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 Sicinivirus A seqs

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  Genus: Sicinivirus

Species: Sicinivirus A

Type: sicinivirus A1
        (SiV-A1) 
 
5' UTR L VP0 VP3 VP1 2A 2B 2C 3A 3B 3C 3D 3' UTR
Type: sicinivirus A2
        (SiV-A2) 
 
5' UTR L VP0 VP3 VP1 2A 2B 2C 3A 3B 3C 3D 3' UTR
Type: sicinivirus A3
        (SiV-A3) 
 
5' UTR L VP0 VP3 VP1 2A 2B 2C 3A 3B 3C 3D 3' UTR
Type: sicinivirus A4
        (SiV-A4) 
 
5' UTR L VP0 VP3 VP1 2A 2B 2C 3A 3B 3C 3D 3' UTR
Type: sicinivirus A5
        (SiV-A5) 
 
5' UTR L VP0 VP3 VP1 2A 2B 2C 3A 3B 3C 3D 3' UTR

Proposed type classification (N.J. Knowles, unpublished data)

(White areas indicate genes which haven't yet been sequenced completely; grey areas are where only partial sequences exist)

Virus Strain Region Length Accession No. Reference Comments

sicinivirus A1 (SiV-1)

SiV-1 ch/UCC001/Eire CG(p) 9276 KF741227 Bullman et al., 2014 5' end missing
SiV-1 ch/UCC1/Eire/2012 CG(p) 8334 KF366619 Bullman et al., unpub. 5' end missing
SiV-1 ch/Pf-CHK1/HUN/2013 CG(p) 9883 KT880665 Boros et al., 2016  
             

sicinivirus A2 (SiV-2)

SiV-2 ch/JSY/China/2014 CG 9809 KP779642 Zhou et al., 2015  
             

sicinivirus A3 (SiV-3) (aka chicken picornavirus 1)

SiV-3 ch/55C/Hong Kong/2008 CG(p) 8287 KF979331 Lau et al., 2014 5' end missing
SiV-3 ch/RS/BR/2015/2 CG(p) 9128 KY069113 Lima et al., unpub. 5' end missing
             

sicinivirus A4 (SiV-4) (aka chicken picornavirus 1)

SiV-4 ch/100C/Hong Kong/2009 CG(p) 8331 KF979332 Lau et al., 2014 5' end missing
             

sicinivirus A5 (SiV-5)

SiV-5 ch/RS/BR/2015/1 CG(p) 9253 KY069112 Lima et al., unpub. 5' end missing
             

sicinivirus 10 (candiate new type)

SiV ch/SiV 10 VP0(p)-2A(p) 2557 KX100567 Morgan et al., unpub.  
             

unclassified siciniviruses

SiV ch/RS/BR/2015/7R-2   1023 MG846466 Lima et al., 2018  
SiV ch/RS/BR/2015/7R-3   1025 MG846467 Lima et al., 2018  
SiV ch/RS/BR/2015/7R-1   1065 MG846468 Lima et al., 2018  
SiV ch/RS/BR/2015/2R-5   1073 MG846469 Lima et al., 2018  
SiV ch/RS/BR/2015/2S-2   1131 MG846470 Lima et al., 2018  
SiV ch/RS/BR/2015/2R-3   1149 MG846471 Lima et al., 2018  
SiV ch/RS/BR/2015/1R-2   1236 MG846472 Lima et al., 2018  
SiV ch/RS/BR/2015/2R-4   1502 MG846473 Lima et al., 2018  
SiV ch/RS/BR/2015/3S-4   1548 MG846474 Lima et al., 2018  
SiV ch/RS/BR/2015/2R-2   1696 MG846475 Lima et al., 2018  
SiV ch/RS/BR/2015/3S-3   1723 MG846476 Lima et al., 2018  
SiV ch/RS/BR/2015/3S-2   2587 MG846477 Lima et al., 2018  
SiV ch/RS/BR/2015/2R-1 2C(p) to 3'UTR 3832 MG846478 Lima et al., 2018  
SiV ch/RS/BR/2015/3S-1 5'UTR(p) to VP1 4486 MG846479 Lima et al., 2018  
SiV ch/RS/BR/2015/2S-1 CG(p) 8710 MG846480 Lima et al., 2018  
SiV ch/RS/BR/2015/4R CG(p) 9075 MG846481 Lima et al., 2018  
SiV ch/RS/BR/2015/3R CG(p) 9240 MG846482 Lima et al., 2018  
SiV ch/RS/BR/2015/1R-1 CG(p) 9270 MG846483 Lima et al., 2018  
SiV ch/RS/BR/2015/7S CG(p) 9471 MG846484 Lima et al., 2018  
SiV ch/RS/BR/2015/4S CG(p) 9547 MG846485 Lima et al., 2018  
SiV ch/RS/BR/2015/5S CG(p) 9711 MG846486 Lima et al., 2018  
SiV ch/RS/BR/2015/5R CG(p) 9874 MG846487 Lima et al., 2018  
SiV ch/UT-G-Khajehnasiri/Iran/2017 CG(p) 9277 MT215487 Zamani et al., unpub.  
SiV ch/UT-G-Masoumi/Iran/2017 CG(p) 9884 MT225405 Zamani et al., unpub.  
SiV ch/GA/1472/2004/USA CG(p) 9775 MN873045 Goraichuk et al., unpub.  
SiV ch/GA/1477/2005/USA CG(p) 9687 MN873046 Goraichuk et al., unpub.  
SiV ch/GA/1478/2003/USA CG(p) 9670 MN873047 Goraichuk et al., unpub.  
SiV ch/GA/1479/2004/USA CG(p) 9806 MN873048 Goraichuk et al., unpub.  
SiV ch/B1203/Mexico/2019 CG(p) 9706 MT345550 Parris, unpub.
             

Pacific black duck sicini-like virus

  pbd/4111nt/PBD05.18-AU-2018   4111 MT247839 Vibin et al., 2020 Anas superciliosa
  pbd/4792nt/PBD05.18-AU-2018   4792 MT247840 Vibin et al., 2020 Anas superciliosa
             
CG = complete genome
(p) = partial gene sequence

References

Boros, A., Pankovics, P., Adonyi, A., Fenyvesi, H., Day, J.M., Phan, T.G., Delwart, E. and Reuter, G. (2016). A diarrheic chicken simultaneously co-infected with multiple picornaviruses: Complete genome analysis of avian picornaviruses representing up to six genera. Virology 489: 63-74. Epub 2015 Dec 18.

Bullman, S., Kearney, K., O'Mahony, M., Kelly, L., Whyte, P., Fanning, S. and Morgan, J.G. (2014). Identification and genetic characterisation of a novel picornavirus from chickens. J. Gen. Virol. 95: 1094-1103.

Lau, S.K., Woo, P.C., Yip, C.C., Li, K.S., Fan, R.Y., Bai, R., Huang, Y., Chan, K.H. and Yuen, K.Y. (2014). Chickens host diverse picornaviruses originated from potential interspecies transmission with recombination. J. Gen. Virol. 95: 1929-1944.

Lima DA, Cibulski SP, Tochetto C, Varela APM, Finkler F, Teixeira TF, Loiko MR, Cerva C, Junqueira DM, Mayer FQ, Roehe PM. The intestinal virome of malabsorption syndrome-affected and unaffected broilers through shotgun metagenomics. Virus Res. 2018 Dec 10. pii: S0168-1702(18)30482-9. doi: 10.1016/j.virusres.2018.12.005. [Epub ahead of print] PubMed PMID: 30543873.

Vibin J, Chamings A, Klaassen M, Bhatta TR, Alexandersen S. Metagenomic characterisation of avian parvoviruses and picornaviruses from Australian wild ducks. Sci Rep. 2020 Jul 30;10(1):12800. doi: 10.1038/s41598-020-69557-z. PMID: 32733035; PMCID: PMC7393117.

Zhou, H., Zhu, S., Quan, R., Wang, J., Wei, L., Yang, B., Xu, F., Wang, J., Chen, F. and Liu, J. (2015). Identification and genome characterization of the first sicinivirus isolate from chickens in mainland China by using viral metagenomics. PLoS One 10: e0139668.

 

 
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