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Lee WL, Armas F, Guarneri F, Gu X, Formenti N, Wu F, Chandra F, Parisio G, Chen H, Xiao A, Romeo C, Scali F, Tonni M, Leifels M, Chua FJD, Kwok GW, Tay JY, Pasquali P, Thompson J, Alborali GL, Alm EJ. Rapid displacement of SARS-CoV-2 variant Delta by Omicron revealed by allele-specific PCR in wastewater. WATER RESEARCH 2022; 221:118809. [PMID: 35841797 PMCID: PMC9250349 DOI: 10.1016/j.watres.2022.118809] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 06/18/2022] [Accepted: 07/01/2022] [Indexed: 05/06/2023]
Abstract
On November 26, 2021, the B.1.1.529 COVID-19 variant was classified as the Omicron variant of concern (VOC). Reports of higher transmissibility and potential immune evasion triggered flight bans and heightened health control measures across the world to stem its distribution. Wastewater-based surveillance has demonstrated to be a useful complement for clinical community-based tracking of SARS-CoV-2 variants. Using design principles of our previous assays that detect SARS-CoV-2 variants (Alpha and Delta), we developed an allele-specific RT-qPCR assay which simultaneously targets the stretch of mutations from Q493R to Q498R for quantitative detection of the Omicron variant in wastewater. We report their validation against 10-month longitudinal samples from the influent of a wastewater treatment plant in Italy. SARS-CoV-2 RNA concentrations and variant frequencies in wastewater determined using these variant assays agree with clinical cases, revealing rapid displacement of the Delta variant by the Omicron variant within three weeks. These variant trends, when mapped against vaccination rates, support clinical studies that found the rapid emergence of SARS-CoV-2 Omicron variant being associated with an infection advantage over Delta in vaccinated persons. These data reinforce the versatility, utility and accuracy of these open-sourced methods using allele-specific RT-qPCR for tracking the dynamics of variant displacement in communities through wastewater for informed public health responses.
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Affiliation(s)
- Wei Lin Lee
- Antimicrobial Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, Singapore; Campus for Research Excellence and Technological Enterprise (CREATE), Singapore
| | - Federica Armas
- Antimicrobial Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, Singapore; Campus for Research Excellence and Technological Enterprise (CREATE), Singapore
| | - Flavia Guarneri
- Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna "Bruno Ubertini" (IZSLER), Italy
| | - Xiaoqiong Gu
- Antimicrobial Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, Singapore; Campus for Research Excellence and Technological Enterprise (CREATE), Singapore
| | - Nicoletta Formenti
- Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna "Bruno Ubertini" (IZSLER), Italy
| | - Fuqing Wu
- Center for Infectious Disease, Department of Epidemiology, Human Genetics, and Environmental Sciences, University of Texas School of Public Health, Houston, TX, USA
| | - Franciscus Chandra
- Antimicrobial Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, Singapore; Campus for Research Excellence and Technological Enterprise (CREATE), Singapore
| | - Giovanni Parisio
- Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna "Bruno Ubertini" (IZSLER), Italy
| | - Hongjie Chen
- Antimicrobial Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, Singapore; Campus for Research Excellence and Technological Enterprise (CREATE), Singapore
| | - Amy Xiao
- Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, USA; Department of Biological Engineering, Massachusetts Institute of Technology, USA
| | - Claudia Romeo
- Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna "Bruno Ubertini" (IZSLER), Italy
| | - Federico Scali
- Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna "Bruno Ubertini" (IZSLER), Italy
| | - Matteo Tonni
- Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna "Bruno Ubertini" (IZSLER), Italy
| | - Mats Leifels
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore
| | - Feng Jun Desmond Chua
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore
| | - Germaine Wc Kwok
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore
| | - Joey Yr Tay
- Antimicrobial Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, Singapore; Campus for Research Excellence and Technological Enterprise (CREATE), Singapore
| | - Paolo Pasquali
- Dipartimento di Sicurezza Alimentare, Nutrizione e Sanità Pubblica Veterinaria, Istituto Superiore di Sanità, Italy
| | - Janelle Thompson
- Campus for Research Excellence and Technological Enterprise (CREATE), Singapore; Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore; Asian School of the Environment, Nanyang Technological University, Singapore.
| | - Giovanni Loris Alborali
- Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna "Bruno Ubertini" (IZSLER), Italy
| | - Eric J Alm
- Antimicrobial Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, Singapore; Campus for Research Excellence and Technological Enterprise (CREATE), Singapore; Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, USA; Department of Biological Engineering, Massachusetts Institute of Technology, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA.
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Salehi-Vaziri M, Fazlalipour M, Seyed Khorrami SM, Azadmanesh K, Pouriayevali MH, Jalali T, Shoja Z, Maleki A. The ins and outs of SARS-CoV-2 variants of concern (VOCs). Arch Virol 2022; 167:327-344. [PMID: 35089389 PMCID: PMC8795292 DOI: 10.1007/s00705-022-05365-2] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Accepted: 11/16/2021] [Indexed: 02/07/2023]
Abstract
SARS-CoV-2, a newly emerging coronavirus that caused the COVID-19 epidemic, has been spreading quickly throughout the world. Despite immunization and some fairly effective therapeutic regimens, SARS-CoV-2 has been ravaging patients, health workers, and the economy. SARS-CoV-2 mutates and evolves to adapt to its host as a result of extreme selection pressure. As a consequence, new SARS-CoV-2 variants have emerged, some of which are classified as variants of concern (VOC) because they exhibit greater transmissibility, cause more-severe disease, are better able to escape immunity, or cause higher mortality than the original Wuhan strain. Here, we introduce these VOCs and review their characteristics, such as transmissibility, immune escape, mortality risk, and diagnostics.
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Affiliation(s)
- Mostafa Salehi-Vaziri
- COVID-19 National Reference Laboratory, Pasteur Institute of Iran, 69 Pasteur Ave, 1316943551, Tehran, Iran
- Department of Arboviruses and Viral Hemorrhagic Fevers (National Reference Laboratory), Pasteur Institute of Iran, Tehran, Iran
- Research Center for Emerging and Reemerging Infectious Diseases, Pasteur Institute of Iran, Tehran, Iran
| | - Mehdi Fazlalipour
- COVID-19 National Reference Laboratory, Pasteur Institute of Iran, 69 Pasteur Ave, 1316943551, Tehran, Iran
| | | | - Kayhan Azadmanesh
- Research Center for Emerging and Reemerging Infectious Diseases, Pasteur Institute of Iran, Tehran, Iran
- Department of Molecular Virology, Pasteur Institute of Iran, Tehran, Iran
| | - Mohammad Hassan Pouriayevali
- COVID-19 National Reference Laboratory, Pasteur Institute of Iran, 69 Pasteur Ave, 1316943551, Tehran, Iran
- Department of Arboviruses and Viral Hemorrhagic Fevers (National Reference Laboratory), Pasteur Institute of Iran, Tehran, Iran
| | - Tahmineh Jalali
- COVID-19 National Reference Laboratory, Pasteur Institute of Iran, 69 Pasteur Ave, 1316943551, Tehran, Iran
- Department of Arboviruses and Viral Hemorrhagic Fevers (National Reference Laboratory), Pasteur Institute of Iran, Tehran, Iran
| | - Zabihollah Shoja
- Department of Molecular Virology, Pasteur Institute of Iran, Tehran, Iran
| | - Ali Maleki
- COVID-19 National Reference Laboratory, Pasteur Institute of Iran, 69 Pasteur Ave, 1316943551, Tehran, Iran.
- Department of Molecular Virology, Pasteur Institute of Iran, Tehran, Iran.
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Buchta C, Camp JV, Jovanovic J, Radler U, Benka B, Puchhammer-Stöckl E, Müller MM, Griesmacher A, Aberle SW, Görzer I. Inadequate design of mutation detection panels prevents interpretation of variants of concern: results of an external quality assessment for SARS-CoV-2 variant detection. Clin Chem Lab Med 2021; 60:291-298. [PMID: 34751522 DOI: 10.1515/cclm-2021-0889] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 10/21/2021] [Indexed: 11/15/2022]
Abstract
OBJECTIVES Mutation-specific PCR assays have quickly found their way into laboratory diagnostics due to their capacity to be a fast, easy to implement and high-throughput method for the detection of known SARS-CoV-2 variants of concern (VoCs). However, little is known about the performance of such assays in routine laboratory analysis. METHODS The results reported in a recent round of an external quality assessment (EQA) scheme for SARS-CoV-2 mutation-specific PCR were retrospectively analyzed. For the determination of individual variant-specific sequences as well as for the interpretation results for certain virus variants, correct, incorrect, and unreported results were evaluated, and their possible causes were investigated. RESULTS A total of 34 laboratories participated in this study. For five samples containing the VoC Alpha + E484K, Beta, Gamma, Delta, or B.1.1.318 (as a variant of interest), 848 results for SARS-2-CoV mutation detection were reported, 824 (97.2%, range per sample 88-100%) of which were correct. Melting curve assays gave 99% correct results, real-time RT-qPCR 94%, microarray-based assays 100%, and MALDI-TOF MS 96%. A total of 122/167 (73%) reported results for SARS-CoV-2 variant determination were correct. Of the 45 inconclusive or incorrect results, 33 (73%) were due to inadequate selection of targets that did not allow identification of contemporary VoC, 11 (24%) were due to incorrect results, and one (3%) was due to correct results of mutation-specific PCR. CONCLUSIONS Careful and up-to-date selection of the targets used in mutation-specific PCR is essential for successful detection of current SARS-CoV-2 variants.
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Affiliation(s)
- Christoph Buchta
- Austrian Association for Quality Assurance and Standardization of Medical and Diagnostic Tests (ÖQUASTA), Vienna, Austria
| | - Jeremy V Camp
- Center for Virology, Medical University of Vienna, Vienna, Austria
| | - Jovana Jovanovic
- Austrian Association for Quality Assurance and Standardization of Medical and Diagnostic Tests (ÖQUASTA), Vienna, Austria
| | - Ulla Radler
- Austrian Association for Quality Assurance and Standardization of Medical and Diagnostic Tests (ÖQUASTA), Vienna, Austria
| | - Bernhard Benka
- Division Public Health, AGES - Austrian Agency for Health and Food Safety, Vienna, Austria
| | | | - Mathias M Müller
- Austrian Association for Quality Assurance and Standardization of Medical and Diagnostic Tests (ÖQUASTA), Vienna, Austria
| | - Andrea Griesmacher
- Austrian Association for Quality Assurance and Standardization of Medical and Diagnostic Tests (ÖQUASTA), Vienna, Austria
| | - Stephan W Aberle
- Center for Virology, Medical University of Vienna, Vienna, Austria
| | - Irene Görzer
- Center for Virology, Medical University of Vienna, Vienna, Austria
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Jacobson KB, Pinsky BA, Rath MEM, Wang H, Miller JA, Skhiri M, Shepard J, Mathew R, Lee G, Bohman B, Parsonnet J, Holubar M. Post-vaccination SARS-CoV-2 infections and incidence of the B.1.427/B.1.429 variant among healthcare personnel at a northern California academic medical center. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2021:2021.04.14.21255431. [PMID: 33907767 PMCID: PMC8077590 DOI: 10.1101/2021.04.14.21255431] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Background Distribution of mRNA-based SARS-CoV-2 vaccines to healthcare personnel (HCP) in the United States began in December 2020, with efficacy ≥ 90%. However, breakthrough infections in fully vaccinated individuals have been reported. Meanwhile, multiple SARS-CoV-2 variants of concern have emerged worldwide, including the B.1.427/B.1.429 variant first described in California. Little is known about the real-world effectiveness of the mRNA-based SARS-CoV-2 vaccines against novel variants including B.1.427/B.1.429. Methods In this quality improvement project, post-vaccine SARS-CoV-2 cases (PVSCs) were defined as individuals with positive SARS-CoV-2 nucleic acid amplification test (NAAT) after receiving at least one dose of a SARS-CoV-2 vaccine. Chart extraction of demographic and clinical information was performed, and available specimens meeting cycle threshold value criteria were tested for L452R, N501Y and E484K mutations by RT-PCR. Results From December 2020 to March 2021, 189 PVSCs were identified out of 22,729 healthcare personnel who received at least one dose of an mRNA-based SARS-CoV-2 vaccine. Of these, 114 (60.3%) occurred within 14 days of first vaccine dose (early post-vaccination), 49 (25.9%) within 14 days of the second vaccine dose (partially vaccinated), and 26 (13.8%) ≥14 days after the second dose (fully vaccinated). Of 115 samples available for mutation testing, 42 were positive for L452R alone, presumptive of B.1.427/B.1.429; three had N501Y mutation alone and none were found with E484K mutation. Though on univariate analysis partially- and fully-vaccinated PVSCs were more likely than early post-vaccination PVSCs to be infected with presumptive B.1.427/B.1.429, when adjusted for community prevalence of B.1.427/B.1.429 at the time of infection, partially- and fully-vaccinated PVSC did not have statistically significantly elevated risk ratios for infection with this variant (RR 1.40, 95% CI 0.81-2.43 and RR 1.13, 95% CI 0.59-2.16, respectively). Conclusions The great majority of PVSCs occurred prior to the expected onset of full, vaccine-derived immunity. Although the B.1.427/B.1.429 variant did not represent a significantly higher proportion of PVSCs than expected, numbers were small and there was a trend towards higher representation in the partially- and fully-vaccinated subset. Continued infection control measures in the workplace and in the community including social distancing and masking, particularly in the early days post-vaccination, as well as continued variant surveillance in PVSCs, is imperative in order to anticipate and control future surges of infection.
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Affiliation(s)
- Karen B Jacobson
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Benjamin A Pinsky
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, CA, USA
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Maria E Montez Rath
- Department of Medicine, Division of Nephrology, Stanford University School of Medicine, Stanford, CA, USA
| | - Hannah Wang
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Jacob A Miller
- Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA, USA
| | - Mehdi Skhiri
- Department of Medicine, Primary Care and Population Health, Stanford University School of Medicine, Stanford, CA, USA
| | - John Shepard
- Department of Quality, Patient Safety and Clinical Effectiveness, Stanford Health Care, Stanford, CA, USA
| | - Roshni Mathew
- Department of Pediatrics, Division of Infectious Diseases, Stanford University School of Medicine, Stanford, CA, USA
| | - Grace Lee
- Department of Pediatrics, Division of Infectious Diseases, Stanford University School of Medicine, Stanford, CA, USA
| | - Bryan Bohman
- Workforce Health and Wellness, Stanford University School of Medicine, Stanford, CA, USA
| | - Julie Parsonnet
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, CA, USA
- Department of Epidemiology and Population Health, Stanford University School of Medicine, Stanford, CA, USA
| | - Marisa Holubar
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, CA, USA
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