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Volume 21, Number 1—January 2015
Research

Protocol for Metagenomic Virus Detection in Clinical Specimens1

Claudia KohlComments to Author , Annika Brinkmann, Piotr W. Dabrowski, Aleksandar Radonić, Andreas Nitsche, and Andreas Kurth
Author affiliations: Robert Koch Institute, Berlin, Germany

Main Article

Table 4

PCRs used to develop a protocol for metagenomic virus detection in infectious disease settings*

Virus or DNA Characteristic Primer Gene, sequence (5′→3′), and reference
Reovirus PCR target – T3/Germany/Bat/342/08 polymerase gene
Forward primer BatReoF CACCATgTCAAgCTgCTCCC
Reverse primer BatReoR ACCgCCATgTATgTCCTCCAg
Probe Bat Reo FAM-CCCAgTCgCggTCATTACCACTCCg-BBQ
Reference – Kohl et al. (11)
Influenza virus PCR target – Generic influenza A virus detection
Forward primer M+ 25 AgATgAgTCTTCTAACCgAggTCg
Reverse primer M-124BB CCW-gCAAARACATCYTCAAgTYTCTg
Probe MGB M+64 FAM-TCAggCCCCCTCAA-MGB
Reference – Schulze et al. (15)
Vaccinia virus PCR target – Generic orthopoxvirus detection
Forward primer OPV F TATTACTTCgATTGCTCATCCAgg
Reverse primer OPV R ACTTCTCACAAATggATTTGAAAATC
Probe OPV TMGB FAM-TCCTTTACgTGATAAATCAT-MGB
Reference – Schroeder and Nitsche (16)
Sendai virus PCR target – Large polymerase gene
Forward primer Sendai F1 gAGCCGCCTggTCTCCTCAgA
Reverse primer Sendai R1 AAggCATggCggACAgTggC
Probe Sendai MGB FAM-CCgTAgACAATTACACAAgT-MGB
Reference – In house design
Chicken DNA PCR target – galTBP gene NM_205103.1
Forward primer galTBP F gTgTCCACggTgAATCTTgg
Reverse primer galTBP R TgCATTCTAACATACTTCTCTTACCTTg
Probe galTBP TM 6-FAM-CgTgCCCGAAATgCTgAATATAATCCCA-BBQ
Reference – Kurth (17)
Mammalian DNA PCR target – c-myc oncogene HUMMYCF03
Forward primer C-myc F gCCAgAggAggAACgAgCT
Reverse primer C-Myc R gggCCTTTTCATTgTTTTCCA
Probe C-Myc TM Cy5-ATgCCCTgCgTgACCAgATCC-NFQ
Reference – Schroeder and Nitsche (16)

*–, not applicable.

Main Article

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Main Article

1Preliminary results of this study were presented at the Biodefense and Emerging Infectious Diseases Meeting, January 29, 2014, Washington DC, USA.

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