Universal viral transport media system

Manufactured by BD

The BD Universal Viral Transport Media system is a collection and transport device designed to maintain the viability of a variety of viruses, including SARS-CoV-2. It provides a sterile, swab-based collection kit and a liquid medium to preserve viral samples during transport to a laboratory for testing.

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Dsp virus pathogen mini kit, by Qiagen (2 mentions) Qiasymphony and the dsp virus pathogen mini kit, by Qiagen (2 mentions)

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BD Universal Viral Transport (10 citations) Viral Transport Media (3 citations) Universal viral transport media (2 citations) BD Universal Viral Transport System (2 citations)

8 protocols using universal viral transport media system

Comparative RNA-seq analysis of viral infections

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We investigated a range of RNA-seq datasets in which primary cells or cell lines were infected with different pathogens including the three betacoronaviruses as well as the influenza virus H3N2, the bacterium Streptococcus pneumonia, Hepatitis C virus, Zika virus, Dengue virus, and Respiratory Syncytial Virus. All these datasets were downloaded from the National Center for Biotechnology Information's (NCBI) Sequence Read Archive (SRA) [19 (link)]. Infection of cell lines or primary cells with virus is a commonly used experimental system to investigate host dependency factors and host restriction factors [20 (link)].
An additional, clinical dataset was analyzed from nasopharyngeal swab specimens (SARS-CoV-2-A) from the New York-Presbyterian Hospital-Weill Cornell Medical Center [27 (link)]. We will refer to this dataset as SARS-CoV-2-A in the text. Briefly, nasopharyngeal swabs were collected using the BD Universal Viral Transport Media system (Becton, Dickinson and Company, Franklin Lakes, NJ) from symptomatic patients. Total Nucleic Acid (TNA) was extracted using automated nucleic acid extraction on the QIAsymphony and the DSP Virus/Pathogen Mini Kit (Qiagen). RNA isolation and library preparation is fully described in Butler, et al. [27 (link)].

Karlebach G., Aronow B., Baylin S.B., Butler D., Foox J., Levy S., Meydan C., Mozsary C., Saravia-Butler A.M., Taylor D.M., Wurtele E., Mason C.E., Beheshti A, & Robinson P.N. (2022). Betacoronavirus-specific alternate splicing. Genomics, 114(2), 110270.

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SARS-CoV-2 Total RNA-seq Analysis

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Samples were collected and processed through the Weill Cornell Medicine Institutional Review Board (IRB) Protocol 19-11021069. Dates of collected data for SARS-CoV-2 suspected patients was extracted from the electronic health records at NYP-CUIMC. We used data collected starting on March 10th, 2020 through April 20th, 2020. We applied this total RNA-seq platform to 732 clinical samples, including 669 confirmed or suspected COVID-19 cases at New York-Presbyterian Hospital-Weill Cornell Medical Center (NYPH-WCMC). Prior to analysis, duplicate samples, environmental samples, and seq control samples were removed. Only samples with over 2 million human genome aligned reads were included in the expression analysis (Figure S1B). Raw data are available at the database of Genotypes and Phenotypes dbGAP (accession #38851 and dbGAP: phs002258.v1.phs).
Patient specimens were collected with patients’ consent at New York-Presbyterian Hospital-Weill Cornell Medical Center (NYPH-WCMC) and then processed for qRT-PCR. Nasopharyngeal (NP) swab specimens were collected using the BD Universal Viral Transport Media system (Becton, Dickinson and Company, Franklin Lakes, NJ) from symptomatic patients. Sex was not a determining factor (nor recorded) since it was the first wave of the pandemic and we took all samples that came to the hospital.

Saravia-Butler A.M., Schisler J.C., Taylor D., Beheshti A., Butler D., Meydan C., Foox J., Hernandez K., Mozsary C., Mason C.E, & Meller R. (2022). Host transcriptional responses in nasal swabs identify potential SARS-CoV-2 infection in PCR negative patients. iScience, 25(11), 105310.

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Transcriptome Analysis of Pathogen-Infected Cells

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We investigated a range of RNA-seq datasets in which primary cells or cell lines were infected with different pathogens including the three betacoronaviruses as well as the influenza virus H3N2, the bacterium Streptococcus pneumonia, Hepatitis C virus, Zika virus, Dengue virus, and Respiratory Syncytial Virus. All these datasets were downloaded from NCBI’s Short Read Archive (SRA) [19 (link)]. Infection of cell lines or primary cells with virus is a commonly used experimental system to investigate host dependency factors and host restriction factors [20 ].
An additional, clinical dataset was analyzed from nasopharyngeal swab specimens (NPSS) from the New York-Presbyterian Hospital-Weill Cornell Medical Center [27 (link)]. We will refer to this dataset as SARS-CoV-2-A in the text. Briefly, nasopharyngeal swabs were collected using the BD Universal Viral Transport Media system (Becton, Dickinson and Company, Franklin Lakes, NJ) from symptomatic patients. Total Nucleic Acid (TNA) was extracted using automated nucleic acid extraction on the QIAsymphony and the DSP Virus/Pathogen Mini Kit (Qiagen). RNA isolation and library preparation is fully described in Butler, et al. [27 (link)].

Karlebach G., Aronow B., Baylin S.B., Butler D., Foox J., Levy S., Meydan C., Mozsary C., Saravia-Butler A.M., Taylor D.M., Wurtele E., Mason C.E., Beheshti A, & Robinson P.N. (2021). Betacoronavirus-specific alternate splicing. bioRxiv.

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Nasopharyngeal Swab SARS-CoV-2 Extraction

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Patient specimens were processed as described in Butler et al. (2021) (link). Briefly, nasopharyngeal swabs were collected using the BD Universal Viral Transport Media system (Becton, Dickinson and Company, Franklin Lakes, NJ) from symptomatic patients. Total Nucleic Acid (TNA) was extracted from using automated nucleic acid extraction on the QIAsymphony and the DSP Virus/Pathogen Mini Kit (QIAGEN).

McDonald J.T., Enguita F.J., Taylor D., Griffin R.J., Priebe W., Emmett M.R., Sajadi M.M., Harris A.D., Clement J., Dybas J.M., Aykin-Burns N., Guarnieri J.W., Singh L.N., Grabham P., Baylin S.B., Yousey A., Pearson A.N., Corry P.M., Saravia-Butler A., Aunins T.R., Sharma S., Nagpal P., Meydan C., Foox J., Mozsary C., Cerqueira B., Zaksas V., Singh U., Wurtele E.S., Costes S.V., Davanzo G.G., Galeano D., Paccanaro A., Meinig S.L., Hagan R.S., Bowman N.M., Wolfgang M.C., Altinok S., Sapoval N., Treangen T.J., Moraes-Vieira P.M., Vanderburg C., Wallace D.C., Schisler J.C., Mason C.E., Chatterjee A., Meller R, & Beheshti A. (2021). Role of miR-2392 in driving SARS-CoV-2 infection. Cell Reports, 37(3), 109839.

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SARS-CoV-2 Nasopharyngeal Specimen Processing

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SARS-CoV-2 RT-PCR from Nasopharyngeal Swabs

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Patient specimens were collected with patients’ consent at New York Presbyterian Hospital (NYPH) and then processed for RT-PCR as described previously^{30 (link)}. Nasopharyngeal (NP) swab specimens were collected using the BD Universal Viral Transport Media system (Becton, Dickinson and Company, Franklin Lakes, NJ) from symptomatic patients.

Ramlall V., Thangaraj P.M., Meydan C., Foox J., Butler D., May B., De Freitas J.K., Glicksberg B.S., Mason C.E., Tatonetti N.P, & Shapira S.D. (2020). Identification of Immune complement function as a determinant of adverse SARS-CoV-2 infection outcome. medRxiv.

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SARS-CoV-2 Diagnostic Workflow

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Patient specimens were collected with patients’ consent at New York-Presbyterian Hospital-Weill Cornell Medical Center (NYPH-WCMC) and then processed for qRT-PCR. Nasopharyngeal (NP) swab specimens were collected using the BD Universal Viral Transport Media system (Becton, Dickinson and Company, Franklin Lakes, NJ) from symptomatic patients. Samples were collected and processed through the Weill Cornell Medicine Institutional Review Board (IRB) Protocol 19-11021069. All relevant ethical regulations for work with human participants were complied with. Observational cohort analysis (ACEI/ARB) was done through the Columbia University IRB Protocol AAAL0601. Oropharyngeal samples data from University Hospital of Tuebingen were collected under IRB 243/2020A.

Butler D., Mozsary C., Meydan C., Foox J., Rosiene J., Shaiber A., Danko D., Afshinnekoo E., MacKay M., Sedlazeck F.J., Ivanov N.A., Sierra M., Pohle D., Zietz M., Gisladottir U., Ramlall V., Sholle E.T., Schenck E.J., Westover C.D., Hassan C., Ryon K., Young B., Bhattacharya C., Ng D.L., Granados A.C., Santos Y.A., Servellita V., Federman S., Ruggiero P., Fungtammasan A., Chin C.S., Pearson N.M., Langhorst B.W., Tanner N.A., Kim Y., Reeves J.W., Hether T.D., Warren S.E., Bailey M., Gawrys J., Meleshko D., Xu D., Couto-Rodriguez M., Nagy-Szakal D., Barrows J., Wells H., O’Hara N.B., Rosenfeld J.A., Chen Y., Steel P.A., Shemesh A.J., Xiang J., Thierry-Mieg J., Thierry-Mieg D., Iftner A., Bezdan D., Sanchez E., Campion TR J.r., Sipley J., Cong L., Craney A., Velu P., Melnick A.M., Shapira S., Hajirasouliha I., Borczuk A., Iftner T., Salvatore M., Loda M., Westblade L.F., Cushing M., Wu S., Levy S., Chiu C., Schwartz R.E., Tatonetti N., Rennert H., Imielinski M, & Mason C.E. (2021). Shotgun transcriptome, spatial omics, and isothermal profiling of SARS-CoV-2 infection reveals unique host responses, viral diversification, and drug interactions. Nature Communications, 12, 1660.

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RT-PCR Analysis of NP Swab Specimens

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Patient specimens were collected with patients’ consent at New York Presbyterian Hospital and then processed for RT–PCR as described previously³⁰. NP swab specimens were collected using the BD Universal Viral Transport Media system (Becton, Dickinson and Company) from symptomatic patients.

Ramlall V., Thangaraj P.M., Meydan C., Foox J., Butler D., Kim J., May B., De Freitas J.K., Glicksberg B.S., Mason C.E., Tatonetti N.P, & Shapira S.D. (2020). Immune complement and coagulation dysfunction in adverse outcomes of SARS-CoV-2 infection. Nature medicine, 26(10), 1609-1615.

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