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. 2022 Mar 12;14(3):585. doi: 10.3390/v14030585

Table 2.

Summary of the DNA and RNA viral diseases ORF characteristics.

Virus Type Pathogen ORF Characteristics Reference
DNA virus ds DNA WSSV ORF75
  • ●

    Number of bp in the repeat unit: 45 bp (type 1), 102 bp (type 2)

  • ●

    Repeat unit sequences:

  • -

    Type 1: GAA GCA GCT CCC CCA CTT AAA GGT GCA CTT GGA CGT AAG AGG CGC

  • -

    Type 2: GAA GCA GCT CCC CCA CTT AAA GGT GCG CTT GGA CGT AAG AGG CGC GAA GCA GAA TCC TTG GAG GAA GAA CTT GTG TCT GCT GAA GAA GAA CGT GAA AAG CGC

  • ●

    Primers:

  • -

    ORF75F (5′-GCC AGA TTT CTT CCC CTA CC-3′)

  • -

    ORF75R (5′-CTC CAT GTA GAG GCA AAG CA-3′)

 [9,13,20,24,164,165,166,167,168,169,170,171,172]
ORF94
  • ●

    Number of bp in the repeat unit: 54 bp

  • ●

    The most informative single genetic marker

  • ●

    Repeat unit sequences:

  • -

    CGC AAA AAG CGT GCC GCA CCT CCA CCT GAG GAT GAA GAA GAG GAT GA G/T TTC TAC

  • ●

    Primers:

  • -

    ORF94-F (5′-TCT ACT CGA GGA GGT GAC GAC-3′)

  • -

    ORF94-R (5′-AGC AGG TGT GTA CAC ATT TCA TG-3′)
ORF125
  • ●

    Number of repeat unit: 69 bp

  • ●

    Repeat unit sequences:

  • -

    AG/TA AAC AAG GAG GAA GAA GAC GCG AGG ATA AAG CGT GTA GCC GTC AGG ACA TTT ACA GCC ATC AGA GAAA

  • ●

    Primers:

  • -

    ORF125F (5′-TGG AAA CAG AGT GAG GGT CA-3′)

  • -

    ORF125R (5′-CAT GTC GAC TAT ACG TTG AAT CC-3′)
ORF14/15
  • ●

    Prone to the recombination region
ORF23/24
  • ●

    Deletion region
ORF109
  • ●

    Nucleotide position: 163996–164238

  • ●

    VP15

  • -

    Location: nucleocapsid

  • -

    Overlaps with ORF110 (11 kDa)
ORF182
  • ●

    Nucleotide position: 290363–289998

  • ●

    VP19

  • -

    Location: envelope
ORF153
  • ●

    VP26

  • -

    Location: nucleocapsid

  • -

    Tegument protein

  • -

    N-terminal anchors in the envelop

  • -

    C-terminal is bound to the nucleocapsid

  • -

    Capable of binding to actin or actin-associated proteins

  • -

    Interacts with VP51
ORF-wsv002
  • ●

    VP24

  • -

    Location: nucleocapsid

  • -

    Major structural protein

  • -

    Chitin-binding protein
ORF-wsv421
  • ●

    VP28

  • -

    Location: envelope

  • -

    Major structural protein

  • -

    Early stages of virus infection

  • -

    Viral attachment protein

  • -

    Helps the virus to enter the cytoplasm
ORF-wsv308
  • ●

    VP51

  • -

    Location: nucleocapsid

  • -

    Molecular mass: 51.9 kDa

  • -

    Encodes a 466 aa protein
ss DNA IHHNV
(Decapod penstylhamaparvovirus 1)		 ORF1
  • ●

    Length: 2001 bp

  • ●

    Starts at nt 648 and terminates with a TAA codon at 2648 nt

  • ●

    Encodes a 666 aa protein with a molecular weight of 75.77 kDa

  • ●

    Coding domain

  • -

    Nonstructural proteins 1

  • -

    Function: enzymatic activities involved in viral transcription and replication

  • ●

    Contained highly conserved replication initiator motifs (rolling-circle replication (RCR) motifs) and NTP-binding and helicase domains (ATPase motifs)

 [57,58,59,85,173,174]
ORF2
  • ●

    Length: 1092 bp

  • ●

    Starts with an ATG codon at 591 nt and terminates with a TAG codon at 1681 nt

  • ●

    Encodes a 363 aa protein with a molecular mass of 42.11 kDa

  • ●

    Coding domain

  • -

    Nonstructural proteins 2

  • -

    Function: viral multiplication
ORF3
  • ●

    Length: 990 bp

  • ●

    Smallest among the three ORFs

  • ●

    Starts with an ATG at 2590 nt, and terminates with an TAA codon at 3577 nt

  • ●

    Encodes a 329 aa protein with a molecular mass of 37.48 kDa

  • ●

    Coding domain: CP
RNA virus ds RNA IMNV
(PsIMNV)		 ORF1
(59 ORF)
  • ●

    Length: 5127 nt

  • ●

    Nucleotide: 136–4953

  • ●

    First half of ORF1

  • -

    Region of the RNA-binding protein

  • -

    Contained a dsRNA-binding motif in the first 60 aa

  • ●

    The second half of ORF1

  • -

    Encodes a capsid protein (molecular mass of 106 kDa)

 [62,73,74,76,83,86]
ORF2
(39 ORF)
  • ●

    Length: 2739 nt

  • ●

    Nucleotides: 5241–7451

  • ●

    Encoded a putative RNA-dependent RNA polymerase (RdRp)
ss RNA YHV ORF1a
  • ●

    Nucleotides: 12,216

  • ●

    Encodes a 4027 aa polyprotein (pp1a)

  • ●

    ORF1a polyprotein (pp1a)

  • -

    15 amino acids longer than GAV pp1a

  • -

    Contains four hydrophobic domains (HD1, HD2, HD3 and HD4)

  • -

    3C-like cysteine protease catalytic domain

  • -

    Papain-like protease (PL1) domain

  • -

    Lacks the canonical α + β fold of the papain-like protease (PLX) domain

  • -

    Autolytic activity

 [1,92,100,104,107,111,114,163,175,176]
ORF1a/ORF1b
  • ●

    Fold into a complex pseudoknot structure

  • ●

    A slippery hepta nucleotide (AAAUUUU)

  • ●

    The ribosomal frame-shift (RFS):

  • -

    Generate polyprotein pp1ab

  • ●

    ORF1a/ORF1b overlaping polyprotein (pp1ab):

  • -

    Overlaps by 37nt

  • -

    15 amino acids longer than GAV pp1ab
ORF1b
  • ●

    Nucleotides: 7887

  • ●

    Encodes a 6688 aa polyprotein (pp1b)

  • ●

    Encodes enzyme of the replication complex:

  • -

    RNA dependent RNA polymerase

  • -

    Cysteine and histidine-rich domain (C/H) Zn fingers

  • -

    Helicase (HEL)

  • -

    Exonuclease

  • -

    Uridylate-specific endoribonuclease

  • -

    Ribose-2′-O-methyl transferase domains

  • ●

    Untranslated region (UTR) between ORF1b and ORF2:

  • -

    352 nt
ORF2
  • ●

    Encodes a 146 aa nucleoprotein (p20)
ORF3
  • ●

    Encodes a 1666 aa polyglycoprotein (pp3):

  • -

    Generates the envelop glycoproteins 22, 64, and 116

  • ●

    Glycoprotein 22 (gp 22)

  • -

    Unknown function

  • ●

    Glycoprotein 64 (gp 64)

  • -

    Major structural protein

  • -

    Form the spike-like projection on the virion surface

  • ●

    Glycoprotein 116 (gp 116)

  • -

    Major structural protein

  • -

    Form the spike-like projection on the virion surface

  • -

    Bind to a 65 kDa protein in the lymphoid organ cells

  • -

    Identity of gp116 with GAV gp116: 73%

  • ●

    Untranslated region (UTR) between ORF3 and the 3‘-poly(A) tail

  • -

    677 nt
ORF4
  • ●

    677 nt region downstream of ORF3

  • ●

    Encodes a 20 aa polypeptide

  • ●

    Interrupted by multiple stop codons
GAV ORF1a
  • ●

    ORF1a polyprotein (pp1a)

  • -

    Encodes 3C-like cysteine protease catalytic domain

  • -

    Identity of pp1a with YHV pp1a: 82.4%

 [1,92,100,107,114,177]
ORF1b
  • ●

    Identity of the ORF1b sequence with YHV ORF1b: ~82%

  • ●

    Untranslated region (UTR) between ORF1b and ORF2

  • -

    93 nt
ORF1a/ORF1b
  • ●

    Identity of pp1ab with YHV pp1ab: 84.9%
ORF2
  • ●

    Encodes a 144 aa polypeptide
ORF3
  • ●

    Encodes a 1640 aa glycoprotein

  • ●

    Identity of the ORF3 sequence with YHV ORF3: ~74%
ORF4
  • ●

    638 nt region downstream of ORF3

  • ●

    An unidentified 83 aa polypeptide
TSV ORF1
  • ●

    Nucleotides: 6324

  • ●

    Amino acid polyprotein: 2107

  • ●

    Molecular mass: 234 kDa

  • ●

    Encode the non-structural proteins

  • -

    Helicase

  • -

    Protease

  • -

    RNA dependent RNA polymerase

 [95,128,130,178]
ORF2
  • ●

    Nucleotides: 3036

  • ●

    Amino acid polyproteins: 1011

  • ●

    Molecular mass: 112 kDa

  • ●

    Encodes 3 major and 1 minor capsid proteins:

  • -

    Major VP1 (55 kDa)

  • -

    Major VP2 (40 kDa)

  • -

    Major VP3 (24 kDa)

  • -

    Minor VP0 (58 kDa)
WTD
(MrNV)		 ORF1
(RNA-1)
  • ●

    Length: 2.9 Kbp

  • ●

    Nucleotides: 3202

  • ●

    Encodes approximately 1000 amino-acids (approximately 100 kDa) and a B protein encoded by the 30 region (13 kDa)

  • ●

    Coding domain:

  • -

    Protein A or RNA-dependent RNA polymerase

  • -

    Protein B2

 [56,140,150,153,156,157]
ORF2
(RNA-2)
  • ●

    Length: 1.26 Kbp

  • ●

    Nucleotides: 1175

  • ●

    Coding domain:

  • -

    Capsid protein (CP-43)
WTD
(XSV)		 XSV genome
  • ●

    Length: 900 bp

  • ●

    Nucleotides: 796

  • ●

    Short poly (A) tail and polyadenylation signal AAUAAA were found

  • ●

    Coding domains:

  • -

    Capsid protein (CP-16 or CP-17)

  • -

    Methionine N-terminal ends for both polypeptides