Host Immune Response." Journal of Virology 90, no. 14 (2016): 6573–82. https://doi.org/10.5281/zenodo.13477650.

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(Uploaded by Plazi for the Bat Literature Project) Bats harbor severe acute respiratory syndrome (SARS)-like coronaviruses (SL-CoVs) from which the causative agent of the 2002-2003 SARS pandemic is thought to have originated. However, despite the fact that a large number of genetically diverse SL-CoV sequences have been detected in bats, only two strains (named WIV1 and WIV16) have been successfully cultured in vitro. These two strains differ from SARS-CoV only in containing an extra open reading frame (ORF) (named ORFX), between ORF6 and ORF7, which has no homology to any known protein sequen

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25

Zeng, Lei-Ping, Yu-Tao Gao, Xing-Yi Ge, et al. "Bat Severe Acute Respiratory Syndrome-Like Coronavirus WIV1 Encodes an Extra Accessory Protein, ORFX, Involved in Modulation of the Host Immune Response." Journal of Virology 90, no. 14 (2016): 6573–82. https://doi.org/10.5281/zenodo.13477650.

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(Uploaded by Plazi for the Bat Literature Project) Bats harbor severe acute respiratory syndrome (SARS)-like coronaviruses (SL-CoVs) from which the causative agent of the 2002-2003 SARS pandemic is thought to have originated. However, despite the fact that a large number of genetically diverse SL-CoV sequences have been detected in bats, only two strains (named WIV1 and WIV16) have been successfully cultured in vitro. These two strains differ from SARS-CoV only in containing an extra open reading frame (ORF) (named ORFX), between ORF6 and ORF7, which has no homology to any known protein sequen

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26

Zeng, Lei-Ping, Yu-Tao Gao, Xing-Yi Ge, et al. "Bat Severe Acute Respiratory Syndrome-Like Coronavirus WIV1 Encodes an Extra Accessory Protein, ORFX, Involved in Modulation of the Host Immune Response." Journal of Virology 90, no. 14 (2016): 6573–82. https://doi.org/10.5281/zenodo.13477650.

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Abstract:

(Uploaded by Plazi for the Bat Literature Project) Bats harbor severe acute respiratory syndrome (SARS)-like coronaviruses (SL-CoVs) from which the causative agent of the 2002-2003 SARS pandemic is thought to have originated. However, despite the fact that a large number of genetically diverse SL-CoV sequences have been detected in bats, only two strains (named WIV1 and WIV16) have been successfully cultured in vitro. These two strains differ from SARS-CoV only in containing an extra open reading frame (ORF) (named ORFX), between ORF6 and ORF7, which has no homology to any known protein sequen

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27

Zeng, Lei-Ping, Yu-Tao Gao, Xing-Yi Ge, et al. "Bat Severe Acute Respiratory Syndrome-Like Coronavirus WIV1 Encodes an Extra Accessory Protein, ORFX, Involved in Modulation of the Host Immune Response." Journal of Virology 90, no. 14 (2016): 6573–82. https://doi.org/10.5281/zenodo.13477650.

Full text

Abstract:

(Uploaded by Plazi for the Bat Literature Project) Bats harbor severe acute respiratory syndrome (SARS)-like coronaviruses (SL-CoVs) from which the causative agent of the 2002-2003 SARS pandemic is thought to have originated. However, despite the fact that a large number of genetically diverse SL-CoV sequences have been detected in bats, only two strains (named WIV1 and WIV16) have been successfully cultured in vitro. These two strains differ from SARS-CoV only in containing an extra open reading frame (ORF) (named ORFX), between ORF6 and ORF7, which has no homology to any known protein sequen

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28

Zeng, Lei-Ping, Yu-Tao Gao, Xing-Yi Ge, et al. "Bat Severe Acute Respiratory Syndrome-Like Coronavirus WIV1 Encodes an Extra Accessory Protein, ORFX, Involved in Modulation of the Host Immune Response." Journal of Virology 90, no. 14 (2016): 6573–82. https://doi.org/10.5281/zenodo.13477650.

Full text

Abstract:

(Uploaded by Plazi for the Bat Literature Project) Bats harbor severe acute respiratory syndrome (SARS)-like coronaviruses (SL-CoVs) from which the causative agent of the 2002-2003 SARS pandemic is thought to have originated. However, despite the fact that a large number of genetically diverse SL-CoV sequences have been detected in bats, only two strains (named WIV1 and WIV16) have been successfully cultured in vitro. These two strains differ from SARS-CoV only in containing an extra open reading frame (ORF) (named ORFX), between ORF6 and ORF7, which has no homology to any known protein sequen

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29

Diaz, Marta, Eva Valdivia, Manuel Martínez-Bueno, et al. "Characterization of a New Operon, as-48EFGH, from the as-48 Gene Cluster Involved in Immunity to Enterocin AS-48." Applied and Environmental Microbiology 69, no. 2 (2003): 1229–36. http://dx.doi.org/10.1128/aem.69.2.1229-1236.2003.

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ABSTRACT Enterocin AS-48 is a cyclic peptide produced by Enterococcus faecalis S-48 whose genetic determinants have been identified in the conjugative plasmid pMB2. A region of 7.8 kb, carrying the minimum information required for production of and immunity against AS-48, had been previously cloned and sequenced in pAM401 (pAM401-52). In this region, the as-48A structural gene and as-48B, as-48C, as-48C1 , as-48D, and as-48D1 genes and open reading frame 6 (ORF6) and ORF7 had been identified. The sequence analysis carried out in this work in the BglII B fragment (6.6-kb) from pMB2 cloned downs

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30

Lipps, Georg. "Molecular biology of the pRN1 plasmid from Sulfolobus islandicus." Biochemical Society Transactions 37, no. 1 (2009): 42–45. http://dx.doi.org/10.1042/bst0370042.

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The pRN1 plasmid is a rather small multicopy plasmid which was isolated from a Sulfolobus islandicus strain in 1993 by Wolfram Zillig and co-workers. Sequence analysis of the genome sequence suggested that three conserved genes are important for plasmid replication. These genes code for two sequence-specific DNA-binding proteins (ORF56 and ORF80) and for a large multifunctional replication protein (ORF904). The protein ORF904 has primase, DNA polymerase and helicase activity. Remarkably, the primase activity is highly sequence specific, and primers are only efficiently synthesized on templates

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31

Elliott, Simon J., Efrosinia O. Krejany, Jay L. Mellies, Roy M. Robins-Browne, Chihiro Sasakawa, and James B. Kaper. "EspG, a Novel Type III System-Secreted Protein from Enteropathogenic Escherichia coli with Similarities to VirA of Shigella flexneri." Infection and Immunity 69, no. 6 (2001): 4027–33. http://dx.doi.org/10.1128/iai.69.6.4027-4033.2001.

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ABSTRACT The function of the rorf2 gene located on the locus of enterocyte effacement (LEE) pathogenicity island of enteropathogenicEscherichia coli (EPEC) has not been described. We report that rorf2 encodes a novel protein, named EspG, which is secreted by the type III secretory system and which is translocated into host epithelial cells. EspG is homologous withShigella flexneri protein VirA, and the clonedespG (rorf2) gene can rescue invasion in a Shigella virA mutant, indicating that these proteins are functionally equivalent in Shigella. An EPECespG mutant had no apparent defects in in vi

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32

Zeng, Lei-Ping, Yu-Tao Gao, Xing-Yi Ge, et al. "Bat Severe Acute Respiratory Syndrome-Like Coronavirus WIV1 Encodes an Extra Accessory Protein, ORFX, Involved in Modulation of the Host Immune Response." Journal of Virology 90, no. 14 (2016): 6573–82. http://dx.doi.org/10.1128/jvi.03079-15.

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ABSTRACTBats harbor severe acute respiratory syndrome (SARS)-like coronaviruses (SL-CoVs) from which the causative agent of the 2002-2003 SARS pandemic is thought to have originated. However, despite the fact that a large number of genetically diverse SL-CoV sequences have been detected in bats, only two strains (named WIV1 and WIV16) have been successfully culturedin vitro. These two strains differ from SARS-CoV only in containing an extra open reading frame (ORF) (named ORFX), between ORF6 and ORF7, which has no homology to any known protein sequences. In this study, we constructed a full-le

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Johnston, Julie C., Mehdi Gasmi, Leland E. Lim, et al. "Minimum Requirements for Efficient Transduction of Dividing and Nondividing Cells by Feline Immunodeficiency Virus Vectors." Journal of Virology 73, no. 6 (1999): 4991–5000. http://dx.doi.org/10.1128/jvi.73.6.4991-5000.1999.

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ABSTRACT The development of gene delivery vectors based on feline immunodeficiency virus (FIV) is an attractive alternative to vectors based on primate sources for the delivery of genes into humans. To investigate the requirements for efficient transduction of dividing and nondividing cells by vector particles based on FIV, a series of packaging and vector constructs was generated for which viral gene expression was minimized and from which unnecessarycis-acting sequences were deleted. Pseudotyped vector particles produced in 293T cells were used to transduce various target cells, including co

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Papazisi, L., S. Frasca, M. Gladd, X. Liao, D. Yogev, and S. J. Geary. "GapA and CrmA Coexpression Is Essential for Mycoplasma gallisepticum Cytadherence and Virulence." Infection and Immunity 70, no. 12 (2002): 6839–45. http://dx.doi.org/10.1128/iai.70.12.6839-6845.2002.

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ABSTRACT It was previously demonstrated that avirulent Mycoplasma gallisepticum strain Rhigh (passage 164) is lacking three proteins that are expressed in its virulent progenitor, strain Rlow (passage 15). These proteins were identified as the cytadhesin molecule GapA, the putative cytadhesin-related molecule CrmA, and a component of a high-affinity transporter system, HatA. Complementation of Rhigh with wild-type gapA restored expression in the transformant (GT5) but did not restore the cytadherence phenotype and maintained avirulence in chickens. These results suggested that CrmA might play

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Poss, Mary, Howard A. Ross, Sally L. Painter, et al. "Feline Lentivirus Evolution in Cross-Species Infection Reveals Extensive G-to-A Mutation and Selection on Key Residues in the Viral Polymerase." Journal of Virology 80, no. 6 (2006): 2728–37. http://dx.doi.org/10.1128/jvi.80.6.2728-2737.2006.

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ABSTRACT Factors that restrict a virus from establishing productive infection in a new host species are important to understand because cross-species transmission events are often associated with emergent viral diseases. To determine the evolutionary pressures on viruses in new host species, we evaluated the molecular evolution of a feline immunodeficiency virus derived from a wild cougar, Puma concolor, during infection of domestic cats. Analyses were based on the coding portion of genome sequences recovered at intervals over 37 weeks of infection of six cats inoculated by either intravenous

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Pavesi, Angelo, and Fabio Romerio. "Extending the Coding Potential of Viral Genomes with Overlapping Antisense ORFs: A Case for the De Novo Creation of the Gene Encoding the Antisense Protein ASP of HIV-1." Viruses 14, no. 1 (2022): 146. http://dx.doi.org/10.3390/v14010146.

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Gene overprinting occurs when point mutations within a genomic region with an existing coding sequence create a new one in another reading frame. This process is quite frequent in viral genomes either to maximize the amount of information that they encode or in response to strong selective pressure. The most frequent scenario involves two different reading frames in the same DNA strand (sense overlap). Much less frequent are cases of overlapping genes that are encoded on opposite DNA strands (antisense overlap). One such example is the antisense ORF, asp in the minus strand of the HIV-1 genome

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O’Keeffe, Triona, Colin Hill, and R. Paul Ross. "Characterization and Heterologous Expression of the Genes Encoding Enterocin A Production, Immunity, and Regulation inEnterococcus faecium DPC1146." Applied and Environmental Microbiology 65, no. 4 (1999): 1506–15. http://dx.doi.org/10.1128/aem.65.4.1506-1515.1999.

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ABSTRACT Enterocin A is a small, heat-stable, antilisterial bacteriocin produced by Enterococcus faecium DPC1146. The sequence of a 10,879-bp chromosomal region containing at least 12 open reading frames (ORFs), 7 of which are predicted to play a role in enterocin biosynthesis, is presented. The genes entA,entI, and entF encode the enterocin A prepeptide, the putative immunity protein, and the induction factor prepeptide, respectively. The deduced proteins EntK and EntR resemble the histidine kinase and response regulator proteins of two-component signal transducing systems of the AgrC-AgrA ty

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Bykova, Anastassia, Andreu Saura, Galina V. Glazko, Abiel Roche-Lima, Vyacheslav Yurchenko, and Igor B. Rogozin. "The 29-nucleotide deletion in SARS-CoV: truncated versions of ORF8 are under purifying selection." BMC Genomics 24, no. 1 (2023). http://dx.doi.org/10.1186/s12864-023-09482-3.

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Abstract Background Accessory proteins have diverse roles in coronavirus pathobiology. One of them in SARS-CoV (the causative agent of the severe acute respiratory syndrome outbreak in 2002–2003) is encoded by the open reading frame 8 (ORF8). Among the most dramatic genomic changes observed in SARS-CoV isolated from patients during the peak of the pandemic in 2003 was the acquisition of a characteristic 29-nucleotide deletion in ORF8. This deletion cause splitting of ORF8 into two smaller ORFs, namely ORF8a and ORF8b. Functional consequences of this event are not entirely clear. Results Here,

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Filipe, Pereira. "Evolutionary dynamics of the SARS-CoV-2 ORF8 accessory gene." November 1, 2020. https://doi.org/10.1016/j.meegid.2020.104525.

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The new SARS-CoV-2 poses a significant threat to human health but many aspects of its basic biology remain unknown. Its genome encodes accessory genes that differ significantly within coronaviruses and contribute to the virus pathogenicity. Among accessory genes, open reading frame 8 (ORF8) stands out by being highly variable and showing structural changes suspected to be related with the virus ability to spread. However, the function of ORF8 remains to be elucidated, making it less studied than other SARS-CoV-2 genes. Here I show that ORF8 is poorly conserved among related coronaviruses. The

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López-Ayllón, Blanca D., Ana de Lucas-Rius, Laura Mendoza-García, et al. "SARS-CoV-2 accessory proteins involvement in inflammatory and profibrotic processes through IL11 signaling." Frontiers in Immunology 14 (July 20, 2023). http://dx.doi.org/10.3389/fimmu.2023.1220306.

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SARS-CoV-2, the cause of the COVID-19 pandemic, possesses eleven accessory proteins encoded in its genome. Their roles during infection are still not completely understood. In this study, transcriptomics analysis revealed that both WNT5A and IL11 were significantly up-regulated in A549 cells expressing individual accessory proteins ORF6, ORF8, ORF9b or ORF9c from SARS-CoV-2 (Wuhan-Hu-1 isolate). IL11 is a member of the IL6 family of cytokines. IL11 signaling-related genes were also differentially expressed. Bioinformatics analysis disclosed that both WNT5A and IL11 were involved in pulmonary f

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Ponde, Nicole O., Karsen E. Shoger, Mst Shamima Khatun, et al. "SARS-CoV-2 ORF8 Mediates Signals in Macrophages and Monocytes through MyD88 Independently of the IL-17 Receptor." Journal of Immunology, June 2, 2023. http://dx.doi.org/10.4049/jimmunol.2300110.

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Abstract SARS-CoV-2 has caused an estimated 7 million deaths worldwide to date. A secreted SARS-CoV-2 accessory protein, known as open reading frame 8 (ORF8), elicits inflammatory pulmonary cytokine responses and is associated with disease severity in COVID-19 patients. Recent reports proposed that ORF8 mediates downstream signals in macrophages and monocytes through the IL-17 receptor complex (IL-17RA, IL-17RC). However, generally IL-17 signals are found to be restricted to the nonhematopoietic compartment, thought to be due to rate-limiting expression of IL-17RC. Accordingly, we revisited th

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Filipe, Pereira. "SARS-CoV-2 variants lacking a functional ORF8 may reduce accuracy of serological testing." October 31, 2020. https://doi.org/10.1016/j.jim.2020.112906.

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Serological testing can be used for diagnosis, retrospective assessment of the efficacy of control measures and testing the response to a future vaccine (Weissleder et al., 2020). Most antibody detection assays to estimate SARS-CoV-2 prevalence and incidence probe for the nucleocapsid (N) or spike (S) proteins (Weissleder et al., 2020). A recent study proposed the use of ORF8 and ORF3b antibodies as serological markers of early and late SARS-CoV-2 infection (Hachim et al., 2020). The study is an important step towards standardization of serological assays for COVID-19 and a better understandin

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Wang, Xiaohui, Joy-Yan Lam, Wan-Man Wong, et al. "Accurate Diagnosis of COVID-19 by a Novel Immunogenic Secreted SARS-CoV-2 orf8 Protein." mBio 11, no. 5 (2020). http://dx.doi.org/10.1128/mbio.02431-20.

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ABSTRACT An accurate diagnostic test for early severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection is the key weapon to control the coronavirus disease 2019 (COVID-19) pandemic. We previously reported that the SARS-CoV-2 genome contains a unique orf8 accessory gene absent from other human-pathogenic coronaviruses. Here, we characterized the SARS-CoV-2 orf8 as a novel immunogenic secreted protein and utilized it for the accurate diagnosis of COVID-19. Extracellular orf8 protein was detected in cell culture supernatant and in sera of COVID-19 patients. In addition, orf8 was fo

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Mohammed, Mohammed Elimam Ahamed. "SARS-CoV-2 proteins: Are they useful as targets for COVID-19 drugs and vaccines?" Current Molecular Medicine 21 (February 23, 2021). http://dx.doi.org/10.2174/1566524021666210223143243.

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: The proteins of coronavirus are classified to nonstructural, structural, and accessory. There are 16 nonstructural viral proteins beside their precursors (1a and 1ab polyproteins). The nonstructural proteins are named as nsp1 to nsp16 and they act as enzymes, coenzymes, and binding proteins to facilitate the replication, transcription, and translation of the virus. The structural proteins are bound to the RNA in the nucleocapsid (N- protein) or to the lipid bilayer membrane of the viral envelope. The lipid bilayer proteins include the membrane protein (M), envelope protein (E), and spike pro

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Geng, Hua, Saravanan Subramanian, Longtao Wu та ін. "SARS-CoV-2 ORF8 Forms Intracellular Aggregates and Inhibits IFNγ-Induced Antiviral Gene Expression in Human Lung Epithelial Cells". Frontiers in Immunology 12 (9 червня 2021). http://dx.doi.org/10.3389/fimmu.2021.679482.

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Infection with the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causes COVID-19, a disease that involves significant lung tissue damage. How SARS-CoV-2 infection leads to lung injury remains elusive. The open reading frame 8 (ORF8) protein of SARS-CoV-2 (ORF8SARS-CoV-2) is a unique accessory protein, yet little is known about its cellular function. We examined the cellular distribution of ORF8SARS-CoV-2 and its role in the regulation of human lung epithelial cell proliferation and antiviral immunity. Using live imaging and immunofluorescent staining analyses, we found that ecto

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Nawaz, Rabia, Muhammad Ali Arif, Zainab Ahmad, et al. "An ncRNA transcriptomics-based approach to design siRNA molecules against SARS-CoV-2 double membrane vesicle formation and accessory genes." BMC Infectious Diseases 23, no. 1 (2023). http://dx.doi.org/10.1186/s12879-023-08870-0.

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Abstract Background The corona virus SARS-CoV-2 is the causative agent of recent most global pandemic. Its genome encodes various proteins categorized as non-structural, accessory, and structural proteins. The non-structural proteins, NSP1–16, are located within the ORF1ab. The NSP3, 4, and 6 together are involved in formation of double membrane vesicle (DMV) in host Golgi apparatus. These vesicles provide anchorage to viral replicative complexes, thus assist replication inside the host cell. While the accessory genes coded by ORFs 3a, 3b, 6, 7a, 7b, 8a, 8b, 9b, 9c, and 10 contribute in cell e

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Si, Fusheng, Bingqing Chen, Xiaoxia Hu, et al. "Porcine Epidemic Diarrhea Virus ORF3 Protein Is Transported through the Exocytic Pathway." Journal of Virology 94, no. 17 (2020). http://dx.doi.org/10.1128/jvi.00808-20.

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ABSTRACT Accessory genes occurring between the S and E genes of coronaviruses have been studied quite intensively during the last decades. In porcine epidemic diarrhea virus (PEDV), the only gene at this location, ORF3, encodes a 224-residue membrane protein shown to exhibit ion channel activity and to enhance virus production. However, little is known about its intracellular trafficking or about its function during PEDV infection. In this study, two recombinant PEDVs were rescued by targeted RNA recombination, one carrying the full-length ORF3 gene and one from which the gene had been deleted

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Heise, Mark, Terence S. Dermody, Arturo Casadevall, Rozanne M. Sandri-Goldin, and Patrick D. Schloss. "The Decision to Publish Gutierrez-Alvarez et al., “Middle East Respiratory Syndrome Coronavirus Gene 5 Modulates Pathogenesis in Mice”." Journal of Virology, November 3, 2020. http://dx.doi.org/10.1128/jvi.02118-20.

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The paper “Middle East respiratory syndrome coronavirus Gene 5 modulates pathogenesis in mice” by Gutierrez-Alvarez et al., in this issue of the Journal of Virology (1), demonstrates that the MERS-CoV accessory protein, Gene 5, also known as ORF5, plays a major role in MERS-CoV pathogenesis.…

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Kitai, Yuki, Shohei Kojima, Aikeda Aishajiang, et al. "Changes in ORF4 of HCoV-229E under different culture conditions." Journal of General Virology 106, no. 7 (2025). https://doi.org/10.1099/jgv.0.002131.

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The genome of human coronavirus 229E (HCoV-229E), a causative agent of human respiratory infections, encodes a unique accessory gene, ORF4. Analysis of laboratory strains and clinical specimens has suggested that HCoV-229E acquires truncating mutations in ORF4 under standard laboratory culture conditions. This study confirmed that HCoV-229E from patients with acute respiratory infections harboured a full-length ORF4 (219 amino acids). In contrast, virus stocks derived from the same patients and passaged in conventional cultured cells [LLC-MK2, human embryonic fibroblast (HEF); HEF, HeLa] exhib

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Lowery, Shea A., Noah Schuster, Lok-Yin Roy Wong, et al. "Mouse hepatitis virus JHMV I protein is required for maximal virulence." Journal of Virology, August 19, 2024. http://dx.doi.org/10.1128/jvi.00680-24.

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ABSTRACT Betacoronaviruses encode a conserved accessory gene within the +1 open reading frame (ORF) of nucleocapsid called the internal N gene. This gene is referred to as “I” for mouse hepatitis virus (MHV), ORF9b for severe acute respiratory CoV (SARS-CoV) and SARS-CoV-2, and ORF8b for Middle East respiratory syndrome CoV (MERS-CoV). Previous studies have shown ORF8b and ORF9b have immunoevasive properties, while the only known information for MHV I is its localization within the virion of the hepatotropic/neurotropic A59 strain of MHV. Whether MHV I is an innate immune antagonist or has oth

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