qPCR for Nairobi sheep disease orthonairovirus & Ganjam (Nairoviridae - family: incl. CCHFV)

[qPCR4vir]

Bunyavirales - order (Phylum:Negarnaviricota; Subphylum:Polyploviricotina; Class:Ellioviricetes)

Nairoviridae - family

Orthonairovirus - genus

Nairobi sheep disease orthonairovirus - specie. Taxonomy ID: 194540. Important tick-borne pathogen of sheep and goats in Africa, also present in Asia

• seq. GB 93 seq
  L, 6 CG, 28 total bis 90% (NC_034387,.. + Ganjam: KU925464, HQ286601, EU697949). Next not Nairobi - specie: 70%: Tofla, Hazara, Dubge, CCHFV, Kupe. Possible PCR: 6877-6994 or -7141
  M, 7 CG bis 78% (NC_034391=KM464725, MH791450, EU697952, ... + Ganjam: KU925465, HQ286599, EU697950), Not Naironbi bis 70% : Tofla, Hazara, Dubge, CCHFV, Kupe
  S, CG ~11, 23 total (18 diff) bis 85% (NC_034386,.. + Ganjam: KU925466, HQ286602, AF504294, HQ286609, ). Next not Nairobi - specie: 76%: Tofla, Hazara, Dubge, CCHFV, Kupe. Possible PCR: 241-522
• primers Literatur
• oligos
• primers, PCR
• exp

*** Ganjam virus - isolate (IP 4081, UG MP 5689) (Nairobi sheep disease orthonairovirus - specie)

• seq. GB 3 seq but... = txid1810948 in GenBank, but not well defined - many are marked as Nairobi sheep disease virus, with Taxonomy ID: 194540
  L, 3 CG bis 99% (KU925464, HQ286601, EU697949) - one strain of Nairobi sheep disease orthonairovirus - specie. Next Nairobi 90%. Next not Nairobi - specie: 70%: Tofla, Hazara, Dubge, CCHFV, Kupe
  M, 3 CG bis 99% (KU925465, HQ286599, EU697950), other 6 seq. bis 95%. Next Nairobi - 78%. Not Naironbi bis 69% : Tofla, Hazara, Dubge, CCHFV, Kupe
  S, CG ~7 bis 94% (KU925466, HQ286602, AF504294, HQ286609, ). Next Nairobi - 90%. Next not Nairobi - specie: 76%: Tofla, Hazara, Dubge, CCHFV, Kupe
• primers Literatur
• oligos
• primers, PCR
• exp

our CCHF-qPCR
CCHF-s_S-f Genome position: 1,068–1,095
CCHF-s_S-p Genome position: 1,172–1,198
CCHF-s_S-r Genome position: 1,223–1,248