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Jang YA, Wu HY, Hsu YT, Chen YK, Chiou HY, Sytwu HK, Chen WJ, Tsou HH. Beyond the waves: Unraveling pandemic outcomes with genomic insights and immunity analysis - Evidence from 14 countries. Prev Med 2024; 178:107820. [PMID: 38092329 DOI: 10.1016/j.ypmed.2023.107820] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 12/08/2023] [Accepted: 12/09/2023] [Indexed: 12/24/2023]
Abstract
OBJECTIVE Although the World Health Organization and many governments have recategorized COVID-19 as a generally mild to moderately severe disease, consecutive pandemic waves driven by immune escape variants have underscored the need for timely and accurate prediction of the next outbreak. Nevertheless, little attention has been paid to translating genomic data and infection- and vaccine-induced immunity into direct estimates. METHODS We retrieved epidemiologic and genomic data shortly before pandemic waves across 14 developed countries from late 2021 to mid-2022 and examined associations between early-stage variant competition, infection- and vaccine-induced immunity, and the time intervals between wave peaks. We applied regression analysis and the generalized estimating equation method to construct an inferential model. RESULTS Each per cent increase in the proportion of a new variant was associated with a 1.0% reduction in interpeak intervals on average. Curvilinear associations between vaccine-induced immunity and outcome variables were observed, suggesting that reaching a critical vaccine distribution rate may decrease the caseload of the upcoming wave. CONCLUSIONS By leveraging readily accessible pre-outbreak genomic and epidemiologic data, our results not only substantiate the predictive potential of early variant fractions but also propose that immunity acquired through infection alone may not sufficiently mitigate transmission. Conversely, a rapid and widespread vaccination initiative appears to be correlated with a decrease in disease incidence.
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Affiliation(s)
- Yung-An Jang
- Institute of Population Health Sciences, National Health Research Institutes, Zhunan, Miaoli County, Taiwan
| | - Hsiao-Yu Wu
- Institute of Population Health Sciences, National Health Research Institutes, Zhunan, Miaoli County, Taiwan
| | - Ya-Ting Hsu
- Institute of Population Health Sciences, National Health Research Institutes, Zhunan, Miaoli County, Taiwan
| | - Yi-Kai Chen
- Institute of Population Health Sciences, National Health Research Institutes, Zhunan, Miaoli County, Taiwan
| | - Hung-Yi Chiou
- Institute of Population Health Sciences, National Health Research Institutes, Zhunan, Miaoli County, Taiwan; School of Public Health, College of Public Health, Taipei Medical University, Taiwan; Master Program in Applied Epidemiology, College of Public Health, Taipei Medical University, Taiwan
| | - Huey-Kang Sytwu
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Taiwan
| | - Wei J Chen
- Center for Neuropsychiatric Research, National Health Research Institutes, Taiwan; Institute of Epidemiology and Preventive Medicine, College of Public Health, National Taiwan University, Taiwan.
| | - Hsiao-Hui Tsou
- Institute of Population Health Sciences, National Health Research Institutes, Zhunan, Miaoli County, Taiwan; Graduate Institute of Biostatistics, College of Public Health, China Medical University, Taiwan.
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Saksena NK, Reddy SB, Miranda-Saksena M, Cardoso THS, Silva EMA, Ferreira JC, Rabeh WM. SARS-CoV-2 variants, its recombinants and epigenomic exploitation of host defenses. Biochim Biophys Acta Mol Basis Dis 2023; 1869:166836. [PMID: 37549720 DOI: 10.1016/j.bbadis.2023.166836] [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] [Received: 01/30/2023] [Revised: 07/17/2023] [Accepted: 07/31/2023] [Indexed: 08/09/2023]
Abstract
Since 2003, we have seen the emergence of novel viruses, such as SARS-CoV-1, MERS, ZIKA, swine flu virus H1N1, Marburg, Monkeypox, Ebola, and SARS-CoV-2, but none of them gained pandemic proportions similar to SARS-CoV-2. This could be attributed to unique viral traits, allowing its rapid global dissemination following its emergence in October 2019 in Wuhan, China, which appears to be primarily driven by the emergence of highly transmissible and virulent variants that also associate, in some cases, with severe disease and considerable mortality caused by fatal pneumonia, acute respiratory distress syndrome (ARDS) in infected individuals. Mechanistically, several factors are involved in viral pathogenesis, and epigenetic alterations take the front seat in host-virus interactions. The molecular basis of all viral infections, including SARS-CoV-2, tightly hinges on the transitory silencing of the host gene machinery via epigenetic modulation. SARS-CoV-2 also hijacks and subdues the host gene machinery, leading to epigenetic modulation of the critical host elements responsible for antiviral immunity. Epigenomics is a powerful, unexplored avenue that can provide a profound understanding of virus-host interactions and lead to the development of epigenome-based therapies and vaccines to counter viruses. This review discusses current developments in SARS-CoV-2 variation and its role in epigenetic modulation in infected hosts. This review provides an overview, especially in the context of emerging viral strains, their recombinants, and their possible roles in the epigenetic exploitation of host defense and viral pathogenesis. It provides insights into host-virus interactions at the molecular, genomic, and immunological levels and sheds light on the future of epigenomics-based therapies for SARS-CoV-2 infection.
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Affiliation(s)
- Nitin K Saksena
- Victoria University, Footscray Campus, Melbourne, VIC. Australia.
| | - Srinivasa Bonam Reddy
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | | | - Thyago H S Cardoso
- OMICS Centre of Excellence, G42 Healthcare, Mazdar City, Abu Dhabi, United Arab Emirates.
| | - Edson M A Silva
- Science Division, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Juliana C Ferreira
- Science Division, New York University Abu Dhabi, PO Box 129188, Abu Dhabi, United Arab Emirates.
| | - Wael M Rabeh
- Science Division, New York University Abu Dhabi, PO Box 129188, Abu Dhabi, United Arab Emirates.
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3
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Kramer AM, Thornlow B, Ye C, De Maio N, McBroome J, Hinrichs AS, Lanfear R, Turakhia Y, Corbett-Detig R. Online Phylogenetics with matOptimize Produces Equivalent Trees and is Dramatically More Efficient for Large SARS-CoV-2 Phylogenies than de novo and Maximum-Likelihood Implementations. Syst Biol 2023; 72:1039-1051. [PMID: 37232476 PMCID: PMC10627557 DOI: 10.1093/sysbio/syad031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 05/14/2023] [Accepted: 06/22/2023] [Indexed: 05/27/2023] Open
Abstract
Phylogenetics has been foundational to SARS-CoV-2 research and public health policy, assisting in genomic surveillance, contact tracing, and assessing emergence and spread of new variants. However, phylogenetic analyses of SARS-CoV-2 have often relied on tools designed for de novo phylogenetic inference, in which all data are collected before any analysis is performed and the phylogeny is inferred once from scratch. SARS-CoV-2 data sets do not fit this mold. There are currently over 14 million sequenced SARS-CoV-2 genomes in online databases, with tens of thousands of new genomes added every day. Continuous data collection, combined with the public health relevance of SARS-CoV-2, invites an "online" approach to phylogenetics, in which new samples are added to existing phylogenetic trees every day. The extremely dense sampling of SARS-CoV-2 genomes also invites a comparison between likelihood and parsimony approaches to phylogenetic inference. Maximum likelihood (ML) and pseudo-ML methods may be more accurate when there are multiple changes at a single site on a single branch, but this accuracy comes at a large computational cost, and the dense sampling of SARS-CoV-2 genomes means that these instances will be extremely rare because each internal branch is expected to be extremely short. Therefore, it may be that approaches based on maximum parsimony (MP) are sufficiently accurate for reconstructing phylogenies of SARS-CoV-2, and their simplicity means that they can be applied to much larger data sets. Here, we evaluate the performance of de novo and online phylogenetic approaches, as well as ML, pseudo-ML, and MP frameworks for inferring large and dense SARS-CoV-2 phylogenies. Overall, we find that online phylogenetics produces similar phylogenetic trees to de novo analyses for SARS-CoV-2, and that MP optimization with UShER and matOptimize produces equivalent SARS-CoV-2 phylogenies to some of the most popular ML and pseudo-ML inference tools. MP optimization with UShER and matOptimize is thousands of times faster than presently available implementations of ML and online phylogenetics is faster than de novo inference. Our results therefore suggest that parsimony-based methods like UShER and matOptimize represent an accurate and more practical alternative to established ML implementations for large SARS-CoV-2 phylogenies and could be successfully applied to other similar data sets with particularly dense sampling and short branch lengths.
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Affiliation(s)
- Alexander M Kramer
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Bryan Thornlow
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Cheng Ye
- Department of Electrical and Computer Engineering, University of California San Diego, San Diego, CA 92093, USA
| | - Nicola De Maio
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Cambridge CB10 1SD, UK
| | - Jakob McBroome
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Angie S Hinrichs
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Robert Lanfear
- Department of Ecology and Evolution, Research School of Biology, Australian National University, Canberra, ACT 2601, Australia
| | - Yatish Turakhia
- Department of Electrical and Computer Engineering, University of California San Diego, San Diego, CA 92093, USA
| | - Russell Corbett-Detig
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
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4
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Gallagher KE, Nyiro J, Agoti CN, Maitha E, Nyagwange J, Karani A, Bottomley C, Murunga N, Githinji G, Mutunga M, Ochola‐Oyier LI, Kombe I, Nyaguara A, Kagucia EW, Warimwe G, Agweyu A, Tsofa B, Bejon P, Scott JAG, Nokes DJ. Symptom prevalence and secondary attack rate of SARS-CoV-2 in rural Kenyan households: A prospective cohort study. Influenza Other Respir Viruses 2023; 17:e13185. [PMID: 37752066 PMCID: PMC10522480 DOI: 10.1111/irv.13185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 07/26/2023] [Accepted: 08/07/2023] [Indexed: 09/28/2023] Open
Abstract
BACKGROUND We estimated the secondary attack rate of SARS-CoV-2 among household contacts of PCR-confirmed cases of COVID-19 in rural Kenya and analysed risk factors for transmission. METHODS We enrolled incident PCR-confirmed cases and their household members. At baseline, a questionnaire, a blood sample, and naso-oropharyngeal swabs were collected. Household members were followed 4, 7, 10, 14, 21 and 28 days after the date of the first PCR-positive in the household; naso-oropharyngeal swabs were collected at each visit and used to define secondary cases. Blood samples were collected every 1-2 weeks. Symptoms were collected in a daily symptom diary. We used binomial regression to estimate secondary attack rates and survival analysis to analyse risk factors for transmission. RESULTS A total of 119 households with at least one positive household member were enrolled between October 2020 and September 2022, comprising 503 household members; 226 remained in follow-up at day 14 (45%). A total of 43 secondary cases arose within 14 days of identification of the primary case, and 81 household members remained negative. The 7-day secondary attack rate was 4% (95% CI 1%-10%), the 14-day secondary attack rate was 28% (95% CI 17%-40%). Of 38 secondary cases with data, eight reported symptoms (21%, 95% CI 8%-34%). Antibody to SARS-CoV-2 spike protein at enrolment was not associated with risk of becoming a secondary case. CONCLUSION Households in our setting experienced a lower 7-day attack rate than a recent meta-analysis indicated as the global average (23%-43% depending on variant), and infection is mostly asymptomatic in our setting.
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Affiliation(s)
- Katherine E. Gallagher
- KEMRI‐Wellcome Trust Research Programme (KWTRP)KilifiKenya
- Department of Infectious Diseases EpidemiologyLondon School of Hygiene and Tropical MedicineLondonUK
| | - Joyce Nyiro
- KEMRI‐Wellcome Trust Research Programme (KWTRP)KilifiKenya
| | | | - Eric Maitha
- Ministry of HealthGovernment of KenyaNairobiKenya
| | | | - Angela Karani
- KEMRI‐Wellcome Trust Research Programme (KWTRP)KilifiKenya
| | - Christian Bottomley
- Department of Infectious Diseases EpidemiologyLondon School of Hygiene and Tropical MedicineLondonUK
| | | | | | - Martin Mutunga
- KEMRI‐Wellcome Trust Research Programme (KWTRP)KilifiKenya
| | | | - Ivy Kombe
- KEMRI‐Wellcome Trust Research Programme (KWTRP)KilifiKenya
| | - Amek Nyaguara
- KEMRI‐Wellcome Trust Research Programme (KWTRP)KilifiKenya
| | | | - George Warimwe
- KEMRI‐Wellcome Trust Research Programme (KWTRP)KilifiKenya
- Nuffield Department of MedicineOxford UniversityOxfordUK
| | - Ambrose Agweyu
- KEMRI‐Wellcome Trust Research Programme (KWTRP)KilifiKenya
- Department of Infectious Diseases EpidemiologyLondon School of Hygiene and Tropical MedicineLondonUK
| | - Benjamin Tsofa
- KEMRI‐Wellcome Trust Research Programme (KWTRP)KilifiKenya
| | - Philip Bejon
- KEMRI‐Wellcome Trust Research Programme (KWTRP)KilifiKenya
- Nuffield Department of MedicineOxford UniversityOxfordUK
| | - J. Anthony G. Scott
- KEMRI‐Wellcome Trust Research Programme (KWTRP)KilifiKenya
- Department of Infectious Diseases EpidemiologyLondon School of Hygiene and Tropical MedicineLondonUK
- Nuffield Department of MedicineOxford UniversityOxfordUK
| | - David James Nokes
- KEMRI‐Wellcome Trust Research Programme (KWTRP)KilifiKenya
- School of Life Sciences and the Zeeman Institute for Systems Biology & Infectious Disease Epidemiology Research (SBIDER)University of WarwickCoventryUK
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Miteva D, Kitanova M, Batselova H, Lazova S, Chervenkov L, Peshevska-Sekulovska M, Sekulovski M, Gulinac M, Vasilev GV, Tomov L, Velikova T. The End or a New Era of Development of SARS-CoV-2 Virus: Genetic Variants Responsible for Severe COVID-19 and Clinical Efficacy of the Most Commonly Used Vaccines in Clinical Practice. Vaccines (Basel) 2023; 11:1181. [PMID: 37514997 PMCID: PMC10385722 DOI: 10.3390/vaccines11071181] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 06/22/2023] [Accepted: 06/27/2023] [Indexed: 07/30/2023] Open
Abstract
Although the chief of the World Health Organization (WHO) has declared the end of the coronavirus disease 2019 (COVID-19) as a global health emergency, the disease is still a global threat. To be able to manage such pandemics in the future, it is necessary to develop proper strategies and opportunities to protect human life. The data on the SARS-CoV-2 virus must be continuously analyzed, and the possibilities of mutation and the emergence of new, more infectious variants must be anticipated, as well as the options of using different preventive and therapeutic techniques. This is because the fast development of severe acute coronavirus 2 syndrome (SARS-CoV-2) variants of concern have posed a significant problem for COVID-19 pandemic control using the presently available vaccinations. This review summarizes data on the SARS-CoV-2 variants that are responsible for severe COVID-19 and the clinical efficacy of the most commonly used vaccines in clinical practice. The consequences after the disease (long COVID or post-COVID conditions) continue to be the subject of studies and research, and affect social and economic life worldwide.
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Affiliation(s)
- Dimitrina Miteva
- Department of Genetics, Faculty of Biology, Sofia University "St. Kliment Ohridski", 8 Dragan Tzankov str., 1164 Sofia, Bulgaria
| | - Meglena Kitanova
- Department of Genetics, Faculty of Biology, Sofia University "St. Kliment Ohridski", 8 Dragan Tzankov str., 1164 Sofia, Bulgaria
| | - Hristiana Batselova
- Department of Epidemiology and Disaster Medicine, University Hospital "Saint George", Medical University, 6000 Plovdiv, Bulgaria
| | - Snezhina Lazova
- Pediatric Department, University Hospital "N. I. Pirogov," 21 "General Eduard I. Totleben" Blvd, 1606 Sofia, Bulgaria
- Department of Healthcare, Faculty of Public Health "Prof. Tsekomir Vodenicharov, MD, DSc", Medical University of Sofia, Bialo More 8 str., 1527 Sofia, Bulgaria
| | - Lyubomir Chervenkov
- Department of Diagnostic Imaging, Medical University Plovdiv, Bul. Vasil Aprilov 15A, 4000 Plovdiv, Bulgaria
| | - Monika Peshevska-Sekulovska
- Department of Gastroenterology, University Hospital Lozenetz, 1407 Sofia, Bulgaria
- Medical Faculty, Sofia University St. Kliment Ohridski, 1407 Sofia, Bulgaria
| | - Metodija Sekulovski
- Medical Faculty, Sofia University St. Kliment Ohridski, 1407 Sofia, Bulgaria
- Department of Anesthesiology and Intensive Care, University Hospital Lozenetz, 1 Kozyak str., 1407 Sofia, Bulgaria
| | - Milena Gulinac
- Department of General and Clinical Pathology, Medical University of Plovdiv, Bul. Vasil Aprilov 15A, 4000 Plovdiv, Bulgaria
| | - Georgi V Vasilev
- Clinic of Endocrinology and Metabolic Disorders, UMHAT "Sv. Georgi", 4000 Plovdiv, Bulgaria
| | - Luchesar Tomov
- Department of Informatics, New Bulgarian University, Montevideo 21 str., 1618 Sofia, Bulgaria
| | - Tsvetelina Velikova
- Medical Faculty, Sofia University St. Kliment Ohridski, 1407 Sofia, Bulgaria
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Nicot F, Trémeaux P, Latour J, Carcenac R, Demmou S, Jeanne N, Ranger N, De Smet C, Raymond S, Dimeglio C, Izopet J. Whole-genome single molecule real-time sequencing of SARS-CoV-2 Omicron. J Med Virol 2023; 95:e28564. [PMID: 36756931 DOI: 10.1002/jmv.28564] [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] [Received: 01/06/2023] [Revised: 01/30/2023] [Accepted: 02/06/2023] [Indexed: 02/10/2023]
Abstract
New variants and genetic mutations of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genome can only be identified using accurate sequencing methods. Single molecule real-time (SMRT) sequencing has been used to characterize Alpha and Delta variants, but not Omicron variants harboring numerous mutations in the SARS-CoV-2 genome. This study assesses the performance of a target capture SMRT sequencing protocol for whole genome sequencing (WGS) of SARS-CoV-2 Omicron variants and compared it to that of an amplicon SMRT sequencing protocol optimized for Omicron variants. The failure rate of the target capture protocol (6%) was lower than that of the amplicon protocol (34%, p < 0.001) on our data set, and the median genome coverage with the target capture protocol (98.6% [interquartile range (IQR): 86-99.4]) was greater than that with the amplicon protocol (76.6% [IQR: 66-89.6], [p < 0.001]). The percentages of samples with >95% whole genome coverage were 64% with the target capture protocol and 19% with the amplicon protocol (p < 0.05). The clades of 96 samples determined with both protocols were 93% concordant and the lineages of 59 samples were 100% concordant. Thus, target capture SMRT sequencing appears to be an efficient method for WGS, genotyping and detecting mutations of SARS-CoV-2 Omicron variants.
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Affiliation(s)
- Florence Nicot
- Virology Laboratory, Toulouse University Hospital, Toulouse, France
| | - Pauline Trémeaux
- Virology Laboratory, Toulouse University Hospital, Toulouse, France
| | - Justine Latour
- Virology Laboratory, Toulouse University Hospital, Toulouse, France
| | - Romain Carcenac
- Virology Laboratory, Toulouse University Hospital, Toulouse, France
| | - Sofia Demmou
- Virology Laboratory, Toulouse University Hospital, Toulouse, France
| | - Nicolas Jeanne
- Virology Laboratory, Toulouse University Hospital, Toulouse, France
| | - Noémie Ranger
- Virology Laboratory, Toulouse University Hospital, Toulouse, France
| | | | - Stéphanie Raymond
- Virology Laboratory, Toulouse University Hospital, Toulouse, France
- INSERM UMR 1291-CNRS UMR 5051, Toulouse Institute for Infectious and Inflammatory Diseases (INFINITy), Toulouse, France
| | - Chloé Dimeglio
- Virology Laboratory, Toulouse University Hospital, Toulouse, France
- INSERM UMR 1291-CNRS UMR 5051, Toulouse Institute for Infectious and Inflammatory Diseases (INFINITy), Toulouse, France
| | - Jacques Izopet
- Virology Laboratory, Toulouse University Hospital, Toulouse, France
- INSERM UMR 1291-CNRS UMR 5051, Toulouse Institute for Infectious and Inflammatory Diseases (INFINITy), Toulouse, France
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7
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Wang C, Huang X, Lau EHY, Cowling BJ, Tsang TK. Association Between Population-Level Factors and Household Secondary Attack Rate of SARS-CoV-2: A Systematic Review and Meta-analysis. Open Forum Infect Dis 2022; 10:ofac676. [PMID: 36655186 PMCID: PMC9835764 DOI: 10.1093/ofid/ofac676] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 12/14/2022] [Indexed: 12/23/2022] Open
Abstract
Background Accurate estimation of household secondary attack rate (SAR) is crucial to understand the transmissibility of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The impact of population-level factors, such as transmission intensity in the community, on SAR estimates is rarely explored. Methods In this study, we included articles with original data to compute the household SAR. To determine the impact of transmission intensity in the community on household SAR estimates, we explored the association between SAR estimates and the incidence rate of cases by country during the study period. Results We identified 163 studies to extract data on SARs from 326 031 cases and 2 009 859 household contacts. The correlation between the incidence rate of cases during the study period and SAR estimates was 0.37 (95% CI, 0.24-0.49). We found that doubling the incidence rate of cases during the study period was associated with a 1.2% (95% CI, 0.5%-1.8%) higher household SAR. Conclusions Our findings suggest that the incidence rate of cases during the study period is associated with higher SAR. Ignoring this factor may overestimate SARs, especially for regions with high incidences, which further impacts control policies and epidemiological characterization of emerging variants.
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Affiliation(s)
- Can Wang
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Xiaotong Huang
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Eric H Y Lau
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China,Laboratory of Data Discovery for Health Limited, Hong Kong Science and Technology Park, New Territories, Hong Kong Special Administrative Region, China
| | - Benjamin J Cowling
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China,Laboratory of Data Discovery for Health Limited, Hong Kong Science and Technology Park, New Territories, Hong Kong Special Administrative Region, China
| | - Tim K Tsang
- Correspondence: Tim K. Tsang, PhD, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, 7 Sassoon Road, Pokfulam, Hong Kong Special Administrative Region, China ()
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8
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Marquez C, Kerkhoff AD, Schrom J, Rojas S, Black D, Mitchell A, Wang CY, Pilarowski G, Ribeiro S, Jones D, Payan J, Manganelli S, Rojas S, Lemus J, Jain V, Chamie G, Tulier-Laiwa V, Petersen M, DeRisi J, Havlir DV. COVID-19 Symptoms and Duration of Rapid Antigen Test Positivity at a Community Testing and Surveillance Site During Pre-Delta, Delta, and Omicron BA.1 Periods. JAMA Netw Open 2022; 5:e2235844. [PMID: 36215069 PMCID: PMC9552893 DOI: 10.1001/jamanetworkopen.2022.35844] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/02/2022] [Accepted: 08/24/2022] [Indexed: 12/04/2022] Open
Abstract
Importance Characterizing the clinical symptoms and evolution of community-based SARS-CoV-2 infections may inform health practitioners and public health officials in a rapidly changing landscape of population immunity and viral variants. Objectives To compare COVID-19 symptoms among people testing positive with a rapid antigen test (RAT) during the Omicron BA.1 variant period (December 1, 2021, to January 30, 2022) with the pre-Delta (January 10 to May 31, 2021) and Delta (June 1 to November 30, 2021) variant periods and to assess the duration of RAT positivity during the Omicron BA.1 surge. Design, Setting, and Participants This cross-sectional study was conducted from January 10, 2021, to January 31, 2022, at a walk-up community COVID-19 testing site in San Francisco, California. Participants included children and adults seeking COVID-19 testing with an RAT, regardless of age, vaccine status, or symptoms. Main Outcomes and Measures Fisher exact tests or χ2 tests were used to compare COVID-19 symptoms during the Omicron BA.1 period with the pre-Delta and Delta periods for vaccination status and age group. Among people returning for repeated testing during the Omicron period, the proportion with a positive RAT between 4 and 14 days from symptom onset or since first positive test if asymptomatic was estimated. Results Among 63 277 persons tested (median [IQR] age, 32 [21-44] years, with 12.0% younger than 12 years; 52.0% women; and 68.5% Latinx), a total of 18 301 people (28.9%) reported symptoms, of whom 4565 (24.9%) tested positive for COVID-19. During the Omicron BA.1 period, 3032 of 7283 symptomatic participants (41.6%) tested positive, and the numbers of these reporting cough and sore throat were higher than during pre-Delta and Delta periods (cough: 2044 [67.4%] vs 546 [51.3%] of 1065 participants, P < .001 for pre-Delta, and 281 [60.0%] of 468 participants, P = .002, for Delta; sore throat: 1316 [43.4%] vs 315 [29.6%] of 1065 participants, P < .001 for pre-Delta, and 136 [29.1%] of 468 participants, P < .001, for Delta). Compared with the 1065 patients with positive test results in the pre-Delta period, congestion among the 3032 with positive results during the Omicron BA.1 period was more common (1177 [38.8%] vs 294 [27.6%] participants, P < .001), and loss of taste or smell (160 [5.3%] vs 183 [17.2%] participants, P < .001) and fever (921 [30.4%] vs 369 [34.7%] participants, P = .01) were less common. In addition, during the Omicron BA.1 period, fever was less common among the people with positive test results who had received a vaccine booster compared with those with positive test results who were unvaccinated (97 [22.5%] of 432 vs 42 [36.2%] of 116 participants, P = .003), and fever and myalgia were less common among participants who had received a booster compared with those with positive results who had received only a primary series (fever: 97 [22.5%] of 432 vs 559 [32.8%] of 1705 participants, P < .001; myalgia: 115 [26.6%] of 432 vs 580 [34.0%] of 1705 participants, P = .003). During the Omicron BA.1 period, 5 days after symptom onset, 507 of 1613 people (31.1%) with COVID-19 stated that their symptoms were similar, and 95 people (5.9%) reported worsening symptoms. Among people testing positive, 80.2% of participants who were symptomatic and retested remained positive 5 days after symptom onset. Conclusions and Relevance In this cross-sectional study, COVID-19 upper respiratory tract symptoms were more commonly reported during the Omicron BA.1 period than during the pre-Delta and Delta periods, with differences by vaccination status. Rapid antigen test positivity remained high 5 days after symptom onset, supporting guidelines requiring a negative test to inform the length of the isolation period.
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Affiliation(s)
- Carina Marquez
- Division of HIV, Infectious Diseases and Global Medicine, Zuckerberg San Francisco General Hospital, University of California, San Francisco, San Francisco
| | - Andrew D. Kerkhoff
- Division of HIV, Infectious Diseases and Global Medicine, Zuckerberg San Francisco General Hospital, University of California, San Francisco, San Francisco
| | - John Schrom
- Division of HIV, Infectious Diseases and Global Medicine, Zuckerberg San Francisco General Hospital, University of California, San Francisco, San Francisco
| | - Susana Rojas
- The San Francisco Latino Task Force-Response to COVID-19, San Francisco, California
| | - Douglas Black
- Division of HIV, Infectious Diseases and Global Medicine, Zuckerberg San Francisco General Hospital, University of California, San Francisco, San Francisco
| | | | | | | | | | | | | | | | - Susy Rojas
- Unidos en Salud, San Francisco, California
| | | | - Vivek Jain
- Division of HIV, Infectious Diseases and Global Medicine, Zuckerberg San Francisco General Hospital, University of California, San Francisco, San Francisco
| | - Gabriel Chamie
- Division of HIV, Infectious Diseases and Global Medicine, Zuckerberg San Francisco General Hospital, University of California, San Francisco, San Francisco
| | - Valerie Tulier-Laiwa
- The San Francisco Latino Task Force-Response to COVID-19, San Francisco, California
| | - Maya Petersen
- Division of Biostatistics, School of Public Health, University of California, Berkeley, Berkeley
| | | | - Diane V. Havlir
- Division of HIV, Infectious Diseases and Global Medicine, Zuckerberg San Francisco General Hospital, University of California, San Francisco, San Francisco
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Shi J, Zheng J, Zhang X, Tai W, Odle AE, Perlman S, Du L. RBD-mRNA vaccine induces broadly neutralizing antibodies against Omicron and multiple other variants and protects mice from SARS-CoV-2 challenge. Transl Res 2022; 248:11-21. [PMID: 35489692 PMCID: PMC9045870 DOI: 10.1016/j.trsl.2022.04.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/02/2022] [Revised: 04/19/2022] [Accepted: 04/21/2022] [Indexed: 02/05/2023]
Abstract
Multiple SARS-CoV-2 variants are identified with higher rates of transmissibility or greater disease severity. Particularly, recent emergence of Omicron variant with rapid human-to-human transmission posts new challenges to the current prevention strategies. In this study, following vaccination with an mRNA vaccine encoding SARS-CoV-2 receptor-binding domain (RBD-mRNA), we detected serum antibodies that neutralized pseudoviruses expressing spike (S) protein harboring single or multiple mutations, as well as authentic SARS-CoV-2 variants, and evaluated its protection against SARS-CoV-2 infection. The vaccine induced durable antibodies that potently neutralized prototypic strain and B.1.1.7 lineage variant pseudoviruses containing N501Y or D614G mutations alone or in combination with a N439K mutation (B.1.258 lineage), with a L452R mutation (B.1.427 or B.1.429 lineage), or a L452R-E484Q double mutation (B.1.617.1 variant), although neutralizing activity against B.1.1.7 lineage variant containing 10 amino acid changes in the S protein was slightly reduced. The RBD-mRNA-induced antibodies exerted moderate neutralization against authentic B.1.617.2 and B.1.1.529 variants, and pseudotyped B.1.351 and P.1 lineage variants containing K417N/T, E484K, and N501Y mutations, the B.1.617.2 lineage variant harboring L452R, T478K, and P681R mutations, and the B.1.1.529 lineage variant containing 38 mutations in the S protein. Particularly, RBD-mRNA vaccine completely protected mice from challenge with a virulent mouse-adapted SARS-CoV-2 variant. Among these lineages, B.1.1.7, B.1.351, P.1, B.1.617.2, and B.1.1.529 belong to Alpha, Beta, Gamma, Delta, and Omicron variants, respectively. Our observations reveal that RBD-mRNA vaccine is promising and highlights the need to design novel vaccines with improved neutralization against current and future pandemic SARS-CoV-2 variants.
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Key Words
- ace2, angiotensin converting enzyme 2
- covid-19, coronavirus disease 2019
- e, envelope
- i.d., intradermally
- lnps, lipid nanoparticles
- n, nucleocapsid
- ntd, n-terminal domain
- m, membrane
- pfu, plaque-forming unit
- prnt, plaque reduction neutralization assay
- rbd, receptor-binding domain
- s, spike
- sars-cov-2, severe acute respiratory syndrome coronavirus-2
- vlps, virus-like particles
- vocs, variants of concern
- vois, variants of interest
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Affiliation(s)
- Juan Shi
- Institute for Biomedical Sciences, Georgia State University, Atlanta, Georgia; Lindsley F. Kimball Research Institute, New York Blood Center, New York, New York
| | - Jian Zheng
- Department of Microbiology and Immunology, and Department of Pediatrics, University of Iowa, Iowa City, Iowa
| | - Xiujuan Zhang
- Lindsley F. Kimball Research Institute, New York Blood Center, New York, New York
| | - Wanbo Tai
- Lindsley F. Kimball Research Institute, New York Blood Center, New York, New York
| | - Abby E Odle
- Department of Microbiology and Immunology, and Department of Pediatrics, University of Iowa, Iowa City, Iowa
| | - Stanley Perlman
- Department of Microbiology and Immunology, and Department of Pediatrics, University of Iowa, Iowa City, Iowa.
| | - Lanying Du
- Institute for Biomedical Sciences, Georgia State University, Atlanta, Georgia; Lindsley F. Kimball Research Institute, New York Blood Center, New York, New York.
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10
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Replacement of SARS-CoV-2 strains with variants carrying N501Y and L452R mutations in Japan: an epidemiological surveillance assessment. Western Pac Surveill Response J 2022; 13:1-10. [PMID: 36688179 PMCID: PMC9831602 DOI: 10.5365/wpsar.2022.13.3.943] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Objective Monitoring the prevalence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants is important due to concerns regarding infectivity, transmissibility, immune evasion and disease severity. We evaluated the temporal and regional replacement of previous SARS-CoV-2 variants by the emergent strains, Alpha and Delta. Methods We obtained the results of polymerase chain reaction screening tests for variants conducted in multiple commercial laboratories. Assuming that all previous strains would be replaced by one variant, the new variant detection rate was estimated by fitting a logistic growth model. We estimated the transmission advantage of each new variant over the pre-existing virus strains. Results The variant with the N501Y mutation was first identified in the Kinki region in early February 2021, and by early May, it had replaced more than 90% of the previous strains. The variant with the L452R mutation was first detected in the Kanto-Koshin region in mid-May, and by early August, it comprised more than 90% of the circulating strains. Compared with pre-existing strains, the variant with the N501Y mutation showed transmission advantages of 48.2% and 40.3% in the Kanto-Koshin and Kinki regions, respectively, while the variant with the L452R mutation showed transmission advantages of 60.1% and 71.9%, respectively. Discussion In Japan, Alpha and Delta variants displayed regional differences in the replacement timing and their relative transmission advantages. Our method is efficient in monitoring and estimating changes in the proportion of variant strains in a timely manner in each region.
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11
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Nicot F, Trémeaux P, Latour J, Jeanne N, Ranger N, Raymond S, Dimeglio C, Salin G, Donnadieu C, Izopet J. Whole-genome sequencing of SARS-CoV-2: Comparison of target capture and amplicon single molecule real-time sequencing protocols. J Med Virol 2022; 95:e28123. [PMID: 36056719 PMCID: PMC9539136 DOI: 10.1002/jmv.28123] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 08/17/2022] [Accepted: 08/30/2022] [Indexed: 01/11/2023]
Abstract
Fast, accurate sequencing methods are needed to identify new variants and genetic mutations of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genome. Single-molecule real-time (SMRT) Pacific Biosciences (PacBio) provides long, highly accurate sequences by circular consensus reads. This study compares the performance of a target capture SMRT PacBio protocol for whole-genome sequencing (WGS) of SARS-CoV-2 to that of an amplicon PacBio SMRT sequencing protocol. The median genome coverage was higher (p < 0.05) with the target capture protocol (99.3% [interquartile range, IQR: 96.3-99.5]) than with the amplicon protocol (99.3% [IQR: 69.9-99.3]). The clades of 65 samples determined with both protocols were 100% concordant. After adjusting for Ct values, S gene coverage was higher with the target capture protocol than with the amplicon protocol. After stratification on Ct values, higher S gene coverage with the target capture protocol was observed only for samples with Ct > 17 (p < 0.01). PacBio SMRT sequencing protocols appear to be suitable for WGS, genotyping, and detecting mutations of SARS-CoV-2.
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Affiliation(s)
- Florence Nicot
- Virology LaboratoryToulouse University HospitalToulouseFrance
| | | | - Justine Latour
- Virology LaboratoryToulouse University HospitalToulouseFrance
| | - Nicolas Jeanne
- Virology LaboratoryToulouse University HospitalToulouseFrance
| | - Noémie Ranger
- Virology LaboratoryToulouse University HospitalToulouseFrance
| | - Stéphanie Raymond
- Virology LaboratoryToulouse University HospitalToulouseFrance,Toulouse Institute for Infectious and Inflammatory Diseases (INFINITy)INSERM UMR 1291 – CNRS UMR 5051ToulouseFrance
| | - Chloé Dimeglio
- Virology LaboratoryToulouse University HospitalToulouseFrance,Toulouse Institute for Infectious and Inflammatory Diseases (INFINITy)INSERM UMR 1291 – CNRS UMR 5051ToulouseFrance
| | - Gérald Salin
- Genotoul‐Genome & Transcriptome—Plateforme Génomique (GeT‐PlaGe), US INRAe 1426Castanet‐TolosanFrance
| | - Cécile Donnadieu
- Genotoul‐Genome & Transcriptome—Plateforme Génomique (GeT‐PlaGe), US INRAe 1426Castanet‐TolosanFrance
| | - Jacques Izopet
- Virology LaboratoryToulouse University HospitalToulouseFrance,Toulouse Institute for Infectious and Inflammatory Diseases (INFINITy)INSERM UMR 1291 – CNRS UMR 5051ToulouseFrance
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12
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Schrom J, Marquez C, Pilarowski G, Wang CY, Mitchell A, Puccinelli R, Black D, Rojas S, Ribeiro S, Tulier-Laiwa V, Martinez J, Payan J, Rojas S, Jones D, Martinez D, Nakamura R, Chamie G, Jain V, Petersen M, DeRisi J, Havlir D. Comparison of SARS-CoV-2 Reverse Transcriptase Polymerase Chain Reaction and BinaxNOW Rapid Antigen Tests at a Community Site During an Omicron Surge : A Cross-Sectional Study. Ann Intern Med 2022; 175:682-690. [PMID: 35286144 PMCID: PMC8943844 DOI: 10.7326/m22-0202] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
BACKGROUND SARS-CoV-2 rapid antigen tests are an important public health tool. OBJECTIVE To evaluate field performance of the BinaxNOW rapid antigen test (Abbott) compared with reverse transcriptase polymerase chain reaction (RT-PCR) for detecting infection with the Omicron variant of SARS-CoV-2. DESIGN Cross-sectional surveillance study. SETTING Free, walk-up, outdoor, urban community testing and vaccine site led by Unidos en Salud, serving a predominantly Latinx community highly impacted by COVID-19. PARTICIPANTS Persons seeking COVID-19 testing in January 2022. MEASUREMENTS Simultaneous BinaxNOW and RT-PCR from nasal, cheek, and throat swabs, including cycle threshold (Ct) measures; a lower Ct value is a surrogate for higher amounts of virus. RESULTS Among 731 persons tested with nasal swabs, there were 296 (40.5%) positive results on RT-PCR; 98.9% were the Omicron variant. BinaxNOW detected 95.2% (95% CI, 91% to 98%) of persons who tested positive on RT-PCR with a Ct value below 30, 82.1% (CI, 77% to 87%) of those who tested positive on RT-PCR with a Ct value below 35, and 65.2% (CI, 60% to 71%) of all who were positive on RT-PCR. Among 75 persons with simultaneous nasal and cheek swabs, BinaxNOW using a cheek swab failed to detect 91% (20 of 22) of specimens that were positive on BinaxNOW with a nasal swab. Among persons with simultaneous nasal and throat swabs who were positive on RT-PCR with a Ct value below 30, 42 of 49 (85.7%) were detected by nasal BinaxNOW, 23 of 49 (46.9%) by throat BinaxNOW, and 44 of 49 (89.8%) by either. LIMITATION Participants were a cross-sectional sample from a community-based sentinel surveillance site, precluding study of viral or symptom dynamics. CONCLUSION BinaxNOW detected persons with high SARS-CoV-2 levels during the Omicron surge, enabling rapid responses to positive test results. Cheek or throat swabs should not replace nasal swabs. As currently recommended, high-risk persons with an initial negative BinaxNOW result should have repeated testing. PRIMARY FUNDING SOURCE University of California, San Francisco.
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Affiliation(s)
- John Schrom
- University of California, San Francisco, San Francisco, California (J.S., C.M., D.B., G.C., V.J., D.H.)
| | - Carina Marquez
- University of California, San Francisco, San Francisco, California (J.S., C.M., D.B., G.C., V.J., D.H.)
| | - Genay Pilarowski
- Unidos en Salud, San Francisco, California (G.P., S.Ribeiro, J.M., J.P., D.J., D.M.)
| | - Chung-Yu Wang
- Chan Zuckerberg Biohub, San Francisco, California (C.W., A.M., J.D.)
| | - Anthea Mitchell
- Chan Zuckerberg Biohub, San Francisco, California (C.W., A.M., J.D.)
| | - Robert Puccinelli
- University of California, Berkeley, Berkeley, California (R.P., M.P.)
| | - Doug Black
- University of California, San Francisco, San Francisco, California (J.S., C.M., D.B., G.C., V.J., D.H.)
| | - Susana Rojas
- Unidos en Salud and San Francisco Latino Task Force for COVID-19, San Francisco, California (Susana Rojas, V.T., Susy Rojas)
| | - Salustiano Ribeiro
- Unidos en Salud, San Francisco, California (G.P., S.Ribeiro, J.M., J.P., D.J., D.M.)
| | - Valerie Tulier-Laiwa
- Unidos en Salud and San Francisco Latino Task Force for COVID-19, San Francisco, California (Susana Rojas, V.T., Susy Rojas)
| | - Jacqueline Martinez
- Unidos en Salud, San Francisco, California (G.P., S.Ribeiro, J.M., J.P., D.J., D.M.)
| | - Joselin Payan
- Unidos en Salud, San Francisco, California (G.P., S.Ribeiro, J.M., J.P., D.J., D.M.)
| | - Susy Rojas
- Unidos en Salud and San Francisco Latino Task Force for COVID-19, San Francisco, California (Susana Rojas, V.T., Susy Rojas)
| | - Diane Jones
- Unidos en Salud, San Francisco, California (G.P., S.Ribeiro, J.M., J.P., D.J., D.M.)
| | - Daniel Martinez
- Unidos en Salud, San Francisco, California (G.P., S.Ribeiro, J.M., J.P., D.J., D.M.)
| | - Robert Nakamura
- California Department of Public Health, Richmond, California (R.N.)
| | - Gabriel Chamie
- University of California, San Francisco, San Francisco, California (J.S., C.M., D.B., G.C., V.J., D.H.)
| | - Vivek Jain
- University of California, San Francisco, San Francisco, California (J.S., C.M., D.B., G.C., V.J., D.H.)
| | - Maya Petersen
- University of California, Berkeley, Berkeley, California (R.P., M.P.)
| | - Joe DeRisi
- Chan Zuckerberg Biohub, San Francisco, California (C.W., A.M., J.D.)
| | - Diane Havlir
- University of California, San Francisco, San Francisco, California (J.S., C.M., D.B., G.C., V.J., D.H.)
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13
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Acharya CB, Schrom J, Mitchell AM, Coil DA, Marquez C, Rojas S, Wang CY, Liu J, Pilarowski G, Solis L, Georgian E, Belafsky S, Petersen M, DeRisi J, Michelmore R, Havlir D. Viral Load Among Vaccinated and Unvaccinated, Asymptomatic and Symptomatic Persons Infected With the SARS-CoV-2 Delta Variant. Open Forum Infect Dis 2022; 9:ofac135. [PMID: 35479304 PMCID: PMC8992250 DOI: 10.1093/ofid/ofac135] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 03/16/2022] [Indexed: 07/21/2023] Open
Abstract
We found no significant difference in cycle threshold values between vaccinated and unvaccinated persons infected with severe acute respiratory syndrome coronavirus 2 Delta, overall or stratified by symptoms. Given the substantial proportion of asymptomatic vaccine breakthrough cases with high viral levels, interventions, including masking and testing, should be considered in settings with elevated coronavirus disease 2019 transmission.
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Affiliation(s)
| | - John Schrom
- Unidos en Salud, San Francisco, California, USA
| | - Anthea M Mitchell
- Chan Zuckerberg Biohub and Department of Biochemistry & Biophysics, University of California, San Francisco, San Francisco, California, USA
| | - David A Coil
- Genome Center, University of California, Davis, Davis, California, USA
| | - Carina Marquez
- Unidos en Salud, San Francisco, California, USA
- Division of HIV, Infectious Disease and Global Medicine, Department of Medicine, University of California, San Francisco, San Francisco, California, USA
| | | | - Chung Yu Wang
- Chan Zuckerberg Biohub and Department of Biochemistry & Biophysics, University of California, San Francisco, San Francisco, California, USA
| | - Jamin Liu
- Joint UCB/UCSF Bioengineering Program, University of California, Berkeley, and University of California, San Francisco, San Francisco, California, USA
| | - Genay Pilarowski
- Unidos en Salud, San Francisco, California, USA
- The Public Health Company, Oakland, California, USA
| | - Leslie Solis
- Genome Center, University of California, Davis, Davis, California, USA
| | | | - Sheri Belafsky
- Department of Public Health Sciences, University of California, Davis, Davis, California, USA
| | - Maya Petersen
- Unidos en Salud, San Francisco, California, USA
- School of Public Health, University of California, Berkeley, Berkeley, California, USA
| | - Joseph DeRisi
- Chan Zuckerberg Biohub and Department of Biochemistry & Biophysics, University of California, San Francisco, San Francisco, California, USA
| | | | - Diane Havlir
- Unidos en Salud, San Francisco, California, USA
- Division of HIV, Infectious Disease and Global Medicine, Department of Medicine, University of California, San Francisco, San Francisco, California, USA
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14
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Jacobson KB, Pinsky BA, Montez Rath ME, Wang H, Miller JA, Skhiri M, Shepard J, Mathew R, Lee G, Bohman B, Parsonnet J, Holubar M. Post-Vaccination Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Infections and Incidence of the Presumptive B.1.427/B.1.429 Variant Among Healthcare Personnel at a Northern California Academic Medical Center. Clin Infect Dis 2022; 74:821-828. [PMID: 34137815 PMCID: PMC8344553 DOI: 10.1093/cid/ciab554] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Indexed: 11/17/2022] Open
Abstract
BACKGROUND Although mRNA-based severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) vaccines report >90% efficacy, breakthrough infections occur. Little is known about their effectiveness against SARS-CoV-2 variants, including the highly prevalent B.1.427/B.1.429 variant. METHODS In this quality improvement project, we collected demographic and clinical information from post-vaccine SARS-CoV-2 cases (PVSCs), defined as healthcare personnel (HCP) with positive SARS-CoV-2 nucleic acid amplification test after receiving ≥1 vaccine dose. Available specimens were tested for L452R, N501Y, and E484K mutations using reverse-transcription polymerase chain reaction. Mutation prevalence was compared among unvaccinated, early post-vaccinated (≤14 days after dose 1), partially vaccinated (positive test >14 days after dose 1 and <14 days after dose 2), and fully vaccinated (>14 days after dose 2) PVSCs. RESULTS From December 2020 to April 2021, ≥23 090 HCP received ≥1 dose of an mRNA-based SARS-CoV-2 vaccine, and 660 HCP cases of SARS-CoV-2 occurred, of which 189 were PVSCs. Among the PVSCs, 114 (60.3%), 49 (25.9%), and 26 (13.8%) were early post-vaccination, partially vaccinated, and fully vaccinated, respectively. Of 261 available samples from vaccinated and unvaccinated HCP, 103 (39.5%), including 42 PVSCs (36.5%), had the L452R mutation presumptive of B.1.427/B.1.429. When adjusted for community prevalence of B.1.427/B.1.429, PVSCs did not have significantly elevated risk of B.1.427/B.1.429 compared with unvaccinated HCP. CONCLUSIONS Most PVSCs occurred prior to expected onset of full, vaccine-derived immunity. Presumptive B.1.427/B.1.429 was not more prevalent in post-vaccine cases than in unvaccinated SARS-CoV-2 HCP. Continued infection control measures, particularly <14 days post-vaccination, and continued variant surveillance in PVSCs are imperative to control future SARS-CoV-2 surges.
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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, California, USA
| | - Benjamin A Pinsky
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, California, USA
- Department of Pathology, Stanford University School of Medicine, Stanford, California, USA
| | - Maria E Montez Rath
- Department of Medicine, Division of Nephrology, Stanford University School of Medicine, Stanford, California, USA
| | - Hannah Wang
- Department of Pathology, Stanford University School of Medicine, Stanford, California, USA
| | - Jacob A Miller
- Department of Radiation Oncology, Stanford University School of Medicine, Stanford, California, USA
| | - Mehdi Skhiri
- Department of Medicine, Primary Care and Population Health, Stanford University School of Medicine, Stanford, California, USA
| | - John Shepard
- Department of Quality, Patient Safety and Clinical Effectiveness, Stanford Health Care, Stanford, California, USA
| | - Roshni Mathew
- Department of Pediatrics, Division of Infectious Diseases, Stanford University School of Medicine, Stanford, California, USA
| | - Grace Lee
- Department of Pediatrics, Division of Infectious Diseases, Stanford University School of Medicine, Stanford, California, USA
| | - Bryan Bohman
- Workforce Health and Wellness, Stanford University School of Medicine, Stanford, California, USA
| | - Julie Parsonnet
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, California, USA
- Department of Epidemiology and Population Health, Stanford University School of Medicine, Stanford, California, USA
| | - Marisa Holubar
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, California, USA
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15
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Stoddard G, Black A, Ayscue P, Lu D, Kamm J, Bhatt K, Chan L, Kistler AL, Batson J, Detweiler A, Tan M, Neff N, DeRisi JL, Corrigan J. Using genomic epidemiology of SARS-CoV-2 to support contact tracing and public health surveillance in rural Humboldt County, California. BMC Public Health 2022; 22:456. [PMID: 35255849 PMCID: PMC8900115 DOI: 10.1186/s12889-022-12790-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Accepted: 01/03/2022] [Indexed: 11/12/2022] Open
Abstract
Background During the COVID-19 pandemic within the United States, much of the responsibility for diagnostic testing and epidemiologic response has relied on the action of county-level departments of public health. Here we describe the integration of genomic surveillance into epidemiologic response within Humboldt County, a rural county in northwest California. Methods Through a collaborative effort, 853 whole SARS-CoV-2 genomes were generated, representing ~58% of the 1,449 SARS-CoV-2-positive cases detected in Humboldt County as of March 12, 2021. Phylogenetic analysis of these data was used to develop a comprehensive understanding of SARS-CoV-2 introductions to the county and to support contact tracing and epidemiologic investigations of all large outbreaks in the county. Results In the case of an outbreak on a commercial farm, viral genomic data were used to validate reported epidemiologic links and link additional cases within the community who did not report a farm exposure to the outbreak. During a separate outbreak within a skilled nursing facility, genomic surveillance data were used to rule out the putative index case, detect the emergence of an independent Spike:N501Y substitution, and verify that the outbreak had been brought under control. Conclusions These use cases demonstrate how developing genomic surveillance capacity within local public health departments can support timely and responsive deployment of genomic epidemiology for surveillance and outbreak response based on local needs and priorities. Supplementary Information The online version contains supplementary material available at 10.1186/s12889-022-12790-0.
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Affiliation(s)
- Gunnar Stoddard
- Humboldt County Department of Health and Human Services - Public Health, CA, Eureka, USA
| | | | | | - Dan Lu
- Chan Zuckerberg Initiative, CA, San Francisco, USA
| | - Jack Kamm
- Chan Zuckerberg Biohub, CA, San Francisco, USA
| | - Karan Bhatt
- Chan Zuckerberg Biohub, CA, San Francisco, USA
| | - Lienna Chan
- Chan Zuckerberg Biohub, CA, San Francisco, USA
| | | | | | | | | | - Norma Neff
- Chan Zuckerberg Biohub, CA, San Francisco, USA
| | - Joseph L DeRisi
- Chan Zuckerberg Biohub, CA, San Francisco, USA.,Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA
| | - Jeremy Corrigan
- Humboldt County Department of Health and Human Services - Public Health, CA, Eureka, USA. .,Humboldt County Public Health Laboratory, CA, Eureka, USA.
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16
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SARS-CoV-2 variant exposures elicit antibody responses with differential cross-neutralization of established and emerging strains including Delta and Omicron. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2021:2021.09.08.21263095. [PMID: 34981075 PMCID: PMC8722618 DOI: 10.1101/2021.09.08.21263095] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
The wide spectrum of SARS-CoV-2 variants with phenotypes impacting transmission and antibody sensitivity necessitates investigation of the immune response to different spike protein versions. Here, we compare the neutralization of variants of concern, including B.1.617.2 (Delta) and B.1.1.529 (Omicron) in sera from individuals exposed to variant infection, vaccination, or both. We demonstrate that neutralizing antibody responses are strongest against variants sharing certain spike mutations with the immunizing exposure. We also observe that exposure to multiple spike variants increases the breadth of variant cross-neutralization. These findings contribute to understanding relationships between exposures and antibody responses and may inform booster vaccination strategies. SUMMARY This study characterizes neutralization of eight different SARS-CoV-2 variants, including Delta and Omicron, with respect to nine different prior exposures, including vaccination, booster, and infections with Delta, Epsilon, and others. Different exposures were found to confer substantially differing neutralization specificity.
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17
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Lhomme S, Latour J, Jeanne N, Trémeaux P, Ranger N, Migueres M, Salin G, Donnadieu C, Izopet J. Prediction of SARS-CoV-2 Variant Lineages Using the S1-Encoding Region Sequence Obtained by PacBio Single-Molecule Real-Time Sequencing. Viruses 2021; 13:v13122544. [PMID: 34960813 PMCID: PMC8707593 DOI: 10.3390/v13122544] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 12/15/2021] [Accepted: 12/16/2021] [Indexed: 12/20/2022] Open
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is the causal agent of the COVID-19 pandemic that emerged in late 2019. The outbreak of variants with mutations in the region encoding the spike protein S1 sub-unit that can make them more resistant to neutralizing or monoclonal antibodies is the main point of the current monitoring. This study examines the feasibility of predicting the variant lineage and monitoring the appearance of reported mutations by sequencing only the region encoding the S1 domain by Pacific Bioscience Single Molecule Real-Time sequencing (PacBio SMRT). Using the PacBio SMRT system, we successfully sequenced 186 of the 200 samples previously sequenced with the Illumina COVIDSeq (whole genome) system. PacBio SMRT detected mutations in the S1 domain that were missed by the COVIDseq system in 27/186 samples (14.5%), due to amplification failure. These missing positions included mutations that are decisive for lineage assignation, such as G142D (n = 11), N501Y (n = 6), or E484K (n = 2). The lineage of 172/186 (92.5%) samples was accurately determined by analyzing the region encoding the S1 domain with a pipeline that uses key positions in S1. Thus, the PacBio SMRT protocol is appropriate for determining virus lineages and detecting key mutations.
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Affiliation(s)
- Sébastien Lhomme
- Infinity, Université Toulouse, CNRS, INSERM, UPS, 31300 Toulouse, France; (M.M.); (J.I.)
- Laboratoire de Virologie, CHU Toulouse, Hôpital Purpan, 31300 Toulouse, France; (J.L.); (N.J.); (P.T.); (N.R.)
- Correspondence: ; Tel.: +33-5-67-69-04-24
| | - Justine Latour
- Laboratoire de Virologie, CHU Toulouse, Hôpital Purpan, 31300 Toulouse, France; (J.L.); (N.J.); (P.T.); (N.R.)
| | - Nicolas Jeanne
- Laboratoire de Virologie, CHU Toulouse, Hôpital Purpan, 31300 Toulouse, France; (J.L.); (N.J.); (P.T.); (N.R.)
| | - Pauline Trémeaux
- Laboratoire de Virologie, CHU Toulouse, Hôpital Purpan, 31300 Toulouse, France; (J.L.); (N.J.); (P.T.); (N.R.)
| | - Noémie Ranger
- Laboratoire de Virologie, CHU Toulouse, Hôpital Purpan, 31300 Toulouse, France; (J.L.); (N.J.); (P.T.); (N.R.)
| | - Marion Migueres
- Infinity, Université Toulouse, CNRS, INSERM, UPS, 31300 Toulouse, France; (M.M.); (J.I.)
- Laboratoire de Virologie, CHU Toulouse, Hôpital Purpan, 31300 Toulouse, France; (J.L.); (N.J.); (P.T.); (N.R.)
| | - Gérald Salin
- INRAE, US 1426, GeT-PlaGe, Genotoul, 31326 Castanet-Tolosan, France; (G.S.); (C.D.)
| | - Cécile Donnadieu
- INRAE, US 1426, GeT-PlaGe, Genotoul, 31326 Castanet-Tolosan, France; (G.S.); (C.D.)
| | - Jacques Izopet
- Infinity, Université Toulouse, CNRS, INSERM, UPS, 31300 Toulouse, France; (M.M.); (J.I.)
- Laboratoire de Virologie, CHU Toulouse, Hôpital Purpan, 31300 Toulouse, France; (J.L.); (N.J.); (P.T.); (N.R.)
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Tao K, Tzou PL, Nouhin J, Gupta RK, de Oliveira T, Kosakovsky Pond SL, Fera D, Shafer RW. The biological and clinical significance of emerging SARS-CoV-2 variants. Nat Rev Genet 2021; 22:757-773. [PMID: 34535792 PMCID: PMC8447121 DOI: 10.1038/s41576-021-00408-x] [Citation(s) in RCA: 605] [Impact Index Per Article: 201.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/28/2021] [Indexed: 12/13/2022]
Abstract
The past several months have witnessed the emergence of SARS-CoV-2 variants with novel spike protein mutations that are influencing the epidemiological and clinical aspects of the COVID-19 pandemic. These variants can increase rates of virus transmission and/or increase the risk of reinfection and reduce the protection afforded by neutralizing monoclonal antibodies and vaccination. These variants can therefore enable SARS-CoV-2 to continue its spread in the face of rising population immunity while maintaining or increasing its replication fitness. The identification of four rapidly expanding virus lineages since December 2020, designated variants of concern, has ushered in a new stage of the pandemic. The four variants of concern, the Alpha variant (originally identified in the UK), the Beta variant (originally identified in South Africa), the Gamma variant (originally identified in Brazil) and the Delta variant (originally identified in India), share several mutations with one another as well as with an increasing number of other recently identified SARS-CoV-2 variants. Collectively, these SARS-CoV-2 variants complicate the COVID-19 research agenda and necessitate additional avenues of laboratory, epidemiological and clinical research.
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Affiliation(s)
- Kaiming Tao
- Division of Infectious Diseases, Department of Medicine, Stanford University, Stanford, CA, USA
| | - Philip L Tzou
- Division of Infectious Diseases, Department of Medicine, Stanford University, Stanford, CA, USA
| | - Janin Nouhin
- Division of Infectious Diseases, Department of Medicine, Stanford University, Stanford, CA, USA
| | - Ravindra K Gupta
- Cambridge Institute for Therapeutic Immunology and Infectious Diseases, University of Cambridge, Cambridge, UK
| | - Tulio de Oliveira
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), University of KwaZulu-Natal, Durban, South Africa
| | | | - Daniela Fera
- Department of Chemistry and Biochemistry, Swarthmore College, Swarthmore, PA, USA
| | - Robert W Shafer
- Division of Infectious Diseases, Department of Medicine, Stanford University, Stanford, CA, USA.
- Department of Pathology, Stanford University, Stanford, CA, USA.
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19
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Huang Y, Yu J, Li D, He K, Liu W, Wang L, Chen Y, Xie C, Wu X. Durable tracking anti-SARS-CoV-2 antibodies in cancer patients recovered from COVID-19. Sci Rep 2021; 11:17381. [PMID: 34462453 PMCID: PMC8405618 DOI: 10.1038/s41598-021-96195-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Accepted: 07/31/2021] [Indexed: 11/09/2022] Open
Abstract
Cancer patients are more susceptible to SARS-CoV-2 infection and generally have higher mortality rate. Anti-SARS-CoV-2 IgG is an important consideration for the patients in this COVID-19 pandemic. Recent researches suggested the rapid decay of anti-SARS-CoV-2 antibodies in the general population, but the decline rate of the antibodies in cancer patients was unknown. In this observational study, we reported the clinical features of the 53 cancer patients infected by SARS-CoV-2 from Wuhan, China and tracked the presence of anti-SARS-CoV-2 antibodies in the patients for more than 12 months. We found the duration (days) of anti-SARS-CoV-2 IgG in the patients was significant longer in chemotherapy (mean: 175; range: 75 to 315) and radiotherapy groups (mean: 168; range: 85 to 265) than in non-chemo- or radio-therapy group (mean: 58; range: 21 to 123) after their recovery from COVID-19. We also used single-cell RNA sequencing to track the immunologic changes in a representative patient recovered from COVID-19 and found that CD8 + effective T cells, memory B cells and plasma cells were persistently activated in the patient undergoing chemotherapy. Together, our findings show that chemotherapy and radiotherapy might be beneficial to extend the duration of anti-SARS-CoV-2 IgG.
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Affiliation(s)
- Yongsheng Huang
- School of Basic Medicine, Peking Union Medical College, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, Beijing, China
| | - Jing Yu
- Department of Radiation and Medical Oncology, Zhongnan Hospital, Wuhan University, Wuhan, 430071, China.,Hubei Cancer Clinical Study Center, Zhongnan Hospital, Wuhan University, Wuhan, China
| | - Dan Li
- National Cancer Center/Cancer Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Kai He
- Guangdong Provincial Key Laboratory of Single Cell Technology and Application, School of Basic Medical Science, Southern Medical University, Guangzhou, China
| | - Wenyang Liu
- National Cancer Center/Cancer Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Lin Wang
- School of Basic Medicine, Peking Union Medical College, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, Beijing, China
| | - Yeshan Chen
- Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430000, China.
| | - Conghua Xie
- Department of Radiation and Medical Oncology, Zhongnan Hospital, Wuhan University, Wuhan, 430071, China. .,Hubei Cancer Clinical Study Center, Zhongnan Hospital, Wuhan University, Wuhan, China.
| | - Xiaowei Wu
- Department of Thoracic Surgery, TongJi Hospital, TongJi Medical College, Huazhong University of Science and Technology, Wuhan, 430000, China.
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20
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Madewell ZJ, Yang Y, Longini IM, Halloran ME, Dean NE. Factors Associated With Household Transmission of SARS-CoV-2: An Updated Systematic Review and Meta-analysis. JAMA Netw Open 2021; 4:e2122240. [PMID: 34448865 PMCID: PMC8397928 DOI: 10.1001/jamanetworkopen.2021.22240] [Citation(s) in RCA: 98] [Impact Index Per Article: 32.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Accepted: 06/19/2021] [Indexed: 12/14/2022] Open
Abstract
Importance A previous systematic review and meta-analysis of household transmission of SARS-CoV-2 that summarized 54 published studies through October 19, 2020, found an overall secondary attack rate (SAR) of 16.6% (95% CI, 14.0%-19.3%). However, the understanding of household secondary attack rates for SARS-CoV-2 is still evolving, and updated analysis is needed. Objective To use newly published data to further the understanding of SARS-CoV-2 transmission in the household. Data Sources PubMed and reference lists of eligible articles were used to search for records published between October 20, 2020, and June 17, 2021. No restrictions on language, study design, time, or place of publication were applied. Studies published as preprints were included. Study Selection Articles with original data that reported at least 2 of the following factors were included: number of household contacts with infection, total number of household contacts, and secondary attack rates among household contacts. Studies that reported household infection prevalence (which includes index cases), that tested contacts using antibody tests only, and that included populations overlapping with another included study were excluded. Search terms were SARS-CoV-2 or COVID-19 with secondary attack rate, household, close contacts, contact transmission, contact attack rate, or family transmission. Data Extraction and Synthesis Meta-analyses were performed using generalized linear mixed models to obtain SAR estimates and 95% CIs. The Preferred Reporting Items for Systematic Reviews and Meta-analyses (PRISMA) reporting guideline was followed. Main Outcomes and Measures Overall household SAR for SARS-CoV-2, SAR by covariates (contact age, sex, ethnicity, comorbidities, and relationship; index case age, sex, symptom status, presence of fever, and presence of cough; number of contacts; study location; and variant), and SAR by index case identification period. Results A total of 2722 records (2710 records from database searches and 12 records from the reference lists of eligible articles) published between October 20, 2020, and June 17, 2021, were identified. Of those, 93 full-text articles reporting household transmission of SARS-CoV-2 were assessed for eligibility, and 37 studies were included. These 37 new studies were combined with 50 of the 54 studies (published through October 19, 2020) from our previous review (4 studies from Wuhan, China, were excluded because their study populations overlapped with another recent study), resulting in a total of 87 studies representing 1 249 163 household contacts from 30 countries. The estimated household SAR for all 87 studies was 18.9% (95% CI, 16.2%-22.0%). Compared with studies from January to February 2020, the SAR for studies from July 2020 to March 2021 was higher (13.4% [95% CI, 10.7%-16.7%] vs 31.1% [95% CI, 22.6%-41.1%], respectively). Results from subgroup analyses were similar to those reported in a previous systematic review and meta-analysis; however, the SAR was higher to contacts with comorbidities (3 studies; 50.0% [95% CI, 41.4%-58.6%]) compared with previous findings, and the estimated household SAR for the B.1.1.7 (α) variant was 24.5% (3 studies; 95% CI, 10.9%-46.2%). Conclusions and Relevance The findings of this study suggest that the household remains an important site of SARS-CoV-2 transmission, and recent studies have higher household SAR estimates compared with the earliest reports. More transmissible variants and vaccines may be associated with further changes.
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Affiliation(s)
| | - Yang Yang
- Department of Biostatistics, University of Florida, Gainesville
| | - Ira M. Longini
- Department of Biostatistics, University of Florida, Gainesville
| | - M. Elizabeth Halloran
- Fred Hutchinson Cancer Research Center, Seattle, Washington
- Department of Biostatistics, University of Washington, Seattle
| | - Natalie E. Dean
- Department of Biostatistics, University of Florida, Gainesville
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21
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Kepczynski CM, Genigeski JA, Koski RR, Bernknopf AC, Konieczny AM, Klepser ME. A systematic review comparing at-home diagnostic tests for SARS-CoV-2: Key points for pharmacy practice, including regulatory information. J Am Pharm Assoc (2003) 2021; 61:666-677.e2. [PMID: 34274214 PMCID: PMC8196235 DOI: 10.1016/j.japh.2021.06.012] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2021] [Revised: 05/19/2021] [Accepted: 06/08/2021] [Indexed: 11/19/2022]
Abstract
BACKGROUND Home-based rapid diagnostic testing can play an integral role in controlling the spread of coronavirus disease 2019 (COVID-19). OBJECTIVES This review aimed to identify and compare at-home diagnostic tests that have been granted Emergency Use Authorizations (EUAs) and convey details about COVID-19 diagnostic tests, including regulatory information, pertinent to pharmacy practice. METHODS The Food and Drug Administration (FDA) online resources pertaining to COVID-19 tests, EUAs, and medical devices were consulted, as were linked resources from FDA's webpages. Homepages of the 9 COVID-19 home tests with EUAs were comprehensively reviewed. PubMed literature searches were performed, most recently in May 2021, to locate literature about the identified home tests, as were searches of Google Scholar, medRxiv, and bioRxiv. Studies were included if they were performed at home or if subjects self-tested at study sites. Samples were collected by a parent or guardian for patients under 18 years of age. Positive percent agreement (PPA) and negative percent agreement (NPA) for the clinical diagnosis of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus was evaluated. RESULTS Limited data have been published for these home tests given that they are available through EUAs that do not require clinical trials. Fifteen studies were located from searching the literature, but only 2 met the inclusion criteria. Review of the home tests' websites yielded a single study for each test, with the 3 BinaxNOW platforms using the same study for their EUAs. The 9 COVID-19 home tests with EUAs as of May 7, 2021, include 3 molecular tests and 6 antigen tests. These tests had similar performance on the basis of PPA ranging from 83.5% to 97.4% and NPA ranging from 97% to 100%. CONCLUSION The 9 SARS-CoV-2 home tests demonstrated satisfactory performance in comparison with laboratory real time reverse-transcription polymerase chain reaction tests. The convenience and ease of use of these tests make them well-suited for home-based rapid SARS-CoV-2 testing.
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22
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Boehm E, Kronig I, Neher RA, Eckerle I, Vetter P, Kaiser L. Novel SARS-CoV-2 variants: the pandemics within the pandemic. Clin Microbiol Infect 2021; 27:1109-1117. [PMID: 34015535 PMCID: PMC8127517 DOI: 10.1016/j.cmi.2021.05.022] [Citation(s) in RCA: 227] [Impact Index Per Article: 75.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 05/05/2021] [Accepted: 05/09/2021] [Indexed: 11/29/2022]
Abstract
Background Many new variants of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have been termed variants of concern/interest (VOC/I) because of the greater risk they pose due to possible enhanced transmissibility and/or severity, immune escape, diagnostic and/or treatment failure, and reduced vaccine efficacy. Aims We sought to review the current knowledge of emerging SARS-CoV-2 variants, particularly those deemed VOC/Is: B.1.351, B.1.1.7, and P.1. Sources MEDLINE and BioRxiv databases, as well as the grey literature, were searched for reports of SARS-CoV-2 variants since November 2020. Relevant articles and their references were screened. Content Mutations on the spike protein in particular may affect both affinity for the SARS-CoV-2 cell receptor ACEII and antibody binding. These VOC/Is often share similar mutation sets. The N501Y mutation is shared by the three main VOCs: B.1.1.7, first identified in the United Kingdom, P.1, originating from Brazil, and B.1.351, first described in South Africa. This mutation likely increases transmissibility by increasing affinity for ACEII. The B.1.351 and P.1 variants also display the E484K mutation which decreases binding of neutralizing antibodies, leading to partial immune escape; this favours reinfections, and decreases the in vitro efficacy of some antibody therapies or vaccines. Those mutations may also have phenotypical repercussions of greater severity. Furthermore, the accumulation of mutations poses a diagnostic risk (lowered when using multiplex assays), as seen for some assays targeting the S gene. With ongoing surveillance, many new VOC/Is have been identified. The emergence of the E484K mutation independently in different parts of the globe may reflect the adaptation of SARS-CoV-2 to humans against a background of increasing immunity. Implications These VOC/Is are increasing in frequency globally and pose challenges to any herd immunity approach to managing the pandemic. While vaccination is ongoing, vaccine updates may be prudent. The virus continues to adapt to transmission in humans, and further divergence from the initial Wuhan sequences is expected.
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Affiliation(s)
- Erik Boehm
- Geneva Centre for Emerging Viral Diseases, Geneva University Hospitals, 1205 Geneva, Switzerland; Laboratory of Virology, Division of Laboratory Medicine, Geneva University Hospitals & Faculty of Medicine, University of Geneva, 1205 Geneva, Switzerland.
| | - Ilona Kronig
- Geneva Centre for Emerging Viral Diseases, Geneva University Hospitals, 1205 Geneva, Switzerland; Laboratory of Virology, Division of Laboratory Medicine, Geneva University Hospitals & Faculty of Medicine, University of Geneva, 1205 Geneva, Switzerland
| | - Richard A Neher
- Biozentrum, University of Basel, Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Isabella Eckerle
- Geneva Centre for Emerging Viral Diseases, Geneva University Hospitals, 1205 Geneva, Switzerland; Laboratory of Virology, Division of Laboratory Medicine, Geneva University Hospitals & Faculty of Medicine, University of Geneva, 1205 Geneva, Switzerland; Department of Microbiology and Molecular Medicine, University of Geneva, Geneva, Switzerland
| | - Pauline Vetter
- Geneva Centre for Emerging Viral Diseases, Geneva University Hospitals, 1205 Geneva, Switzerland; Laboratory of Virology, Division of Laboratory Medicine, Geneva University Hospitals & Faculty of Medicine, University of Geneva, 1205 Geneva, Switzerland
| | - Laurent Kaiser
- Geneva Centre for Emerging Viral Diseases, Geneva University Hospitals, 1205 Geneva, Switzerland; Laboratory of Virology, Division of Laboratory Medicine, Geneva University Hospitals & Faculty of Medicine, University of Geneva, 1205 Geneva, Switzerland
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23
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Chen X, Chen Z, Azman AS, Sun R, Lu W, Zheng N, Zhou J, Wu Q, Deng X, Zhao Z, Chen X, Ge S, Yang J, Leung DT, Yu H. Comprehensive mapping of neutralizing antibodies against SARS-CoV-2 variants induced by natural infection or vaccination. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2021:2021.05.03.21256506. [PMID: 33972950 PMCID: PMC8109187 DOI: 10.1101/2021.05.03.21256506] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Background Immunity after SARS-CoV-2 infection or vaccination has been threatened by recently emerged SARS-CoV-2 variants. A systematic summary of the landscape of neutralizing antibodies against emerging variants is needed. Methods We systematically searched PubMed, Embase, Web of Science, and 3 pre-print servers for studies that evaluated neutralizing antibodies titers induced by previous infection or vaccination against SARS-CoV-2 variants and comprehensively collected individual data. We calculated lineage-specific GMTs across different study participants and types of neutralization assays. Findings We identified 56 studies, including 2,483 individuals and 8,590 neutralization tests, meeting the eligibility criteria. Compared with lineage B, we estimate a 1.5-fold (95% CI: 1.0-2.2) reduction in neutralization against the B.1.1.7, 8.7-fold (95% CI: 6.5-11.7) reduction against B.1.351 and 5.0-fold (95% CI: 4.0-6.2) reduction against P.1. The estimated neutralization reductions for B.1.351 compared to lineage B were 240.2-fold (95% CI: 124.0-465.6) reduction for non-replicating vector platform, 4.6-fold (95% CI: 4.0-5.2) reduction for RNA platform, and 1.6-fold (95% CI: 1.2-2.1) reduction for protein subunit platform. The neutralizing antibodies induced by administration of inactivated vaccines and mRNA vaccines against lineage P.1 were also remarkably reduced by an average of 5.9-fold (95% CI: 3.7-9.3) and 1.5-fold (95% CI: 1.2-1.9). Interpretation Our findings indicate that the antibody response established by natural infection or vaccination might be able to effectively neutralize B.1.1.7, but neutralizing titers against B.1.351 and P.1 suffered large reductions. Standardized protocols for neutralization assays, as well as updating immune-based prevention and treatment, are needed. Funding Chinese National Science Fund for Distinguished Young Scholars.
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Affiliation(s)
- Xinhua Chen
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China
| | - Zhiyuan Chen
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China
| | - Andrew S. Azman
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
- Unit of Population Epidemiology, Division of Primary Care Medicine, Geneva University Hospitals, Switzerland
- Institute of Global Health, Faculty of Medicine, University of Geneva, Switzerland
| | - Ruijia Sun
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China
| | - Wanying Lu
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China
| | - Nan Zheng
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China
| | - Jiaxin Zhou
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China
| | - Qianhui Wu
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China
| | - Xiaowei Deng
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China
| | - Zeyao Zhao
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China
| | - Xinghui Chen
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China
| | - Shijia Ge
- Department of Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China
| | - Juan Yang
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China
| | - Daniel T. Leung
- Division of Infectious Diseases, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Hongjie Yu
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China
- Department of Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China
- Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai, China
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24
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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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Thornlow B, Hinrichs AS, Jain M, Dhillon N, La S, Kapp JD, Anigbogu I, Cassatt-Johnstone M, McBroome J, Haeussler M, Turakhia Y, Chang T, Olsen HE, Sanford J, Stone M, Vaske O, Bjork I, Akeson M, Shapiro B, Haussler D, Kilpatrick AM, Corbett-Detig R. A new SARS-CoV-2 lineage that shares mutations with known Variants of Concern is rejected by automated sequence repository quality control. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021:2021.04.05.438352. [PMID: 33851162 PMCID: PMC8043452 DOI: 10.1101/2021.04.05.438352] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
We report a SARS-CoV-2 lineage that shares N501Y, P681H, and other mutations with known variants of concern, such as B.1.1.7. This lineage, which we refer to as B.1.x (COG-UK sometimes references similar samples as B.1.324.1), is present in at least 20 states across the USA and in at least six countries. However, a large deletion causes the sequence to be automatically rejected from repositories, suggesting that the frequency of this new lineage is underestimated using public data. Recent dynamics based on 339 samples obtained in Santa Cruz County, CA, USA suggest that B.1.x may be increasing in frequency at a rate similar to that of B.1.1.7 in Southern California. At present the functional differences between this variant B.1.x and other circulating SARS-CoV-2 variants are unknown, and further studies on secondary attack rates, viral loads, immune evasion and/or disease severity are needed to determine if it poses a public health concern. Nonetheless, given what is known from well-studied circulating variants of concern, it seems unlikely that the lineage could pose larger concerns for human health than many already globally distributed lineages. Our work highlights a need for rapid turnaround time from sequence generation to submission and improved sequence quality control that removes submission bias. We identify promising paths toward this goal.
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Affiliation(s)
- Bryan Thornlow
- Department of Biomolecular Engineering, University of California, Santa Cruz
- Genomics Institute, University of California, Santa Cruz
| | | | - Miten Jain
- Department of Biomolecular Engineering, University of California, Santa Cruz
- Genomics Institute, University of California, Santa Cruz
| | - Namrita Dhillon
- Molecular Diagnostics Laboratory, University of California, Santa Cruz
| | - Scott La
- Molecular Diagnostics Laboratory, University of California, Santa Cruz
| | - Joshua D. Kapp
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz
| | - Ikenna Anigbogu
- Department of Biomolecular Engineering, University of California, Santa Cruz
| | | | - Jakob McBroome
- Department of Biomolecular Engineering, University of California, Santa Cruz
- Genomics Institute, University of California, Santa Cruz
| | | | - Yatish Turakhia
- Genomics Institute, University of California, Santa Cruz
- Howard Hughes Medical Institute, University of California, Santa Cruz
| | - Terren Chang
- Molecular Diagnostics Laboratory, University of California, Santa Cruz
| | - Hugh E Olsen
- Department of Biomolecular Engineering, University of California, Santa Cruz
- Genomics Institute, University of California, Santa Cruz
| | - Jeremy Sanford
- Genomics Institute, University of California, Santa Cruz
- Molecular Diagnostics Laboratory, University of California, Santa Cruz
- Department of Molecular Cellular and Developmental Biology, University of California, Santa Cruz
| | - Michael Stone
- Molecular Diagnostics Laboratory, University of California, Santa Cruz
- Department of Chemistry and Biochemistry, University of California, Santa Cruz
| | - Olena Vaske
- Genomics Institute, University of California, Santa Cruz
- Molecular Diagnostics Laboratory, University of California, Santa Cruz
- Department of Molecular Cellular and Developmental Biology, University of California, Santa Cruz
| | - Isabel Bjork
- Genomics Institute, University of California, Santa Cruz
| | - Mark Akeson
- Department of Biomolecular Engineering, University of California, Santa Cruz
| | - Beth Shapiro
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz
- Howard Hughes Medical Institute, University of California, Santa Cruz
| | - David Haussler
- Department of Biomolecular Engineering, University of California, Santa Cruz
- Genomics Institute, University of California, Santa Cruz
- Howard Hughes Medical Institute, University of California, Santa Cruz
| | - A. Marm Kilpatrick
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz
| | - Russell Corbett-Detig
- Department of Biomolecular Engineering, University of California, Santa Cruz
- Genomics Institute, University of California, Santa Cruz
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Folkerts ML, Lemmer D, Pfeiffer A, Vasquez D, French C, Jones A, Nguyen M, Larsen B, Porter WT, Sheridan K, Bowers JR, Engelthaler DM. Methods for sequencing the pandemic: benefits of rapid or high-throughput processing. F1000Res 2021; 10:ISCB Comm J-48. [PMID: 35342619 PMCID: PMC8921685 DOI: 10.12688/f1000research.28352.2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 02/11/2022] [Indexed: 12/21/2022] Open
Abstract
Genomic epidemiology has proven successful for real-time and retrospective monitoring of small and large-scale outbreaks. Here, we report two genomic sequencing and analysis strategies for rapid-turnaround or high-throughput processing of metagenomic samples. The rapid-turnaround method was designed to provide a quick phylogenetic snapshot of samples at the heart of active outbreaks, and has a total turnaround time of <48 hours from raw sample to analyzed data. The high-throughput method, first reported here for SARS-CoV2, was designed for semi-retrospective data analysis, and is both cost effective and highly scalable. Though these methods were developed and utilized for the SARS-CoV-2 pandemic response in Arizona, U.S, we envision their use for infectious disease epidemiology in the 21 st Century.
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Affiliation(s)
- Megan L. Folkerts
- Pathogen Genomics Division, Translational Genomics Research Institute, Flagstaff, AZ, 86005, USA
| | - Darrin Lemmer
- Pathogen Genomics Division, Translational Genomics Research Institute, Flagstaff, AZ, 86005, USA
| | - Ashlyn Pfeiffer
- Pathogen Genomics Division, Translational Genomics Research Institute, Flagstaff, AZ, 86005, USA
| | - Danielle Vasquez
- Pathogen Genomics Division, Translational Genomics Research Institute, Flagstaff, AZ, 86005, USA
| | - Chris French
- Pathogen Genomics Division, Translational Genomics Research Institute, Flagstaff, AZ, 86005, USA
| | - Amber Jones
- Pathogen Genomics Division, Translational Genomics Research Institute, Flagstaff, AZ, 86005, USA
| | - Marjorie Nguyen
- Pathogen Genomics Division, Translational Genomics Research Institute, Flagstaff, AZ, 86005, USA
| | - Brendan Larsen
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, 85721, USA
| | - W. Tanner Porter
- Pathogen Genomics Division, Translational Genomics Research Institute, Flagstaff, AZ, 86005, USA
| | - Krystal Sheridan
- Pathogen Genomics Division, Translational Genomics Research Institute, Flagstaff, AZ, 86005, USA
| | - Jolene R. Bowers
- Pathogen Genomics Division, Translational Genomics Research Institute, Flagstaff, AZ, 86005, USA
| | - David M. Engelthaler
- Pathogen Genomics Division, Translational Genomics Research Institute, Flagstaff, AZ, 86005, USA
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