Table 1. Nomenclature and reading frames for overlapping gene candidates in SARS-CoV-2 ORF3a.
| Gene* | Reading frame† | Genome positions, Wuhan-Hu-1 (CDS positions, ORF3a)‡ |
Length | Description | References |
|---|---|---|---|---|---|
| ORF3a | ss11 (reference) | 25393–26220 (1-828) |
276 codons (828 nt) |
Ion channel formation and virus release in SARS-CoV infection; host cell apoptosis; triggers inflammation; antagonizes interferon | Lu et al., 2010; Cui et al., 2019 |
| ORF3c | ss13 | 25457–25582 (65-190) |
42 codons (126 nt) |
Features suggestive of a viroporin (Cagliani et al., 2020); lowest πN/πS ratio estimated for any gene in our between-host selection analysis (Figure 5); overlaps codons 22–64 of ORF3a | First discovered by Cagliani et al., 2020 as ORF3h; ORF3c in Firth, 2020; ORF3c in Jungreis et al., 2020; ORF3a.iORF1 in Finkel et al., 2020; ORF3b in Pavesi, 2020 |
| ORF3d | ss12 | 25524–25697 (132-305) |
58 codons (174 nt) |
Aligned to and named ORF3b by Chan et al., 2020 but is not homologous to ORF3b; interferon antagonism has not been demonstrated; binds STOML2 mitochondrial protein (Gordon et al., 2020); contains a predicted signal peptide in the region encoding ORF3d-2; contains an X motif in pangolin-CoV but not SARS-CoV-2 (Michel et al., 2020); may contribute to differences between SARS-CoV and SARS-CoV-2 in immune response as a unique antigenic target (Hachim et al., 2020; Niloufar Kavian, pers. comm.); overlaps codons 44–102 of ORF3a | Present study; first discovered by Chan et al., 2020 but misclassified as ORF3b; ORF3b in Gordon et al., 2020, Hachim et al., 2020, and citing studies; ‘hypothetical protein’ in Pavesi, 2020; ‘a completely different ORF’ in Michel et al., 2020 |
| ORF3d-2 | ss12 | 25596–25697 (204-305) |
34 codons (102 nt) |
A shorter isoform of ORF3d that starts after the first 24 codons, where the majority of premature STOP codons in SARS-CoV-2 are located; contains a predicted signal peptide (Finkel et al., 2020); likely expressed at higher levels than full-length ORF3d (Figure 2A) overlaps codons 68–102 of ORF3a | Discovered by Finkel et al., 2020 as ORF3a-iORF2 |
| ORF3a-2 | ss11 (reference) | 25765–26220 (373-828) |
152 codons (456 nt) |
A shorter isoform of ORF3a that starts after the first 124 codons; evidence of expression separate from that of ORF3a (Davidson et al., 2020); has also been conflated with ORF3b; equivalent to codons 124–276 of ORF3a | Discovered by Davidson et al., 2020 (pers. comm.) but referred to as ORF3b |
| ORF3b region§ | ss13 | 25814–26281; four ORFs at 25814–82, 25910–84, 26072–170, and 26183–281 (422-889; ORFs at 422–90, 518–92, 680–778, and 791–889) | 156 codons (468 nt); the four ORFs are 23, 25, 33, and 33 codons (69, 75, 99, and 99 nt) |
Full-length in some related viruses, but truncated by multiple in-frame STOP codons in SARS-CoV-2; longer forms function as an interferon antagonist in SARS-related viruses; may contribute to differences between SARS-CoV and SARS-CoV-2 in immune response; although aligned to ORF3d by Chan et al., 2020, the two are not homologous; overlaps codons 141–276 of ORF3a (first ORF overlaps codons 141–164) | Konno et al., 2020 claim functionality for the first (23-codon) ORF in SARS-CoV-2; the first ORF is also mentioned by Wu et al., 2020a |
*Genes are listed by position of start site in the genome from 5′ (top) to 3′ (bottom).
†Nomenclature as described in Wei and Zhang, 2015 and Nelson et al., 2020a: ss = sense-sense (same strand); ss12 = codon position 1 of the reference frame overlaps codon position 2 of the overlapping frame on the same strand; ss13 = codon position 1 of the reference frame overlaps codon position 3 of the overlapping frame on the same strand. Frame is indicated from the perspective of ORF3a as the reference gene, i.e. ORF3d starts at codon position 3 of ORF3a, while ORF3c and ORF3b start at codon position 2 of ORF3a.
‡Positions and counts include STOP codons. Positions or sequences were indicated by the original publications or verified by personal communication if ambiguous.
§The SARS-CoV-2 region homologous to ORF3b of SARS-CoV contains four premature STOP codons and four distinct ORFs (AUG-to-STOP); see Figure 4, Figure 6, and Supplementary file 1.