Tests and Services Manual: Virus Identification

APTIMA HIV-
1 QUANT ASSAY
Specimen: Human plasma
Method: Transcription-Mediated Amplification
Turn Around Time: 5 – 8 days
Special Requirements: Authorization needs to be obtained prior to submission — contact the laboratory at 212-447-2864

Plasma collected in Becton-Dickinson EDTA Plasma Preparation Tubes (PPT).

Minimum volume of plasma is 4mL. Ship with cold gel packs within 72 hours from the time collected. Alternatively, store at -70° C and ship with dry ice.
Laboratory Test Request Form: HIV Testing (PDF)
BIOFIRE FILM ARRAY-
GASTROINTESTINAL (GI)
PANEL ASSAY
Specimen: Human stool collected in Cary Blair transport medium
Method: Film Array
Turn Around Time: Within 24 hours
Special Requirements: Contact the Bureau of Communicable Diseases at 347-396-2600 for submission requirements.

Minimum volume required is 1 mL.

Ship with cold gel packs within 48 hours from the time collected. Alternatively, store at -70° C and ship with dry ice.
Laboratory Test Request Form: General Testing Service (PDF)
BIOFIRE FILM ARRAY-
RESPIRATORY (RP)
PANEL ASSAY
Specimen: Nasopharyngeal (NP) swabs in Viral Transport Medium
Method: Film Array
Turn Around Time: Within 24 hours
Special Requirements: Contact the Bureau of Communicable Diseases at 347-396-2600 for submission requirements.

Minimum volume required is 3mL.

Ship with cold gel packs within 48 hours from the time collected. Alternatively, store at -70° C and ship with dry ice.
Laboratory Test Request Form: General Testing Service (PDF)
CHIKUNGUNYA
REAL-TIME RT-PCR
Specimen: Human serum or plasma
Method: Real-time RT-PCR
Turn Around Time: 3 - 5 days
Special Requirements: Contact the Bureau of Communicable Diseases at 347-396-2600 for submission requirements.

Blood sample must be taken during the acute period of the disease (first 7 days of symptoms).

Minimum volume required is 3 ml. Keep samples frozen at -20º C. Ship with cold gel pack or dry ice.
Laboratory Test Request Form: General Testing Service (PDF)
COBAS®AMPLIPREP/
COBAS®TAQM
TAQMAN®HIV-1 TEST,
VERSION 2.0
Specimen: Plasma
Method: in vitro nucleic acid amplification test for the quantitation of human HIV-1
Turn Around Time: 3-6 business days
Special Requirements: Authorization needs to be obtained prior to submission-contact the laboratory at 212-447-2864

Plasma collected in Becton-Dickinson EDTA Plasma Preparation Tubes (PPT).

Minimum volume of plasma is 4mL. Ship with cold gel packs within 72 hours from the time collected. Alternatively, store at -70° C and ship with dry ice.
Laboratory Test Request Form: HIV Testing (PDF)
DENGUE VIRUS
real-time RT-PCR
Specimen: Human serum or plasma
Method: Real-time RT-PCR
Turn Around Time: 3 - 5 days
Special Requirements: Contact the Bureau of Communicable Disease at (347) 396-2600 for submission requirements.

Blood sample must be taken during the acute period of the disease (first 7 days of symptoms). Minimum volume required is 3 ml. Keep samples frozen at -20º C. Ship with cold gel pack or dry ice
Laboratory Test Request Form: General Testing Service (PDF)
EBOLA VIRUS
REAL-TIME RT-PCR –
CDC ASSAY
Specimen: Whole blood
Plasma
Serum
Urine (cannot be the sole specimen)
Method: Real-time RT-PCR
Turn Around Time: Within 24 hours
Special Requirements: Must contact the Bureau of Communicable Diseases at 347-396-2600 immediately if there is any suspect case.

Follow the guidelines on specimen collection and storage, provided by Bureau of Communicable Diseases. NYC Public Health Laboratory will pick up the specimen. Also refer to CDC “Guidance for Collection, Transport and Submission of Specimens for Ebola Virus Testing” for details.

Minimum specimen volume required is 4 mL (≥2mL for pediatric samples) for either whole blood, plasma or serum.
Laboratory Test Request Form: General Testing Service (PDF)
HIV-2 DNA
real-time PCR
Specimen:

Whole blood

Method: Real-time PCR
Turn Around Time: 7 - 10 days
Special Requirements: Authorization needs to be obtained prior to submission-contact the laboratory at (212) 447-2864.

Minimum specimen volume required is 7 ml (or ≥2mL for pediatric samples), in a single ACD (acid citrate dextrose) tube. A lavender top tube with EDTA is also acceptable.
Specimens must be received by PHL within 6 hours of blood draw.
Laboratory Test Request Form: Contact Laboratory
HIV-1 RNA
QUALITATIVE ASSAY
(Nucleic Acid
Amplification
Test; NAAT)
Specimen: Plasma
Method: Transcription-Mediated Amplification
Turn Around Time: 5 days
Special Requirements: (212) 447-2864

Plasma collected in EDTA Plasma Preparation Tube (PPT). Minimum volume of plasma is 4 ml. Ship with cold gel packs within 72 hours from the time collected. Alternatively, store at -70º C and ship with dry ice.
Laboratory Test Request Form: HIV Testing (PDF)
INFLUENZA Virus
real-time RT-PCR
Specimen: Respiratory swabs in viral transport medium including Nasopharyngeal swab, nasal swab, nasal aspirate dual nasophayngeal swab/throat swab in viral transport medium
Method: Real-time RT-PCR
Turn Around Time: 3 - 5 days
Special Requirements: Contact the Bureau of Communicable Disease at (347) 396-2600 for submission requirements.

Minimum volume required is 3 ml. Ship with cold gel packs within 48 hours from the time collected. Alternatively, store at -70º C and ship with dry ice.
Laboratory Test Request Form: General Testing Service (PDF)
MEASLES VIRUS
real–time RT-PCR
Specimen: Nasopharyngeal swab, throat swab in viral transport medium
Method: Real-time RT-PCR
Turn Around Time: 3 - 5 days
Special Requirements: Contact the Bureau of Immunization at (347) 396-2402 for submission requirements.

Minimum volume required is 3 ml. Ship with cold gel packs within 48hours from time collected. Alternatively, store at 70º C and ship with dry ice.
Laboratory Test Request Form: General Testing Service (PDF)
MERS-CoV
real-time RT-PCR
Specimen: Nasopharyngeal swab, oropharyngeal swab, sputum, lower respiratory tract aspirates/washes, in viral transport medium
Method: Real-time RT-PCR
Turn Around Time: 3 - 5 days
Special Requirements: Contact the Bureau of Communicable Disease at (347) 396-2600 for submission requirements.

Minimum volume required is 3 ml. Ship with cold gel packs within 48 hours from the time collected. Alternatively, store at -70º C and ship with dry ice.
Laboratory Test Request Form: MERs Co-V (PDF)
MUMPS VIRUS
real-time RT-PCR
Specimen: Oral/buccal swab, oropharyngeal swab in viral transport medium
Method: Real-time RT-PCR
Turn Around Time: 3 - 5 days
Special Requirements: Contact the Bureau of Immunization at (347) 396-2402 for submission requirements.

Minimum volume required is 3 ml. Ship with cold gel packs within 48 hours from time collected. Alternatively, store at 70º C and ship with dry ice.
Laboratory Test Request Form: General Testing Service (PDF)
NOROVIRUSES
GENOGROUP I (GI) and
GENOGROUP II (GII)
real-time RT-PCR
Specimen: Stool
Method: Real-time RT-PCR
Turn Around Time: 3 - 5 days.
Special Requirements: Contact the Bureau of Communicable Disease at (347) 396-2600 for submission requirements.

Store at 4º C and ship with cold gel packs within 72 hours from the time collected. Alternatively, store at -70º C and ship with dry ice.
Laboratory Test Request Form: General Testing Service (PDF))
ORTHOPOX
VIRUS/NON-VARIOLA
OTHOPOX VIRUS PCR
(DOHMH Refferrals Only)


SPECIMEN:
Dried vesicular fluid on slide (touch prep), skin, or crust from roof of vesicle, dry or wet lesion swab, cellular material from tissue culture demonstrating cytopathic effect. Store at 2º - 8º C and ship with cold gel packs.
Method: Real-time PCR
Turn Around Time: 1 - 2 days
Special Requirements: Contact the Bureau of Communicable Disease at (347) 396-2600 for submission requirements.
Laboratory Test Request Form: General Testing Service (PDF)
VIRUS ISOLATION/
DETECTION
(RESPIRATORY
VIRUSES)
Specimen: Nasal swab in viral transport medium (VTM)
Nasopharyngeal swabs in VTM
Nasal aspirates/nasopharyngeal aspirate
Throat swab (tonsillar area & posterior nasopharynx) in VTM
Bronchoalveolar lavage (BAL)
Pleural fluid
Tissue (e.g. lung biopsy) in VTM
Buccal swab (mumps) in VTM
Method: Conventional tube culture

Centrifuge-enhanced culture
Turn Around Time: Conventional tube culture: 14 days to rule out negatives

Centrifuge-enhanced culture: 24 to 48 hours
Special Requirements: Contact the Bureau of Communicable Disease at (347) 396-2600 for submission requirements.

Swab specimens should be collected using flocked swabs or Dacron ® tipped aluminum or plastic shaft.  Calcium alginate- or cotton-tipped swabs are not acceptable.
Keep specimens at 4º C and deliver within 24 to 48 hours after collection.
Laboratory Test Request Form: General Testing Service (PDF)
Note: (Respiratory Virus Screening: RSV, Flu A, Flu B, Parainfluenza 1, 2, 3, Adenovirus)
VIRUS ISOLATION/
DETECTION
(GENERAL)
Specimen: Enteroviruses: Stool or rectal swab in VTM, CSF (if CNS involvement is suspected)

Other Viruses: lesion swab or aspirate; brain tissue; nasopharyngeal, tracheal, buccal, throat, genital swabs; urine (CMV); pleural, pericardial fluid. All swabs and aspirates should be in VTM. Urine (no VTM).
Method: Conventional tube culture Centrifuge-enhanced culture
Turn Around Time: Conventional tube culture: 14-21 days to rule out negatives

Centrifuge-enhanced culture: 1-5 days
Special Requirements: Specimens: keep specimens at 4º C and deliver within 24 to 48 hours after collection.

CSF: Do not dilute with VTM. Store specimen at -70º C. Deliver to the laboratory with dry ice.

Do not freeze urine.
Laboratory Test Request Form: General Testing Service (PDF)
Note: Enterovirus Screening: Enterovirus, ECHO, Coxsackie A, Coxsackie B, Polio

Other viruses: HSV 1, HSV 2, CMV, VZV, Measles, Mumps.
ViroSEq HIV-1
Genotyping Systems (protease, reverse transcriptase, and integrase)
Specimen requirements: Plasma collected in Becton-Dickinson EDTA Plasma Preparation Tubes (PPT). Minimum volume of plasma is 4mL. Plasma must be separated no later than 2 hours after blood draw, and shipped with cold gel packs within 24 hours from the time collected. Alternatively, store separated plasma at -70° C and ship with dry ice.
Method: Reverse Transcription-Polymerase Chain Reaction followed by Sanger Sequencing and data analysis using ViroSeq HIV-1 Genotyping Software, for the detection of antiretroviral drug resistance mutations in HIV-1 from HIV-1 positive patients
Turn Around Time: 5-7 days; up to 2 weeks if repeat testing is required.
Special Requirements: Physicians can request this test for all patients newly diagnosed with HIV-1 infection.
Laboratory Test Request Form: HIV Testing (PDF)
WNV real-time PCR Specimen: Mosquito pool
Method: Real-time RT-PCR
Turn Around Time: 24 - 48 hrs.
Special Requirements: Mosquito pools must be frozen at -70º C.
Laboratory Test Request Form: N/A (Samples accepted from DOHMH Vector Control only)
ZIKA VIRUS
REAL-TIME RT-PCR
Specimen: Human serum and urine
Method: Real-time RT-PCR
Turn Around Time: 3 - 5 days
Special Requirements: Call the Provider Access Line for submission requirements and to order testing.

Blood sample must be taken during the acute period of the disease (first 7 days from onset of the symptoms).

Serum sample must be collected in SST or red top tubes and spun down prior to specimen submission. Serum (but not the whole blood) can be shipped with cold icepacks within 48 hours of blood draw or dry ice if longer than 48 hours.

If whole blood is to be submitted without centrifugation, the sample must be collected in SST or red top tubes and sent with cold icepack (not dry ice) and received by PHL within 6 hours of blood draw.

Minimum volume required for serum is 3 ml for serum and 5 ml for whole blood.

Clean voided urine specimens (5-10ml) must be collected in sterile containers with external cap and internal O-ring seal.

Urine specimens must be delivered with cold ice packs within 48 hours from the time collected, or with dry ice if longer than 48 hours.
Laboratory Test Request Form: Call Provider Access Line to order testing: (PAL) 866-692-3641
ZIKA VIRUS
REAL-TIME RT-PCR
FOR MOSQUITO
POOLS
Specimen: Mosquito pool, Aedes species only
  Method: Real-time RT-PCR
Turn Around Time: 3-5 days
Special Requirements: Mosquito pools must be frozen at -70º C.
Laboratory Test Request Form: N/A (Sample accepted from DOHMH vector control only)
APTIMA ZIKA
VIRUS ASSAY
Specimen: Human serum and urine
Method: NAAT
Turn Around Time: 3 - 5 days
Special Requirements: The NYC Department of Health and Mental Hygiene (DOHMH) requires pre-approval for Zika virus testing conducted by DOHMH’s PHL. Approval for such testing must be obtained by calling the NYC Provider Access Line at 866-692-3641. Specimens submitted to PHL without pre-approval from DOHMH will NOT be tested.

Zika Testing Guidance for Providers (PDF).

Serum sample must be collected in SST or red top tubes and spun down prior to specimen submission. Serum (but not the whole blood) can be shipped with cold icepacks within 72 hours of blood draw or dry ice if longer than 72 hours.

If whole blood is to be submitted without centrifugation, the sample must be collected in SST or red top tubes and sent with cold icepack (not dry ice) and received by PHL within 6 hours of blood draw.

Minimum volume required for serum is 3 ml for serum and 6 ml for whole blood.

Clean voided urine specimens (20 ml) must be collected in sterile containers with external cap and internal O-ring seal.

Urine specimens must be delivered with cold ice packs within 6 hours from the time collected, or with dry ice if longer than 6 hours.