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 Molecular Diagnosis of Infection > Specimen and Report

 Samples for DNA Testing of Infectious Microorganisms

  Test   Sample   Requirement*   Method**   Report**
  Human Papilloma Virus
  (HPV)  DNA
  Liquid cytology     PCR
  qPCR
  RFLP
  Negative, Not detected
  Positive, genotype(s)
  Positive, specific genotype(s)
  unknown, multiple infection
  ThinPrep   4 ml, r.t. or 4°C
  SurePath (Autocyte)   4 ml, r.t. or 4°C
  Cervical/vaginal swab   1 swab, 4°C
  Urethral swab   1 swab, 4°C
  Topical swab   1 pre-wet swab, 4°C
  Urine   20 ml, first void
  Tampon/vaginal insert   1 set, 4°C/frozen
  Hepatitis B Virus (HBV)
  DNA
  Clotted blood   2 ml, less than 6 hr
  at 4°C
  qPCR   Negative, Not detected
  Positive but below limit of
  detection
  Positive, copies & IU/ml
  EDTA blood
  Plasma   1 ml, 4°C or frozen
  Serum
  Hepatitis C Virus (HCV)
  RNA
  EDTA blood   2 ml, less than 6 hr
  at r.t. or 4°C
  RT-qPCR   Negative, Not detected
  Positive but below limit of
  detection
  Positive, copies/ml
  Plasma   1 ml, 4°C or frozen
  Serum
  Epstein Barr Virus (EBV)
  DNA
  EDTA blood
  Plasma
  Serum
  2 ml, less than 6 hr
  at 4°C  1 ml,
  4°C or frozen
  qPCR   Negative, Not detected
  Positive, copies/ml or sample
  Nasal swab   1, 4°C or frozen
  Herpes Simplex Virus
  (HSV)  I & II  DNA
  Liquid cytology     qPCR   Negative, Not detected
  Positive
  Type I and/or II
  ThinPrep   4 ml, r.t. or 4°C
  SurePath (Autocyte)   4 ml, r.t. or 4°C
  Cervical/vaginal swab   1 swab, 4°C
  Urethral swab   1 swab, 4°C
  Topical swab   1 pre-wet swab, 4°C
  CSF   0.5 ml, 4°C /frozen
  Tampon/vaginal insert   1 set, 4°C/frozen
  Varicella Zoster Virus
  (VZV, Shingles)  DNA
  Topical swab   1 pre-wet swab, 4°C   qPCR   Negative, Not detected
  Positive
  CSF   0.5 ml, 4°C /frozen
    
   
  Chlamydia trichomatis (CT)
  DNA
  Liquid cytology     qPCR   Negative, Not detected
  Positive
  ThinPrep   4 ml, r.t. or 4°C
  SurePath (Autocyte)   4 ml, r.t. or 4°C
  Cervical/vaginal swab   1 swab, 4°C
  Urethral swab   1 swab, 4°C
  Topical swab   1 pre-wet swab, 4°C
  Urine   20 ml, first void
  Tampon/vaginal insert   1 set, 4°C/frozen
  Neisseria gonorrhea (NG)
  DNA
  Liquid cytology     qPCR   Negative, Not detected
  Positive
  ThinPrep   4 ml, r.t. or 4°C
  SurePath (Autocyte)   4 ml, r.t. or 4°C
  Cervical/vaginal swab   1 swab, 4°C
  Urethral swab   1 swab, 4°C
  Topical swab   1 pre-wet swab, 4°C
  Urine   20 ml, first void
  Tampon/vaginal insert   1 set, 4°C/frozen
  Mycoplasma genitalium
  (MG)
  Mycoplasma hominis (MH)
  DNA
  Liquid cytology     qPCR   Negative, Not detected
  Positive
  genitarium and/or hominis
  ThinPrep   4 ml, r.t. or 4°C
  SurePath (Autocyte)   4 ml, r.t. or 4°C
  Cervical/vaginal swab   1 swab, 4°C
  Urethral swab   1 swab, 4°C
  Topical swab   1 pre-wet swab, 4°C
  Urine   20 ml, first void
  Tampon/vaginal insert   1 set, 4°C/frozen
  Ureaplasma urealyticum
  parvum; Ureaplasma
  urealyticum T-960  (UU) 
  DNA
  Liquid cytology     qPCR   Negative, Not detected
  Positive
  parvum and/or T-960
  ThinPrep   4 ml, r.t. or 4°C
  SurePath (Autocyte)   4 ml, r.t. or 4°C
  Cervical/vaginal swab   1 swab, 4°C
  Urethral swab   1 swab, 4°C
  Topical swab   1 pre-wet swab, 4°C
  Urine   20 ml, first void
  Tampon/vaginal insert   1 set, 4°C/frozen
  Mycobacterium tuberculosis
  (TB) (MTb complex)  DNA
  Sputum   First in morning   qPCR   Negative, Not detected
  Positive, copies/sample
  Positive but below limit of
  detection
  Urine   20 ml, first void
  Needle biopsy  
  Environmental sample  
* Requirement
  r.t. = room temperature; fridge = 4-8oC (household refrigerator, lower compartment)
frozen = -10oC or less (household freezer, upper compartment)
ThinPrep and SurePath cell suspensions are stable > 2 weeks for cytology at room temperature. But do not keep them for more than
       3 days for DNA testing because it might affect the typing of high risk HPV types; keeping at 4oC or frozen is recommended.
** Method
  Requirements of CLIA:  E.M. Burd (2010). “Validation of Laboratory-Developed Molecular Assays for Infectious Diseases”
       Clinical Microbiology Reviews, July 2010, p. 550-576
qPCR = real time PCR, quantitative PCR;   RT-qPCR = reverse transcription qPCR;   RFLP = restriction fragment length polymorphism