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Merav L, Ofek Shlomai N, Oiknine-Djian E, Caplan O, Livneh A, Sido T, Peri A, Shtoyer A, Amir E, Ben Meir K, Daitch Y, Rivkin M, Kripper E, Fogel I, Horowitz H, Greenberger S, Cohen M, Geal-Dor M, Gordon O, Averbuch D, Ergaz-Shaltiel Z, Eventov Friedman S, Wolf DG, Yassour M. Implementation of pooled saliva tests for universal screening of cCMV infection. Nat Med 2024; 30:1111-1117. [PMID: 38459181 PMCID: PMC11031397 DOI: 10.1038/s41591-024-02873-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Accepted: 02/14/2024] [Indexed: 03/10/2024]
Abstract
Congenital cytomegalovirus (cCMV) is the most common intrauterine infection, leading to neurodevelopmental disabilities. Universal newborn infant screening of cCMV has been increasingly advocated. In the absence of a high-throughput screening test, which can identify all infected newborn infants, the development of an accurate and efficient testing strategy has remained an ongoing challenge. Here we assessed the implementation of pooled saliva polymerase chain reaction (PCR) tests for universal screening of cCMV, in two hospitals of Jerusalem from April 2022 through April 2023. During the 13-month study period, 15,805 infants (93.6% of all live newborn infants) were screened for cCMV using the pooled approach that has since become our routine screening method. The empirical efficiency of the pooling was six (number of tested newborn infants per test), thereby sparing 83% of the saliva tests. Only a minor 3.05 PCR cycle loss of sensitivity was observed for the pooled testing, in accordance with the theoretical prediction for an eight-sample pool. cCMV was identified in 54 newborn infants, with a birth prevalence of 3.4 per 1,000; 55.6% of infants identified with cCMV were asymptomatic at birth and would not have been otherwise targeted for screening. The study demonstrates the wide feasibility and benefits of pooled saliva testing as an efficient, cost-sparing and sensitive approach for universal screening of cCMV.
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Affiliation(s)
- Lior Merav
- School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, Israel
- Department of Microbiology and Molecular Genetics, IMRIC, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
- Clinical Virology Unit, Department of Clinical Microbiology and Infectious Diseases, Hadassah Hebrew University Medical Center, Jerusalem, Israel
| | - Noa Ofek Shlomai
- Department of Neonatology, Hadassah and Hebrew University Medical Center, Jerusalem, Israel
- Hebrew University Faculty of Medicine, Jerusalem, Israel
| | - Esther Oiknine-Djian
- Clinical Virology Unit, Department of Clinical Microbiology and Infectious Diseases, Hadassah Hebrew University Medical Center, Jerusalem, Israel
- Hebrew University Faculty of Medicine, Jerusalem, Israel
- Lautenberg Center for General and Tumor Immunology, Jerusalem, Israel
| | - Orit Caplan
- Clinical Virology Unit, Department of Clinical Microbiology and Infectious Diseases, Hadassah Hebrew University Medical Center, Jerusalem, Israel
| | - Ayala Livneh
- Clinical Virology Unit, Department of Clinical Microbiology and Infectious Diseases, Hadassah Hebrew University Medical Center, Jerusalem, Israel
| | - Tal Sido
- Clinical Virology Unit, Department of Clinical Microbiology and Infectious Diseases, Hadassah Hebrew University Medical Center, Jerusalem, Israel
| | - Amir Peri
- Computing Department of Laboratories and Institutes, Hadassah Hebrew University Medical Center, Jerusalem, Israel
| | - Aviad Shtoyer
- Computing Department of Laboratories and Institutes, Hadassah Hebrew University Medical Center, Jerusalem, Israel
| | - Eden Amir
- Clinical Virology Unit, Department of Clinical Microbiology and Infectious Diseases, Hadassah Hebrew University Medical Center, Jerusalem, Israel
| | - Kerem Ben Meir
- Clinical Virology Unit, Department of Clinical Microbiology and Infectious Diseases, Hadassah Hebrew University Medical Center, Jerusalem, Israel
- Hebrew University Faculty of Medicine, Jerusalem, Israel
- Lautenberg Center for General and Tumor Immunology, Jerusalem, Israel
| | - Yutti Daitch
- Clinical Virology Unit, Department of Clinical Microbiology and Infectious Diseases, Hadassah Hebrew University Medical Center, Jerusalem, Israel
| | - Mila Rivkin
- Clinical Virology Unit, Department of Clinical Microbiology and Infectious Diseases, Hadassah Hebrew University Medical Center, Jerusalem, Israel
| | - Esther Kripper
- Clinical Virology Unit, Department of Clinical Microbiology and Infectious Diseases, Hadassah Hebrew University Medical Center, Jerusalem, Israel
| | - Irit Fogel
- Clinical Virology Unit, Department of Clinical Microbiology and Infectious Diseases, Hadassah Hebrew University Medical Center, Jerusalem, Israel
| | - Hadar Horowitz
- Clinical Virology Unit, Department of Clinical Microbiology and Infectious Diseases, Hadassah Hebrew University Medical Center, Jerusalem, Israel
| | - Sraya Greenberger
- Clinical Virology Unit, Department of Clinical Microbiology and Infectious Diseases, Hadassah Hebrew University Medical Center, Jerusalem, Israel
| | - Mevaseret Cohen
- Clinical Virology Unit, Department of Clinical Microbiology and Infectious Diseases, Hadassah Hebrew University Medical Center, Jerusalem, Israel
- Hebrew University Faculty of Medicine, Jerusalem, Israel
- Lautenberg Center for General and Tumor Immunology, Jerusalem, Israel
| | - Miriam Geal-Dor
- Speech and Hearing Center, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
- Department of Communication Disorders, Hadassah Academic College, Jerusalem, Israel
| | - Oren Gordon
- Hebrew University Faculty of Medicine, Jerusalem, Israel
- Pediatric Infectious Diseases, Pediatric Division, Hadassah Hebrew University Medical Center, Jerusalem, Israel
| | - Diana Averbuch
- Hebrew University Faculty of Medicine, Jerusalem, Israel
- Pediatric Infectious Diseases, Pediatric Division, Hadassah Hebrew University Medical Center, Jerusalem, Israel
| | - Zivanit Ergaz-Shaltiel
- Department of Neonatology, Hadassah and Hebrew University Medical Center, Jerusalem, Israel
- Hebrew University Faculty of Medicine, Jerusalem, Israel
| | - Smadar Eventov Friedman
- Department of Neonatology, Hadassah and Hebrew University Medical Center, Jerusalem, Israel
- Hebrew University Faculty of Medicine, Jerusalem, Israel
| | - Dana G Wolf
- Clinical Virology Unit, Department of Clinical Microbiology and Infectious Diseases, Hadassah Hebrew University Medical Center, Jerusalem, Israel.
- Hebrew University Faculty of Medicine, Jerusalem, Israel.
- Lautenberg Center for General and Tumor Immunology, Jerusalem, Israel.
| | - Moran Yassour
- School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, Israel.
- Department of Microbiology and Molecular Genetics, IMRIC, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel.
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Barak N, Ben-Ami R, Sido T, Perri A, Shtoyer A, Rivkin M, Licht T, Peretz A, Magenheim J, Fogel I, Livneh A, Daitch Y, Oiknine-Djian E, Benedek G, Dor Y, Wolf DG, Yassour M. Lessons from applied large-scale pooling of 133,816 SARS-CoV-2 RT-PCR tests. Sci Transl Med 2021; 13:eabf2823. [PMID: 33619081 PMCID: PMC8099176 DOI: 10.1126/scitranslmed.abf2823] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 12/28/2020] [Accepted: 02/16/2021] [Indexed: 12/28/2022]
Abstract
Pooling multiple swab samples before RNA extraction and real-time reverse transcription polymerase chain reaction (RT-PCR) analysis has been proposed as a strategy to reduce costs and increase throughput of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) tests. However, reports on practical large-scale group testing for SARS-CoV-2 have been scant. Key open questions concern reduced sensitivity due to sample dilution, the rate of false positives, the actual efficiency (number of tests saved by pooling), and the impact of infection rate in the population on assay performance. Here, we report an analysis of 133,816 samples collected between April and September 2020 and tested by Dorfman pooling for the presence of SARS-CoV-2. We spared 76% of RNA extraction and RT-PCR tests, despite the frequently changing prevalence (0.5 to 6%). We observed pooling efficiency and sensitivity that exceeded theoretical predictions, which resulted from the nonrandom distribution of positive samples in pools. Overall, our findings support the use of pooling for efficient large-scale SARS-CoV-2 testing.
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Affiliation(s)
- Netta Barak
- School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Roni Ben-Ami
- Department of Developmental Biology and Cancer Research, IMRIC, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 91121, Israel
- Clinical Virology Unit, Hadassah Hebrew University Medical Center, Jerusalem 91120, Israel
| | - Tal Sido
- Clinical Virology Unit, Hadassah Hebrew University Medical Center, Jerusalem 91120, Israel
- Department of Mathematics, Bar-Ilan University, Ramat-Gan 52900, Israel
| | - Amir Perri
- Computing Department of Laboratories and Institutes, Hadassah Hebrew University Medical Center, Jerusalem 91120, Israel
| | - Aviad Shtoyer
- Computing Department of Laboratories and Institutes, Hadassah Hebrew University Medical Center, Jerusalem 91120, Israel
| | - Mila Rivkin
- Clinical Virology Unit, Hadassah Hebrew University Medical Center, Jerusalem 91120, Israel
| | - Tamar Licht
- Department of Medical Neurobiology, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 91121, Israel
| | - Ayelet Peretz
- Department of Developmental Biology and Cancer Research, IMRIC, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 91121, Israel
| | - Judith Magenheim
- Department of Developmental Biology and Cancer Research, IMRIC, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 91121, Israel
| | - Irit Fogel
- Clinical Virology Unit, Hadassah Hebrew University Medical Center, Jerusalem 91120, Israel
| | - Ayalah Livneh
- Clinical Virology Unit, Hadassah Hebrew University Medical Center, Jerusalem 91120, Israel
| | - Yutti Daitch
- Clinical Virology Unit, Hadassah Hebrew University Medical Center, Jerusalem 91120, Israel
| | - Esther Oiknine-Djian
- Clinical Virology Unit, Hadassah Hebrew University Medical Center, Jerusalem 91120, Israel
| | - Gil Benedek
- Clinical Virology Unit, Hadassah Hebrew University Medical Center, Jerusalem 91120, Israel
- Tissue Typing and Immunogenetics Unit, Hadassah Hebrew University Medical Center, Jerusalem 91121, Israel
| | - Yuval Dor
- Department of Developmental Biology and Cancer Research, IMRIC, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 91121, Israel.
| | - Dana G Wolf
- Clinical Virology Unit, Hadassah Hebrew University Medical Center, Jerusalem 91120, Israel.
- The Lautenberg Centre for Immunology and Cancer Research, IMRIC, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 91121, Israel
| | - Moran Yassour
- School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem 91904, Israel.
- Department of Microbiology and Molecular Genetics, IMRIC, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 91121, Israel
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