Conflicting and ambiguous names of overlapping ORFs in the SARS-CoV-2 genome: A homology-based resolution

Jungreis, Irwin; Nelson, Chase W.; Ardern, Zachary; Finkel, Yaara; Krogan, Nevan J.; Sato, Kei; Ziebuhr, John; Stern-Ginossar, Noam; Pavesi, Angelo; Firth, Andrew E.; Gorbalenya, Alexander E.; Kellis, M

doi:10.1016/j.virol.2021.02.013

Cited by 45 publications

(41 citation statements)

References 73 publications

(70 reference statements)

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“…Previous studies have proposed four other candidate protein-coding ORFs overlapping S and ORF3a, namely ORF2b (39 codons); ORF3d (57 codons); ORF3d-2 (33 codons), a subset of ORF3d starting at a downstream in-frame AUG; and ORF3b (22 codons), a truncated ortholog of SARS-CoV ORF3b 13,[17][18][19][20] . (Note that these ORFs have been referred to by diverse names, with many papers referring to ORF3d as ORF3b 21 .) None of these are conserved in the species Severe acute respiratory syndromerelated coronavirus, showing non-conserved start codon, variable length, and premature stop codons.…”

Section: Resultsmentioning

confidence: 99%

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SARS-CoV-2 gene content and COVID-19 mutation impact by comparing 44 Sarbecovirus genomes

2021

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Despite its clinical importance, the SARS-CoV-2 gene set remains unresolved, hindering dissection of COVID-19 biology. We use comparative genomics to provide a high-confidence protein-coding gene set, characterize evolutionary constraint, and prioritize functional mutations. We select 44 Sarbecovirus genomes at ideally-suited evolutionary distances, and quantify protein-coding evolutionary signatures and overlapping constraint. We find strong protein-coding signatures for ORFs 3a, 6, 7a, 7b, 8, 9b, and a novel alternate-frame gene, ORF3c, whereas ORFs 2b, 3d/3d-2, 3b, 9c, and 10 lack protein-coding signatures or convincing experimental evidence of protein-coding function. Furthermore, we show no other conserved protein-coding genes remain to be discovered. Mutation analysis suggests ORF8 contributes to within-individual fitness but not person-to-person transmission. Cross-strain and within-strain evolutionary pressures agree, except for fewer-than-expected within-strain mutations in nsp3 and S1, and more-than-expected in nucleocapsid, which shows a cluster of mutations in a predicted B-cell epitope, suggesting immune-avoidance selection. Evolutionary histories of residues disrupted by spike-protein substitutions D614G, N501Y, E484K, and K417N/T provide clues about their biology, and we catalog likely-functional co-inherited mutations. Previously reported RNA-modification sites show no enrichment for conservation. Here we report a high-confidence gene set and evolutionary-history annotations providing valuable resources and insights on SARS-CoV-2 biology, mutations, and evolution.

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Section: Resultsmentioning

confidence: 99%

“…NCBI annotates SARS-CoV (NC_004718.3) orthologs of ORFs 3a, 6, 7a, 7b, and 9b, but ORF8 is split into ORF8a and ORF8b, ORF3b is included, and neither ORF9c nor ORF10 are included. Here we use the homology-based ORF nomenclature 21 discussed in Supplementary Note 1.…”

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confidence: 99%

SARS-CoV-2 gene content and COVID-19 mutation impact by comparing 44 Sarbecovirus genomes

2021

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“…HLA-I peptides are derived from internal out-of-frame ORFs in S and N Remarkably, we detected nine HLA-I peptides processed from internal out-of-frame ORFs in the coding region of S and N, termed S.iORF1 (also known as ORF2b; Jungreis et al, 2021) and ORF9b. From S.iORF1/2, we detected three HLA-I peptides (GPMVLRGLIT, GLITLSYHL, and MLLGSMLYM) in HEK293T cells (Figure 5A).…”

Section: Sars-cov-2 Infection Interferes With Cellular Pathways That May Affect Antigen Processingmentioning

confidence: 92%

Profiling SARS-CoV-2 HLA-I peptidome reveals T cell epitopes from out-of-frame ORFs

Weingarten-Gabbay

Klaeger

Sarkizova

et al. 2021

Cell

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T cell-mediated immunity plays an important role in controlling SARS-CoV-2 infection, but the repertoire of naturally processed and presented viral epitopes on class I human leukocyte antigen (HLA-I) remains uncharacterized. Here, we report the first HLA-I immunopeptidome of SARS-CoV-2 in two cell lines at different times post infection using mass spectrometry. We found HLA-I peptides derived not only from canonical open reading frames (ORFs) but also from internal out-of-frame ORFs in spike and nucleocapsid not captured by current vaccines. Some peptides from out-of-frame ORFs elicited T cell responses in a humanized mouse model and individuals with COVID-19 that exceeded responses to canonical peptides, including some of the strongest epitopes reported to date. Whole-proteome analysis of infected cells revealed that early expressed viral proteins contribute more to HLA-I presentation and immunogenicity. These biological insights, as well as the discovery of out-of-frame ORF epitopes, will facilitate selection of peptides for immune monitoring and vaccine development.

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“…ORF3d maps at the 5' end of the ORF3a sequence overlapping the 3' half of ORF3c. Since it was first described as ORF3b by Chan et al (30), literature must be depicted carefully since some reports may have conflated these two ORFs, interchanging the names (31). Nowadays, we know that ORF3b and ORF3d are unrelated and located in different genomic positions (Figure 1).…”

Section: Orf3dmentioning

confidence: 99%

SARS-CoV-2 Accessory Proteins in Viral Pathogenesis: Knowns and Unknowns

et al. 2021

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There are still many unanswered questions concerning viral SARS-CoV-2 pathogenesis in COVID-19. Accessory proteins in SARS-CoV-2 consist of eleven viral proteins whose roles during infection are still not completely understood. Here, a review on the current knowledge of SARS-CoV-2 accessory proteins is summarized updating new research that could be critical in understanding SARS-CoV-2 interaction with the host. Some accessory proteins such as ORF3b, ORF6, ORF7a and ORF8 have been shown to be important IFN-I antagonists inducing an impairment in the host immune response. In addition, ORF3a is involved in apoptosis whereas others like ORF9b and ORF9c interact with cellular organelles leading to suppression of the antiviral response in infected cells. However, possible roles of ORF7b and ORF10 are still awaiting to be described. Also, ORF3d has been reassigned. Relevant information on the knowns and the unknowns in these proteins is analyzed, which could be crucial for further understanding of SARS-CoV-2 pathogenesis and to design strategies counteracting their actions evading immune responses in COVID-19.

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Conflicting and ambiguous names of overlapping ORFs in the SARS-CoV-2 genome: A homology-based resolution

Cited by 45 publications

References 73 publications

SARS-CoV-2 gene content and COVID-19 mutation impact by comparing 44 Sarbecovirus genomes

SARS-CoV-2 gene content and COVID-19 mutation impact by comparing 44 Sarbecovirus genomes

Profiling SARS-CoV-2 HLA-I peptidome reveals T cell epitopes from out-of-frame ORFs

SARS-CoV-2 Accessory Proteins in Viral Pathogenesis: Knowns and Unknowns

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