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Theel ES, Kirby JE, Pollock NR. Testing for SARS-CoV-2: lessons learned and current use cases. Clin Microbiol Rev 2024; 37:e0007223. [PMID: 38488364 DOI: 10.1128/cmr.00072-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2024] Open
Abstract
SUMMARYThe emergence and worldwide dissemination of SARS-CoV-2 required both urgent development of new diagnostic tests and expansion of diagnostic testing capacity on an unprecedented scale. The rapid evolution of technologies that allowed testing to move out of traditional laboratories and into point-of-care testing centers and the home transformed the diagnostic landscape. Four years later, with the end of the formal public health emergency but continued global circulation of the virus, it is important to take a fresh look at available SARS-CoV-2 testing technologies and consider how they should be used going forward. This review considers current use case scenarios for SARS-CoV-2 antigen, nucleic acid amplification, and immunologic tests, incorporating the latest evidence for analytical/clinical performance characteristics and advantages/limitations for each test type to inform current debates about how tests should or should not be used.
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Affiliation(s)
- Elitza S Theel
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - James E Kirby
- Department of Pathology, Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
| | - Nira R Pollock
- Harvard Medical School, Boston, Massachusetts, USA
- Department of Laboratory Medicine, Boston Children's Hospital, Boston, Massachusetts, USA
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Frediani JK, Parsons R, McLendon KB, Westbrook AL, Lam W, Martin G, Pollock NR. The New Normal: Delayed Peak SARS-CoV-2 Viral Loads Relative to Symptom Onset and Implications for COVID-19 Testing Programs. Clin Infect Dis 2024; 78:301-307. [PMID: 37768707 PMCID: PMC10874267 DOI: 10.1093/cid/ciad582] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 09/11/2023] [Accepted: 09/22/2023] [Indexed: 09/29/2023] Open
Abstract
BACKGROUND Early in the coronavirus disease 2019 (COVID-19) pandemic, peak viral loads coincided with symptom onset. We hypothesized that in a highly immune population, symptom onset might occur earlier in infection, coinciding with lower viral loads. METHODS We assessed severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and influenza A viral loads relative to symptom duration in symptomatic adults (≥16 years) presenting for testing in Georgia (4/2022-4/2023; Omicron variant predominant). Participants provided symptom duration and recent testing history. Nasal swabs were tested by Xpert Xpress SARS-CoV-2/Flu/RSV assay and cycle threshold (Ct) values recorded. Nucleoprotein concentrations in SARS-CoV-2 polymerase chain reaction (PCR)-positive samples were measured by single molecule array. To estimate hypothetical antigen rapid diagnostic test (Ag RDT) sensitivity on each day after symptom onset, percentages of individuals with Ct value ≤30 or ≤25 were calculated. RESULTS Of 348 newly-diagnosed SARS-CoV-2 PCR-positive individuals (65.5% women, median 39.2 years), 317/348 (91.1%) had a history of vaccination, natural infection, or both. By both Ct value and antigen concentration measurements, median viral loads rose from the day of symptom onset and peaked on the fourth/fifth day. Ag RDT sensitivity estimates were 30.0%-60.0% on the first day, 59.2%-74.8% on the third day, and 80.0%-93.3% on the fourth day of symptoms.In 74 influenza A PCR-positive individuals (55.4% women; median 35.0 years), median influenza viral loads peaked on the second day of symptoms. CONCLUSIONS In a highly immune adult population, median SARS-CoV-2 viral loads peaked around the fourth day of symptoms. Influenza A viral loads peaked soon after symptom onset. These findings have implications for ongoing use of Ag RDTs for COVID-19 and influenza.
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Affiliation(s)
- Jennifer K Frediani
- Nell Hodgson Woodruff School of Nursing, Emory University, Atlanta, Georgia, USA
| | - Richard Parsons
- Nell Hodgson Woodruff School of Nursing, Emory University, Atlanta, Georgia, USA
| | - Kaleb B McLendon
- Emory/Children's Laboratory for Innovative Assay Development, Department of Pathology, Emory University, Atlanta, Georgia, USA
| | - Adrianna L Westbrook
- Pediatric Biostatistics Core, Department of Pediatrics, Emory University, Atlanta, Georgia, USA
| | - Wilbur Lam
- Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia, USA
- Aflac Cancer and Blood Disorders Center of Children's Healthcare of Atlanta, Atlanta, Georgia, USA
- Wallace H. Coulter Department of Biomedical Engineering, Emory University and Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Greg Martin
- Department of Medicine, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Nira R Pollock
- Department of Laboratory Medicine, Boston Children's Hospital, Boston, Massachusetts, USA
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Alpizar SA, Accini J, Anderson DC, Eysa B, Medina-Piñón I, Ohmagari N, Ostrovskyy MM, Aggrey-Amable A, Beck K, Byrne D, Grayson S, Hwang PMT, Lonchar JD, Strizki J, Xu Y, Paschke A, De Anda CS, Sears PS. Molnupiravir for intra-household prevention of COVID-19: The MOVe-AHEAD randomized, placebo-controlled trial. J Infect 2023; 87:392-402. [PMID: 37690669 DOI: 10.1016/j.jinf.2023.08.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 08/23/2023] [Accepted: 08/31/2023] [Indexed: 09/12/2023]
Abstract
OBJECTIVES To evaluate the efficacy and safety of molnupiravir for intra-household post-exposure prophylaxis (PEP) of COVID-19. METHODS MOVe-AHEAD was a randomized, controlled, double-blind, phase 3 trial comparing molnupiravir (800 mg twice daily for 5 days) with placebo. Eligible participants were adult, unvaccinated, asymptomatic household contacts of patients with laboratory-confirmed COVID-19. The primary efficacy endpoint was the incidence of COVID-19 through day 14 in modified intention-to-treat (MITT) participants (those who received ≥1 dose of study intervention) without detectable SARS-CoV-2 at baseline, termed the MITT-VN population. Superiority of molnupiravir was prespecified as a stratified one-sided p-value of <0.0249 for the treatment difference in this endpoint. RESULTS The MITT population comprised 763 participants randomized to molnupiravir and 764 to placebo; 83.6% had anti-SARS-CoV-2 antibodies at baseline. In the MITT-VN population, COVID-19 rates through day 14 were 6.5% with molnupiravir and 8.5% with placebo (one-sided p-value: 0.0848). In the molnupiravir arm, 25/35 of confirmed COVID-19 events (71.4%) occurred after completion of treatment (versus 17/49 [34.7%] for placebo). Adverse event rates were low and similar between molnupiravir and placebo. CONCLUSIONS Molnupiravir was well-tolerated but did not meet the prespecified superiority criterion, possibly influenced in part by the high pre-existing immunity in the trial population.
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Affiliation(s)
- Sady A Alpizar
- Clinical Research Trials of Florida, 2713 W. Virginia Ave., Tampa 33607, FL, USA.
| | - Jose Accini
- IPS Centro Científico Asistencial, Cra. 45 #85-49, Barranquilla 080020, Colombia.
| | - Duane C Anderson
- Excel Clinical Research LLC, 3059 S Maryland Pkwy., Las Vegas, NV 89109, USA.
| | - Basem Eysa
- National Hepatology and Tropical Medicine Research Institute, 10 Kasr El, Eini St., Fom Al Khalig Sq., Cairo 11796, Egypt.
| | - Isaí Medina-Piñón
- ICARO Investigaciones en Medicina, Calle Ignacio Allende No. 1015, Chihuahua 31000, Mexico.
| | - Norio Ohmagari
- National Center for Global Health and Medicine Hospital, 1-21-1 Toyama, Shinjuku-ku, Tokyo 162-8655, Japan.
| | - Mykola M Ostrovskyy
- Regional Phthisiopulmonological Center, 17 Franka St., Ivano-Frankivsk 76018, Ukraine.
| | | | - Karen Beck
- Merck & Co, Inc., 126 E. Lincoln Ave., Rahway, NJ 07065, USA
| | - Dana Byrne
- Merck & Co, Inc., 126 E. Lincoln Ave., Rahway, NJ 07065, USA
| | - Staci Grayson
- Merck & Co, Inc., 126 E. Lincoln Ave., Rahway, NJ 07065, USA
| | - Peggy M T Hwang
- Merck & Co, Inc., 126 E. Lincoln Ave., Rahway, NJ 07065, USA
| | - Julia D Lonchar
- Merck & Co, Inc., 126 E. Lincoln Ave., Rahway, NJ 07065, USA
| | - Julie Strizki
- Merck & Co, Inc., 126 E. Lincoln Ave., Rahway, NJ 07065, USA
| | - Yayun Xu
- Merck & Co, Inc., 126 E. Lincoln Ave., Rahway, NJ 07065, USA
| | - Amanda Paschke
- Merck & Co, Inc., 126 E. Lincoln Ave., Rahway, NJ 07065, USA
| | | | - Pamela S Sears
- Merck & Co, Inc., 126 E. Lincoln Ave., Rahway, NJ 07065, USA.
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Zhao L, Geng Q, Corchis-Scott R, McKay RM, Norton J, Xagoraraki I. Targeting a free viral fraction enhances the early alert potential of wastewater surveillance for SARS-CoV-2: a methods comparison spanning the transition between delta and omicron variants in a large urban center. Front Public Health 2023; 11:1140441. [PMID: 37546328 PMCID: PMC10400354 DOI: 10.3389/fpubh.2023.1140441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Accepted: 06/30/2023] [Indexed: 08/08/2023] Open
Abstract
Introduction Wastewater surveillance has proven to be a valuable approach to monitoring the spread of SARS-CoV-2, the virus that causes Coronavirus disease 2019 (COVID-19). Recognizing the benefits of wastewater surveillance as a tool to support public health in tracking SARS-CoV-2 and other respiratory pathogens, numerous wastewater virus sampling and concentration methods have been tested for appropriate applications as well as their significance for actionability by public health practices. Methods Here, we present a 34-week long wastewater surveillance study that covers nearly 4 million residents of the Detroit (MI, United States) metropolitan area. Three primary concentration methods were compared with respect to recovery of SARS-CoV-2 from wastewater: Virus Adsorption-Elution (VIRADEL), polyethylene glycol precipitation (PEG), and polysulfone (PES) filtration. Wastewater viral concentrations were normalized using various parameters (flow rate, population, total suspended solids) to account for variations in flow. Three analytical approaches were implemented to compare wastewater viral concentrations across the three primary concentration methods to COVID-19 clinical data for both normalized and non-normalized data: Pearson and Spearman correlations, Dynamic Time Warping (DTW), and Time Lagged Cross Correlation (TLCC) and peak synchrony. Results It was found that VIRADEL, which captures free and suspended virus from supernatant wastewater, was a leading indicator of COVID-19 cases within the region, whereas PEG and PES filtration, which target particle-associated virus, each lagged behind the early alert potential of VIRADEL. PEG and PES methods may potentially capture previously shed and accumulated SARS-CoV-2 resuspended from sediments in the interceptors. Discussion These results indicate that the VIRADEL method can be used to enhance the early-warning potential of wastewater surveillance applications although drawbacks include the need to process large volumes of wastewater to concentrate sufficiently free and suspended virus for detection. While lagging the VIRADEL method for early-alert potential, both PEG and PES filtration can be used for routine COVID-19 wastewater monitoring since they allow a large number of samples to be processed concurrently while being more cost-effective and with rapid turn-around yielding results same day as collection.
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Affiliation(s)
- Liang Zhao
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, MI, United States
| | - Qiudi Geng
- Great Lakes Institute for Environmental Research, University of Windsor, Windsor, ON, Canada
| | - Ryland Corchis-Scott
- Great Lakes Institute for Environmental Research, University of Windsor, Windsor, ON, Canada
| | - Robert Michael McKay
- Great Lakes Institute for Environmental Research, University of Windsor, Windsor, ON, Canada
- Great Lakes Center for Fresh Waters and Human Health, Bowling Green State University, Bowling Green, OH, United States
| | - John Norton
- Great Lakes Water Authority, Detroit, MI, United States
| | - Irene Xagoraraki
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, MI, United States
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Frediani JK, Parsons R, McLendon KB, Westbrook AL, Lam W, Martin G, Pollock NR. The New Normal: Delayed Peak SARS-CoV-2 Viral Loads Relative to Symptom Onset and Implications for COVID-19 Testing Programs. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.05.09.23289735. [PMID: 37214887 PMCID: PMC10197800 DOI: 10.1101/2023.05.09.23289735] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Background Early in the COVID-19 pandemic, peak viral loads coincided with symptom onset. We hypothesized that in a highly immune population, symptom onset might occur earlier in infection, coinciding with lower viral loads. Methods We assessed SARS-CoV-2 and influenza A viral loads relative to symptom duration in recently-tested adults. Symptomatic participants ≥16y presenting to testing sites in Georgia (4/2022-4/2023; Omicron variant predominant) provided symptom duration. Nasal swab samples were tested by the Xpert Xpress SARS-CoV-2/Flu/RSV assay and Ct values recorded. Nucleoprotein concentrations in SARS-CoV-2 PCR-positive samples were measured by Single Molecule Array. To estimate hypothetical antigen rapid diagnostic test (Ag RDT) sensitivity on each day after symptom onset, percentages of individuals with Ct value ≤30 or ≤25 were calculated. Results Of 621 SARS-CoV-2 PCR-positive individuals (64.1% women, median 40.9y), 556/621 (89.5%) had a history of vaccination, natural infection, or both. By both Ct value and antigen concentration measurements, median viral loads rose from the day of symptom onset and peaked on the fourth day. Ag RDT sensitivity estimates were 35.7-71.4% on the first day, 63.9-78.7% on the third day, and 78.6-90.6% on the fourth day of symptoms.In 74 influenza A PCR-positive individuals (55.4% women; median 35.0y), median influenza viral loads peaked on the second day of symptoms. Conclusions In a highly immune adult population, median SARS-CoV-2 viral loads peaked on the fourth day of symptoms. Influenza A viral loads peaked soon after symptom onset. These findings have implications for ongoing use of Ag RDTs for COVID-19 and influenza. Key Points In a highly immune adult population, median SARS-CoV-2 viral loads by cycle threshold and antigen measurements peaked on the fourth day of symptoms, with implications for testing practice. In contrast, viral loads for influenza A peaked soon after symptom onset.
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Affiliation(s)
| | - Richard Parsons
- Nell Hodgson Woodruff School of Nursing, Emory University, Atlanta, GA USA
| | - Kaleb B. McLendon
- Emory/Children’s Laboratory for Innovative Assay Development, Department of Pathology, Emory University, Atlanta, GA USA
| | - Adrianna L. Westbrook
- Pediatric Biostatistics Core, Department of Pediatrics, Emory University, Atlanta, GA USA
| | - Wilbur Lam
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA USA
- Aflac Cancer and Blood Disorders Center of Children’s Healthcare of Atlanta, Atlanta, GA USA
- Wallace H. Coulter Department of Biomedical Engineering, Emory University and Georgia Institute of Technology, Atlanta, GA USA
| | - Greg Martin
- Department of Medicine, Emory University School of Medicine, Atlanta, GA USA
| | - Nira R. Pollock
- Department of Laboratory Medicine, Boston Children’s Hospital, Boston, MA USA
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Kang SW, Park H, Kim JY, Lim SY, Lee S, Bae JY, Kim J, Chang E, Bae S, Jung J, Kim MJ, Chong YP, Lee SO, Choi SH, Kim YS, Park MS, Kim SH. Comparison of the clinical and virological characteristics of SARS-CoV-2 Omicron BA.1/BA.2 and omicron BA.5 variants: A prospective cohort study. J Infect 2023; 86:e148-e151. [PMID: 36669564 PMCID: PMC9846898 DOI: 10.1016/j.jinf.2023.01.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Accepted: 01/12/2023] [Indexed: 01/19/2023]
Affiliation(s)
- Sung-Woon Kang
- Department of Infectious Diseases, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Heedo Park
- Department of Microbiology, Vaccine Innovation Center, Biosafety Center, College of Medicine, Korea University, Seoul, Korea
| | - Ji Yeun Kim
- Department of Infectious Diseases, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - So Yun Lim
- Department of Infectious Diseases, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Sohyun Lee
- Department of Microbiology, Vaccine Innovation Center, Biosafety Center, College of Medicine, Korea University, Seoul, Korea
| | - Joon-Yong Bae
- Department of Microbiology, Vaccine Innovation Center, Biosafety Center, College of Medicine, Korea University, Seoul, Korea
| | - Jeonghun Kim
- Department of Microbiology, Vaccine Innovation Center, Biosafety Center, College of Medicine, Korea University, Seoul, Korea
| | - Euijin Chang
- Department of Infectious Diseases, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Seongman Bae
- Department of Infectious Diseases, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Jiwon Jung
- Department of Infectious Diseases, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Min Jae Kim
- Department of Infectious Diseases, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Yong Pil Chong
- Department of Infectious Diseases, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Sang-Oh Lee
- Department of Infectious Diseases, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Sang-Ho Choi
- Department of Infectious Diseases, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Yang Soo Kim
- Department of Infectious Diseases, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Man-Seong Park
- Department of Microbiology, Vaccine Innovation Center, Biosafety Center, College of Medicine, Korea University, Seoul, Korea.
| | - Sung-Han Kim
- Department of Infectious Diseases, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea.
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Viral dynamics of omicron BA.2.76 variant of SARS-CoV-2 in a cohort of COVID-19 patients. J Infect 2022; 86:154-225. [PMID: 36470410 PMCID: PMC9715459 DOI: 10.1016/j.jinf.2022.11.027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2022] [Accepted: 11/29/2022] [Indexed: 12/03/2022]
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