Clustering of classical swine fever virus isolates by codon pair bias

Leifer, Immanuel; Hoeper, Dirk; Blome, Sandra; Beer, Martin; Ruggli, Nicolas

doi:10.1186/1756-0500-4-521

BMC Research Notes

Table 1 Overview of the CSFV strains used for this study.

From: Clustering of classical swine fever virus isolates by codon pair bias

Isolate	Genotype	Virulence status	GenBank (NCBI) entry	Reference
ALD D49532 hv	1.1	hv	D49532	[11]
Alfort187 × 87939 hv	1.1	hv	X87939	[12]
AlfortA19 U90951 hv	1.1	hv	U90951	[13]
Brescia AF091661 hv	1.2	hv	AF091661	[14]
Brescia M31768 lv¹	1.2	hv	M31768	[14]
BRESCIAX AY578687 hv	1.2	hv	AY578687	[13]
CAP X96550 lv²	1.1	Low virulent	X96550	[15]
cF114 AF333000 hv	1.1	hv	AF333000	[16]
Eystrup AF326963 hv	1.1	hv	AF326963	[17]
Eystrup NC_002657 hv	1.1	hv	NC_002657	[17]
Glentorf U45478 lv³	1.1	Low virulent	U45478	[18]
JL106 EU497410 hv	1.1	hv	EU497410	[19]
Koslov HM237795 hv	1.1	hv	HM237795	[19]
Shimen AF092448 hv	1.1	hv	AF092448	unpublished
Shimen-HVRI AY775178 hv	1.1	hv	AY775178	[19]
SWH DQ127910 hv	1.1	hv	DQ127910	[6]
C_strain AY259122 va	1.1	va	AY259122	[17]
C_strain AY382481 va	1.1	va	AY382481	unpublished
C_strain AY663656 va	1.1	va	AY663656	unpublished
C_strain C-ZJ-2008 va	1.1	va	HM175885	unpublished
C_strain HCLV AF531433 va	1.1	va	AF531433	unpublished
C_strain HVRI AY805221 va	1.1	va	AY805221	unpublished
C_strain U45477 va	1.1	va	U45477	unpublished
C_strain Z46258 va	1.1	va	Z46258	[20]
flc-LOM EU915211 va	1.1	va	EU915211
GPE- D49533 va	1.1	va	D49533	[11]
HCLV AF091507 va	1.1	va	AF091507	[21]
India vaccine EU857642 va	1.1	va	EU857642	unpublished
LOM EU789580 va	1.1	va	EU789580	[22]
LPC AF352565 va	1.1	va	AF352565	[23]
RUCSFPLUM AY578688 va	1.2	va	AY578688	[13]
Thiverval EU490425 va	1.1	va	EU490425	[24]
944IL94TWN AY646427 mv	3.4	mv	AY646427	[25]
Alfort-Tuebingen J04358 mv	2.3	mv	J04358	[26]
Borken GU233731 mv	2.3	mv	GU233731	[3]
CSF 39 AF407339 mv⁴	recombinant	mv-hv	AF407339	[27]
Euskirchen GU233732 mv	2.3	mv	GU233732	[3]
GXW_Z02 AY367767 mv	2.1	mv	AY367767	[27]
Hennef GU233733 mv	2.3	mv	GU233733	[3]
Jambul CSF0864 mv	2.3	mv	HQ148062	[28]
Novska CSF0821 mv	2.3	mv	HQ148061	[28]
Paderborn GQ902941 mv	2.1	mv	GQ902941	[29, 30]
Penevezys CSF1048 mv	2.1	mv	HQ148063	[28]
Roesrath GU233734mv	2.3	mv	GU233734	[3]
Sp01 FJ265020 mv	2.3	mv	FJ265020	unpublished
Uelzen GU324242 mv	2.3	mv	GU324242	[3]
96TD AY554397 uk	2.1	uk	AY554397	unpublished
0406CH01TWN AY568569 uk	2.1	uk	AY568569	unpublished
HEBZ GU592790 uk	2.1	uk	GU592790	unpublished
SXCDK GQ923951 uk	2.1	uk	GQ923951	unpublished
SXYL2006 GQ122383 uk	2.1	uk	GQ122383	unpublished
ZJ0801 FJ529205 uk	2.1	uk	FJ529205	unpublished

Virulence status: highly virulent (hv), moderately virulent (mv), low virulent (lv) or vaccine strains (va), and unknown virulence (uk) is indicated according to the information available. If available, the references to the sequences are indicated.
¹ Brescia M31768 lv¹ is representing the sequence of strain Brescia C1.1.1 which is a low virulent strain obtained after the 30^th passage of strain Brescia on PK-15 cells [31].
² CAP X96550 lv² is described as highly virulent strain in some publications, but was originally described as cell culture adapted strain of low virulence [15].
³ Glentorf U45478 lv³ is described as low virulent or as highly virulent strain, depending on the report. In this study it is considered to be low virulent according to the publication of Handel et al. and Ahrens et al. [18, 32]
⁴ CSF 39 AF407339 mv⁴ is a recombinant CSFV from China [27]. The virulence of this strain cannot be related to a particular genotype because the 5'NTR and the 3'NTR as well as the NS5A/B genes are homologous to genotype 1.1 strains, while the structural genes are homologous to genotype 2.1 strains. Furthermore the sequence of the original isolate is not known since the 32^nd cell culture passage was used for sequence analysis.

Back to article page

ISSN: 1756-0500

Contact us

Submission enquiries: bmcresearchnotes@biomedcentral.com
General enquiries: ORSupport@springernature.com