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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
Type: sicinivirus A6
        (SiV-A6) 
 
5' UTR L VP0 VP3 VP1 2A 2B 2C 3A 3B 3C 3D 3' UTR
Type: sicinivirus A7
        (SiV-A7) 
 
5' UTR L VP0 VP3 VP1 2A 2B 2C 3A 3B 3C 3D 3' UTR
Type: sicinivirus A8
        (SiV-A8) 
 
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Proposed type classification (N.J. Knowles, unpublished data)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;
Gallus gallus domesticus
SiV-1 ch/Pf-CHK1/HUN/2013 CG(p) 9883 KT880665 Boros et al., 2016 Gallus gallus domesticus
SiV ch/RS/BR/2015/5R CG(p) 9874 MG846487 Lima et al., 2018 Gallus gallus domesticus
SiV-1 ch/UT-G-Khajehnasiri/Iran/2017 CG(p) 9277 MT215487 Zamani et al., unpub. Gallus gallus domesticus
SiV-1 ch/UT-G-Masoumi/Iran/2017 CG(p) 9884 MT225405 Zamani et al., unpub. Gallus gallus domesticus
SiV ch/NLD/2019/V_M_017_picorna_4 CG(p) 7782 MW684789 de Rooij et al., unpub. Gallus gallus domesticus
SiV ch/NLD/2019/V_M_019_picorna_4 CG(p) 7634 MW684792 de Rooij et al., unpub. Gallus gallus domesticus
             

sicinivirus A2 (SiV-2)

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

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;
Gallus gallus domesticus
SiV-3 ch/RS/BR/2015/2 CG(p) 9128 KY069113 Lima et al., unpub. 5' end missing;
Gallus gallus domesticus
SiV-3 ch/RS/BR/2015/2R-2   1696 MG846475 Lima et al., 2018 Gallus gallus domesticus
SiV-3 env/NLD/2019/VE_6_picorna_131 CG(p) 5509 MW684780 de Rooij et al., unpub.  
SiV-3 env/NLD/2019/VE_7_picorna_3 CG(p) 9819 MW684781 de Rooij et al., unpub.  
SiV-3 ch/NLD/2019/V_M_040_picorna_3 CG(p) 6257 MW684804 de Rooij et al., unpub. Gallus gallus domesticus
SiV-3 ch/RS/BR/2015/4S CG(p) 9547 MG846485 Lima et al., 2018 Gallus gallus domesticus
SiV-3 ch/RS/BR/2015/5S CG(p) 9711 MG846486 Lima et al., 2018 Gallus gallus domesticus
SiV-3 ch/GA/1479/2004/USA CG(p) 9806 MN873048 Goraichuk et al., 2021 Gallus gallus domesticus
             

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;
Gallus gallus domesticus
             

sicinivirus A5 (SiV-5)

SiV-5 ch/RS/BR/2015/1 CG(p) 9253 KY069112 Lima et al., unpub. 5' end missing;
Gallus gallus domesticus
SiV-5 ch/RS/BR/2015/1R-1 CG(p) 9270 MG846483 Lima et al., 2018 Gallus gallus domesticus
SiV-5 ch/NLD/2019/V_M_005_picorna_5 CG(p) 6502 MW684787 de Rooij et al., unpub. Gallus gallus domesticus
SiV-5 ch/NLD/2019/V_M_034_picorna_3 CG(p) 6421 MW684796 de Rooij et al., unpub. Gallus gallus domesticus
             

sicinivirus 6 (SiV-6)

SiV ch/RS/BR/2015/4R CG(p) 9075 MG846481 Lima et al., 2018 Gallus gallus domesticus
             

sicinivirus 7 (SiV-7)

SiV ch/RS/BR/2015/2S-1 CG(p) 8710 MG846480 Lima et al., 2018 Gallus gallus domesticus
SiV ch/RS/BR/2015/7S CG(p) 9471 MG846484 Lima et al., 2018 Gallus gallus domesticus
SiV ch/GA/1477/2005/USA CG(p) 9687 MN873046 Goraichuk et al., 2021 Gallus gallus domesticus
             
             

sicinivirus 8 (SiV-8)

SiV ch/SiV 10 VP0(p)-2A(p) 2557 KX100567 Morgan et al., unpub. Gallus gallus domesticus
SiV ch/RS/BR/2015/3S-1 5'UTR(p) to VP1 4486 MG846479 Lima et al., 2018 Gallus gallus domesticus
SiV ch/RS/BR/2015/3R CG(p) 9240 MG846482 Lima et al., 2018 Gallus gallus domesticus
SiV ch/RS/BR/2015/7R-2   1023 MG846466 Lima et al., 2018 Gallus gallus domesticus
SiV env/NLD/2019/VE_8_picorna_99 CG(p) 6021 MW684785 de Rooij et al., unpub.  
SiV ch/NLD/2019/V_M_045_picorna_1 CG(p) 6065 MW684806 de Rooij et al., unpub. Gallus gallus domesticus
SiV ch/NLD/2019/V_M_046_picorna_18 CG(p) 6204 MW684808 de Rooij et al., unpub. Gallus gallus domesticus
SiV ch/NLD/2019/V_M_047_picorna_3 CG(p) 7261 MW684809 de Rooij et al., unpub. Gallus gallus domesticus
SiV ch/NLD/2019/V_M_048_picorna_1 CG(p) 7302 MW684810 de Rooij et al., unpub. Gallus gallus domesticus
SiV ch/Belgium/4439_001/2020 CG(p) 7964 MZ367371 Van Borm et al., 2021 Gallus gallus domesticus
SiV ch/GA/1472/2004/USA CG(p) 9775 MN873045 Goraichuk et al., 2021 Gallus gallus domesticus
SiV ch/GA/1478/2003/USA CG(p) 9670 MN873047 Goraichuk et al., 2021 Gallus gallus domesticus
             

sicinivirus ? (candidate new type)

SiV-1 ch/UCC1/Eire/2012 CG(p) 8334 KF366619 Bullman et al., unpub. 5' end missing;
Gallus gallus domesticus
             

sicinivirus ? (candidate new type)

SiV ch/RS/BR/2015/7R-3   1025 MG846467 Lima et al., 2018 Gallus gallus domesticus
SiV ch/RS/BR/2015/2R-4   1502 MG846473 Lima et al., 2018 Gallus gallus domesticus
             

sicinivirus ? (candidate new type)

SiV ch/B1203/Mexico/2019 CG(p) 9706 MT345550 Goraichuk et al., 2021 Gallus gallus domesticus
SiV ch/NLD/2019/V_M_056_picorna_2 CG(p) 5673 MW684816 de Rooij et al., unpub. Gallus gallus domesticus
             

sicinivirus ? (candidate new type)

SiV env/NLD/2019/VE_8_picorna_68 CG(p) 7470 MW684784 de Rooij et al., unpub.  
SiV ch/NLD/2019/V_M_050_picorna_3 CG(p) 7879 MW684813 de Rooij et al., unpub. Gallus gallus domesticus
             

unclassified siciniviruses

SiV ch/RS/BR/2015/7R-1   1065 MG846468 Lima et al., 2018 Gallus gallus domesticus
SiV ch/RS/BR/2015/2R-5   1073 MG846469 Lima et al., 2018 Gallus gallus domesticus
SiV ch/RS/BR/2015/2S-2   1131 MG846470 Lima et al., 2018 Gallus gallus domesticus
SiV ch/RS/BR/2015/2R-3   1149 MG846471 Lima et al., 2018 Gallus gallus domesticus
SiV ch/RS/BR/2015/1R-2   1236 MG846472 Lima et al., 2018 Gallus gallus domesticus
SiV ch/RS/BR/2015/3S-4   1548 MG846474 Lima et al., 2018 Gallus gallus domesticus
SiV ch/RS/BR/2015/3S-3   1723 MG846476 Lima et al., 2018 Gallus gallus domesticus
SiV ch/RS/BR/2015/3S-2   2587 MG846477 Lima et al., 2018 Gallus gallus domesticus
SiV ch/RS/BR/2015/2R-1 2C(p) to 3'UTR 3832 MG846478 Lima et al., 2018 Gallus gallus domesticus
SiV ch/Belgium/4439_001/2020 5'UTR(p)+L(p) 1345 MZ367370 Van Borm et al., 2021 Gallus gallus domesticus
             
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.

Goraichuk IV, Davis JF, Parris DJ, Kariithi HM, Afonso CL, Suarez DL. Near-Complete Genome Sequences of Five Siciniviruses from North America. Microbiol Resour Announc. 2021 May 13;10(19):e00364-21. doi: 10.1128/MRA.00364-21. PMID: 33986098; PMCID: PMC8142584.

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.

Van Borm S, Steensels M, Mathijs E, Vandenbussche F, van den Berg T, Lambrecht B. Metagenomic sequencing determines complete infectious bronchitis virus (avian Gammacoronavirus) vaccine strain genomes and associated viromes in chicken clinical samples. Virus Genes. 2021 Oct 9:112. doi: 10.1007/s11262-021-01872-7. Epub ahead of print. PMID: 34626348; PMCID: PMC8501334.

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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