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 212-671-5890 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. |
|
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. |
|
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. |
|
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. |
|
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 212-671-5890 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. |
|
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 |
|
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. |
|
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 212-671-5890. 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. |
|
HIV-1 RNA QUALITATIVE ASSAY (Nucleic Acid Amplification Test; NAAT) |
Specimen: | Plasma |
Method: | Transcription-Mediated Amplification | |
Turn Around Time: | 5 days | |
Special Requirements: | 212-671-5890
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. |
|
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. |
|
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. |
|
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. |
|
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. |
|
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. |
|
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. | |
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. |
|
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. |
|
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. | |
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) |