Table 1. Nucleotide and amino acid differences from the CV777 reference sequence AF353511.
| Region | Nucleotide (nt) |
AF353511 nt / aa |
ANSES nt / aa |
WBR nt / aa |
DTU nt / aa |
APHA nt / aa |
IZSLER nt / aa |
FLI nt / aa |
|
|---|---|---|---|---|---|---|---|---|---|
| 5'-UTR | 8 | A | G | ** | G | ||||
| 28 | A | ** | G | ||||||
| 72 | A | Del | Del | Del | Del | Del | Del | ||
| 82–85 | TCCT | Del | Del | Del | Del | Del | Del | ||
| ORF1a/1b | 3433 | A / E | Del# | ||||||
| 3434 | G / E | Del# | |||||||
| 3435 | T / S | Del# | |||||||
| 3436 | C / S | Del# | |||||||
| 3437 | T / S | Del# | |||||||
| 3438 | G / E | C / Q | Del# | ||||||
| 4102 | T / V | Y / (A/V) | |||||||
| 4284 | G / G | A / G | |||||||
| 4767 | G / A | T / S | |||||||
| 5170 | A / E | G / G | |||||||
| 6607 | T / L | C / Silent | |||||||
| 7941 | A / S | G / G | |||||||
| 9179 | C / Y | T / Silent | |||||||
| 10715 | T / A | Y / Silent | |||||||
| 11103 | G / A | Y / (A/S) | |||||||
| 13594 | T / V | G / Silent | |||||||
| 13917 | T / V | G / G | G / G | G / G | |||||
| 18113 | A / M | G / V | |||||||
| 20015 | A / I | G / V | |||||||
| Spike (S) | 20887 | G / G | A / S | A / S | |||||
| 20984 | T / I | C / T | C / T | ||||||
| 21348 | T / N | Y / Silent | |||||||
| 21529 | C / H | T / Y | |||||||
| 21680 | A / N | G / S | |||||||
| 21805 | C / P | T / S | |||||||
| 22145 | C / S | T / L | T / L | ||||||
| 22535 | A / E | G / G | |||||||
| 23771 | C / A | T / V | |||||||
| 23800 | C / H | G / D | |||||||
| 24416 | C / T | A / N | |||||||
| 24757 | T / Y | C / H | |||||||
| Spike/ ORF3 | 24765–24816 | * | Del | Del | |||||
| ORF3 | 25201 | A / I | Del | ||||||
| 25202 | T / I | Del## | Del | ||||||
| 25203 | T / I | Del## | Del | ||||||
| Env (E) | 25655 | G / S | K / (S/I) | ||||||
| Mem (M) | 25713 | T / V | C / A | ||||||
| 25992 | G / R | A / H | |||||||
* 52 nt deletion at Spike/ORF3 junction: TTTTGAAAAGGTCCACGTGCAGTGATGTTTCTTGGACTTTTTCAATACACGA. Stop codon of Spike and start codon of ORF3 indicated with underline and italics, respectively.
** the 5´-terminal region of the Br1/87 (DTU) sequence is rearranged upstream of nt 35.
#The 6 nt deletion modifies 3 codons and results in alteration of the encoded amino acid sequence from..NVESEV.. to..NVEV.., i.e. 2 amino acids are deleted.
## The loss of 2 nt results in the formation of a new termination codon that is predicted to result in the truncation of the ORF3 protein (see text for details).
Shared changes are highlighted in grey. Synonymous nt changes are indicated as “silent”. The nt identifier Y is for pyrimidines (C or T) while K denotes G or T.