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Ge X, Zhou H, Shen F, Yang G, Zhang Y, Zhang X, Li H. SARS-CoV-2 subgenomic RNA: formation process and rapid molecular diagnostic methods. Clin Chem Lab Med 2024; 62:1019-1028. [PMID: 38000044 DOI: 10.1515/cclm-2023-0846] [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: 08/04/2023] [Accepted: 11/13/2023] [Indexed: 11/26/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) which caused coronavirus disease-2019 (COVID-19) is spreading worldwide and posing enormous losses to human health and socio-economic. Due to the limitations of medical and health conditions, it is still a huge challenge to develop appropriate discharge standards for patients with COVID-19 and to use medical resources in a timely and effective manner. Similar to other coronaviruses, SARS-CoV-2 has a very complex discontinuous transcription process to generate subgenomic RNA (sgRNA). Some studies support that sgRNA of SARS-CoV-2 can only exist when the virus is active and is an indicator of virus replication. The results of sgRNA detection in patients can be used to evaluate the condition of hospitalized patients, which is expected to save medical resources, especially personal protective equipment. There have been numerous investigations using different methods, especially molecular methods to detect sgRNA. Here, we introduce the process of SARS-CoV-2 sgRNA formation and the commonly used molecular diagnostic methods to bring a new idea for clinical detection in the future.
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Affiliation(s)
- Xiao Ge
- Department of Medical Laboratory, Weifang Medical University, Weifang, Shandong, P.R. China
| | - Huizi Zhou
- Department of Medical Laboratory, Weifang Medical University, Weifang, Shandong, P.R. China
| | - Fangyuan Shen
- Department of Medical Laboratory, Weifang Medical University, Weifang, Shandong, P.R. China
| | - Guimao Yang
- Department of Medical Laboratory, Affiliated Hospital of Weifang Medical University, Weifang, Shandong, P.R. China
| | - Yubo Zhang
- Department of Medical Laboratory, Weifang Medical University, Weifang, Shandong, P.R. China
| | - Xiaoyu Zhang
- Department of Medical Laboratory, Weifang Medical University, Weifang, Shandong, P.R. China
| | - Heng Li
- Department of Medical Laboratory, Weifang Medical University, Weifang, Shandong, P.R. China
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Snedden CE, Lloyd-Smith JO. Predicting the presence of infectious virus from PCR data: A meta-analysis of SARS-CoV-2 in non-human primates. PLoS Pathog 2024; 20:e1012171. [PMID: 38683864 PMCID: PMC11081500 DOI: 10.1371/journal.ppat.1012171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 05/09/2024] [Accepted: 04/03/2024] [Indexed: 05/02/2024] Open
Abstract
Researchers and clinicians often rely on molecular assays like PCR to identify and monitor viral infections, instead of the resource-prohibitive gold standard of viral culture. However, it remains unclear when (if ever) PCR measurements of viral load are reliable indicators of replicating or infectious virus. The recent popularity of PCR protocols targeting subgenomic RNA for SARS-CoV-2 has caused further confusion, as the relationships between subgenomic RNA and standard total RNA assays are incompletely characterized and opinions differ on which RNA type better predicts culture outcomes. Here, we explore these issues by comparing total RNA, subgenomic RNA, and viral culture results from 24 studies of SARS-CoV-2 in non-human primates (including 2167 samples from 174 individuals) using custom-developed Bayesian statistical models. On out-of-sample data, our best models predict subgenomic RNA positivity from total RNA data with 91% accuracy, and they predict culture positivity with 85% accuracy. Further analyses of individual time series indicate that many apparent prediction errors may arise from issues with assay sensitivity or sample processing, suggesting true accuracy may be higher than these estimates. Total RNA and subgenomic RNA showed equivalent performance as predictors of culture positivity. Multiple cofactors (including exposure conditions, host traits, and assay protocols) influence culture predictions, yielding insights into biological and methodological sources of variation in assay outcomes-and indicating that no single threshold value applies across study designs. We also show that our model can accurately predict when an individual is no longer infectious, illustrating the potential for future models trained on human data to guide clinical decisions on case isolation. Our work shows that meta-analysis of in vivo data can overcome longstanding challenges arising from limited sample sizes and can yield robust insights beyond those attainable from individual studies. Our analytical pipeline offers a framework to develop similar predictive tools in other virus-host systems, including models trained on human data, which could support laboratory analyses, medical decisions, and public health guidelines.
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Affiliation(s)
- Celine E. Snedden
- Department of Ecology and Evolutionary Biology, University of California Los Angeles, Los Angeles, California, United States of America
| | - James O. Lloyd-Smith
- Department of Ecology and Evolutionary Biology, University of California Los Angeles, Los Angeles, California, United States of America
- Department of Computational Medicine, University of California Los Angeles, Los Angeles, California, United States of America
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Chen C, Li R, Xing S, Cao L, Qu Y, Lv Q, Li X, Chen Z. Nirmatrelvir and ritonavir combination against COVID-19 caused by omicron BA.2.2 in the elderly: A single-center large observational study. Immun Inflamm Dis 2024; 12:e1232. [PMID: 38578027 PMCID: PMC10996376 DOI: 10.1002/iid3.1232] [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: 11/13/2023] [Revised: 02/03/2024] [Accepted: 03/14/2024] [Indexed: 04/06/2024] Open
Abstract
BACKGROUND Since coronavirus 2019 (COVID-19) swept the world, a variety of novel therapeutic and prevention strategies have been developed, among which nirmatrelvir-ritonavir is highly recommended. We intended to assess the effectiveness and safety of nirmatrelvir-ritonavir in the elderly mild-to-moderate COVID-19 population caused by the omicron BA.2.2 variant in real-world settings. METHODS An observational study was conducted retrospectively to review the outcomes of mild-to-moderate COVID-19 patients admitted between April 26 and June 30, 2022. Patients' baseline characteristics were collected and assessed. Participants in the intervention group were administered nirmatrelvir-ritonavir in addition to standard care, whereas those in the control group only received standard care. The primary outcome was the duration between the initial positive reverse-transcription polymerase chain reaction (RT-PCR) test and the subsequent conversion to a negative result. RESULTS The analysis included 324 patients who were administered nirmatrelvir-ritonavir and an equal number of control patients. The patient characteristics in both groups were evenly matched. The average duration from the initial positive RT-PCR to negative conversion was similar in both groups (16.2 ± 5.0 vs. 16.1 ± 6.3 days, p = .83). Control patients exhibited slower conversion in comparison to patients who received nirmatrelvir-ritonavir treatment within 10 days of symptom onset. CONCLUSIONS These findings suggest that administering nirmatrelvir-ritonavir within 10 days of symptom onset could potentially reduce the time it takes for SARS-CoV-2-infected patients to negative RT-PCR results, thereby expanding the current usage guidelines for nirmatrelvir-ritonavir.
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Affiliation(s)
- Can Chen
- Department of Pharmacy, Zhongshan HospitalFudan UniversityShanghaiChina
| | - Ranyi Li
- Department of Pharmacy, Zhongshan HospitalFudan UniversityShanghaiChina
| | - Shuliang Xing
- Science and Education OfficeShanghai Geriatric Medical CenterShanghaiChina
| | - Lei Cao
- Medical Administration Office, Zhongshan HospitalFudan UniversityShanghaiChina
| | - Yue Qu
- Department of Infectious DiseasesThe Alfred Hospital and Monash UniversityClaytonAustralia
| | - Qianzhou Lv
- Department of Pharmacy, Zhongshan HospitalFudan UniversityShanghaiChina
| | - Xiaoyu Li
- Department of Pharmacy, Zhongshan HospitalFudan UniversityShanghaiChina
| | - Zhangzhang Chen
- Department of Pharmacy, Zhongshan HospitalFudan UniversityShanghaiChina
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Mostafa HH. Is It Possible to Test for Viral Infectiousness?: The Use Case of (SARS-CoV-2). Clin Lab Med 2024; 44:85-93. [PMID: 38280800 DOI: 10.1016/j.cll.2023.10.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2024]
Abstract
Identifying and managing individuals with active or chronic disease, implementing appropriate infection control measures, and mitigating the spread of the COVID-19 pandemic highlighted the need for tests of infectiousness. The gold standard for assessing infectiousness has been the recovery of infectious virus in cell culture. Using cycle threshold values, antigen testing, and SARS-CoV-2, replication intermediate strands were used to assess infectiousness, with many limitations. Infectiousness can be influenced by host factors (eg, preexisting immune responses) and virus factors (eg, evolution).
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Affiliation(s)
- Heba H Mostafa
- Johns Hopkins School of Medicine, Meyer B-121F, 600 North Wolfe Street, Baltimore, MD 21287, USA.
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5
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Bonenfant G, Deyoe JE, Wong T, Grijalva CG, Cui D, Talbot HK, Hassell N, Halasa N, Chappell J, Thornburg NJ, Rolfes MA, Wentworth DE, Zhou B. Surveillance and Correlation of Severe Acute Respiratory Syndrome Coronavirus 2 Viral RNA, Antigen, Virus Isolation, and Self-Reported Symptoms in a Longitudinal Study With Daily Sampling. Clin Infect Dis 2022; 75:1698-1705. [PMID: 35442437 PMCID: PMC9213875 DOI: 10.1093/cid/ciac282] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Accepted: 04/04/2022] [Indexed: 11/14/2022] Open
Abstract
The novel coronavirus pandemic incited unprecedented demand for assays that detect viral nucleic acids, viral proteins, and corresponding antibodies. The 320 molecular diagnostics in receipt of US Food and Drug Administration emergency use authorization mainly focus on viral detection; however, no currently approved test can be used to infer infectiousness, that is, the presence of replicable virus. As the number of tests conducted increased, persistent severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA positivity by reverse-transcription polymerase chain reaction (RT-PCR) in some individuals led to concerns over quarantine guidelines. To this end, we attempted to design an assay that reduces the frequency of positive test results from individuals who do not shed culturable virus. We describe multiplex quantitative RT-PCR assays that detect genomic RNA (gRNA) and subgenomic RNA (sgRNA) species of SARS-CoV-2, including spike, nucleocapsid, membrane, envelope, and ORF8. Viral RNA abundances calculated from these assays were compared with antigen presence, self-reported symptoms, and culture outcome (virus isolation) using samples from a 14-day longitudinal household transmission study. By characterizing the clinical and molecular dynamics of infection, we show that sgRNA detection has higher predictive value for culture outcome compared to detection of gRNA alone. Our findings suggest that sgRNA presence correlates with active infection and may help identify individuals shedding culturable virus.
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Affiliation(s)
- Gaston Bonenfant
- COVID-19 Emergency Response, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
- Oak Ridge Institute for Science and Education, Oak Ridge, Tennessee, USA
| | - Jessica E. Deyoe
- COVID-19 Emergency Response, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
- Oak Ridge Institute for Science and Education, Oak Ridge, Tennessee, USA
| | - Terianne Wong
- COVID-19 Emergency Response, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | | | - Dan Cui
- COVID-19 Emergency Response, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
- General Dynamics Information Technology, Inc, Falls Church, Virginia, USA
| | - H. Keipp Talbot
- Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Norman Hassell
- COVID-19 Emergency Response, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Natasha Halasa
- Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - James Chappell
- Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Natalie J. Thornburg
- COVID-19 Emergency Response, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Melissa A. Rolfes
- COVID-19 Emergency Response, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - David E. Wentworth
- COVID-19 Emergency Response, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Bin Zhou
- COVID-19 Emergency Response, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
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6
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del Valle R, Ballesteros Á, Calvo C, Sainz T, Mendez A, Grasa C, Molina PR, Mellado MJ, Sanz‐Santaeufemia FJ, Herrero B, Calleja L, Soriano‐Arandes A, Melendo S, Rincón‐López E, Hernánz A, Epalza C, García‐Baeza C, Rupérez‐García E, Berzosa A, Ocaña A, Villarroya‐Villalba A, Barrios A, Otheo E, Galán JC, Rodríguez MJ, Mesa JM, Domínguez‐Rodríguez S, Moraleda C, Tagarro A. Comparison of pneumonia features in children caused by SARS-CoV-2 and other viral respiratory pathogens. Pediatr Pulmonol 2022; 57:2374-2382. [PMID: 35754093 PMCID: PMC9349806 DOI: 10.1002/ppul.26042] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 05/01/2022] [Accepted: 06/23/2022] [Indexed: 01/08/2023]
Abstract
BACKGROUND Pneumonia is a frequent manifestation of coronavirus disease 2019 (COVID-19) in hospitalized children. METHODS The study involved 80 hospitals in the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Spanish Pediatric National Cohort. Participants were children <18 years, hospitalized with SARS-CoV-2 community-acquired pneumonia (CAP). We compared the clinical and radiological characteristics of SARS-CoV-2-associated CAP with CAP due to other viral etiologies from ValsDance (retrospective) cohort. RESULTS In total, 151 children with SARS-CoV-2-associated CAP and 138 with other viral CAP were included. Main clinical features of SARS-CoV-2-associated CAP were cough, fever, or dyspnea. Lymphopenia was found in 43% patients and 15% required admission to the pediatric intensive care unit (PICU). Chest X-ray revealed condensation (42%) and other infiltrates (58%). Compared with CAP from other viral pathogens, COVID-19 patients were older, with lower C-reactive protein (CRP) levels, less wheezing, and greater need of mechanical ventilation (MV). There were no differences in the use of continuous positive airway pressure (CPAP) or HVF, or PICU admission between groups. CONCLUSION SARS-CoV-2-associated CAP in children presents differently to other virus-associated CAP: children are older and rarely have wheezing or high CRP levels; they need less oxygen but more CPAP or MV. However, several features overlap and differentiating the etiology may be difficult. The overall prognosis is good.
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Affiliation(s)
- Rut del Valle
- Pediatrics Department, Pediatrics Research Group, Hospital Universitario Infanta SofíaUniversidad Europea de MadridMadridSpain
| | - Álvaro Ballesteros
- Pediatric Research and Clinical Trials Unit (UPIC), Pediatrics Department, Instituto de Investigación Sanitaria Hospital 12 de Octubre (imas12), Fundación de Investigación Biomédica Hospital 12 de OctubreRITIP (Translational Research Network in Paediatric Infectious Diseases)MadridSpain
| | - Cristina Calvo
- Pediatrics, Infectious and Tropical Diseases Department, Hospital Universitario La Paz, Instituto Investigación Hospital La Paz (IDIPaz)RITIP (Translational Research Network in Paediatric Infectious Diseases)MadridSpain
| | - Talía Sainz
- Pediatrics, Infectious and Tropical Diseases Department, Hospital Universitario La Paz, Instituto Investigación Hospital La Paz (IDIPaz)RITIP (Translational Research Network in Paediatric Infectious Diseases)MadridSpain
- Research Center, Centro de Investigación en Red en Enfermedades Infecciosas (CIBERINFEC)Instituto de Salud Carlos III, Madrid, SpainMadridSpain
| | - Ana Mendez
- Pediatrics, Infectious and Tropical Diseases Department, Hospital Universitario La Paz, Instituto Investigación Hospital La Paz (IDIPaz)RITIP (Translational Research Network in Paediatric Infectious Diseases)MadridSpain
| | - Carlos Grasa
- Pediatrics, Infectious and Tropical Diseases Department, Hospital Universitario La Paz, Instituto Investigación Hospital La Paz (IDIPaz)RITIP (Translational Research Network in Paediatric Infectious Diseases)MadridSpain
| | - Paula R. Molina
- Pediatrics, Infectious and Tropical Diseases Department, Hospital Universitario La Paz, Instituto Investigación Hospital La Paz (IDIPaz)RITIP (Translational Research Network in Paediatric Infectious Diseases)MadridSpain
| | - María J. Mellado
- Pediatrics, Infectious and Tropical Diseases Department, Hospital Universitario La Paz, Instituto Investigación Hospital La Paz (IDIPaz)RITIP (Translational Research Network in Paediatric Infectious Diseases)MadridSpain
| | | | - Blanca Herrero
- Pediatrics DepartmentHospital Universitario Niño JesúsMadridSpain
| | - Lourdes Calleja
- Pediatrics DepartmentHospital Universitario Niño JesúsMadridSpain
| | - Antoni Soriano‐Arandes
- Infectious Diseases and Pediatric Immunology Unit, Department of PediatricsHospital Universitario Vall d'HebronBarcelonaSpain
| | - Susana Melendo
- Infectious Diseases and Pediatric Immunology Unit, Department of PediatricsHospital Universitario Vall d'HebronBarcelonaSpain
| | - Elena Rincón‐López
- Pediatric Infectious Diseases Unit, Department of PediatricsHospital Universitario Gregorio MarañónMadridSpain
| | - Alicia Hernánz
- Pediatric Infectious Diseases Unit, Department of PediatricsHospital Universitario Gregorio MarañónMadridSpain
- Research CenterGregorio Marañón Research Institute (IiSGM)MadridSpain
| | - Cristina Epalza
- Pediatric Research and Clinical Trials Unit (UPIC), Pediatrics Department, Instituto de Investigación Sanitaria Hospital 12 de Octubre (imas12), Fundación de Investigación Biomédica Hospital 12 de OctubreRITIP (Translational Research Network in Paediatric Infectious Diseases)MadridSpain
- Pediatric Infectious Diseases Unit, Department of PediatricsHospital Universitario 12 de OctubreMadridSpain
| | - Carmen García‐Baeza
- Pediatric Infectious Diseases Unit, Department of PediatricsHospital Universitario 12 de OctubreMadridSpain
| | | | - Arantxa Berzosa
- Pediatrics DepartmentHospital Universitario Clínico San CarlosMadridSpain
| | - Angustias Ocaña
- Pediatric Intensive Care Unit DepartmentHospital La MoralejaMadridSpain
| | - Alvaro Villarroya‐Villalba
- Pediatric Infectious Diseases Unit, Pediatrics DepartmentHospital Universitari i Politècnic La FeValenciaSpain
| | - Ana Barrios
- Pediatrics Department, Pediatrics Research Group, Hospital Universitario Infanta SofíaUniversidad Europea de MadridMadridSpain
| | - Enrique Otheo
- Pediatrics Department, Hospital Universitario Ramón y CajalUniversidad de Alcalá MadridMadridSpain
| | - Juan C. Galán
- Microbiology Department, Hospital Universitario Ramón y CajalInstituto Ramón y Cajal para la Investigación Sanitaria (IRYCIS)MadridSpain
- Centro de Investigación Biomédica en Red en Epidemiología y Salud Pública (CIBERESP)MadridSpain
| | - Mario José Rodríguez
- Microbiology Department, Hospital Universitario Ramón y CajalInstituto Ramón y Cajal para la Investigación Sanitaria (IRYCIS)MadridSpain
- Centro de Investigación Biomédica en Red en Epidemiología y Salud Pública (CIBERESP)MadridSpain
| | - Juan M. Mesa
- Pediatrics Department, Pediatrics Research Group, Hospital Universitario Infanta SofíaUniversidad Europea de MadridMadridSpain
| | - Sara Domínguez‐Rodríguez
- Pediatric Research and Clinical Trials Unit (UPIC), Pediatrics Department, Instituto de Investigación Sanitaria Hospital 12 de Octubre (imas12), Fundación de Investigación Biomédica Hospital 12 de OctubreRITIP (Translational Research Network in Paediatric Infectious Diseases)MadridSpain
| | - Cinta Moraleda
- Pediatric Research and Clinical Trials Unit (UPIC), Pediatrics Department, Instituto de Investigación Sanitaria Hospital 12 de Octubre (imas12), Fundación de Investigación Biomédica Hospital 12 de OctubreRITIP (Translational Research Network in Paediatric Infectious Diseases)MadridSpain
| | - Alfredo Tagarro
- Pediatrics Department, Pediatrics Research Group, Hospital Universitario Infanta SofíaUniversidad Europea de MadridMadridSpain
- Pediatric Research and Clinical Trials Unit (UPIC), Pediatrics Department, Instituto de Investigación Sanitaria Hospital 12 de Octubre (imas12), Fundación de Investigación Biomédica Hospital 12 de OctubreRITIP (Translational Research Network in Paediatric Infectious Diseases)MadridSpain
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Krogstad P, Contreras D, Ng H, Tobin N, Chambers CD, Bertrand K, Bode L, Aldrovandi GM. No infectious SARS-CoV-2 in breast milk from a cohort of 110 lactating women. Pediatr Res 2022; 92:1140-1145. [PMID: 35042956 PMCID: PMC9586866 DOI: 10.1038/s41390-021-01902-y] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 08/30/2021] [Accepted: 09/17/2021] [Indexed: 01/21/2023]
Abstract
BACKGROUND Genomic RNA of severe acute respiratory syndrome-associated coronavirus type 2 (SARS-CoV-2) has been detected in the breast milk of lactating women, but its pathological significance has remained uncertain due to the small size of prior studies. METHODS Breast milk from 110 lactating women was analyzed by reverse transcription-polymerase chain reaction (285 samples) and viral culture (160 samples). Those containing SARS-CoV-2 viral RNA (vRNA) were examined for the presence of subgenomic RNA (sgRNA), a putative marker of infectivity. RESULTS Sixty-five women had a positive SARS-CoV-2 diagnostic test, 9 had symptoms but negative diagnostic tests, and 36 symptomatic women were not tested. SARS-CoV-2 vRNA was detected in the milk of 7 (6%) women with either a confirmed infection or symptomatic illness, including 6 of 65 (9%) women with a positive SARS-CoV-2 diagnostic test. Infectious virus was not detected in any culture and none had detectable sgRNA. In control experiments, infectious SARS-CoV-2 could be cultured after addition to breastmilk despite several freeze-thaw cycles, as it occurs in the storage and usage of human milk. CONCLUSIONS SARS-CoV-2 RNA can be found infrequently in the breastmilk after recent infection, but we found no evidence that breastmilk contains an infectious virus or that breastfeeding represents a risk factor for transmission of infection to infants. IMPACT This article goes beyond prior small studies to provide evidence that infectious SARS-CoV-2 is not present in the milk of lactating women with recent infection, even when SARS-CoV-2 RNA is detected. Recent SARS-CoV-2 infection or detection of its RNA in human milk is not a contraindication to breastfeeding.
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Affiliation(s)
- Paul Krogstad
- Department of Pediatrics, David Geffen Scool of Medicine at UCLAs, University of California, Los Angeles, CA, USA.
- Departments of Molecular and Medical Pharmacology, David Geffen School of Medicine at UCLA, University of California, Los Angeles, CA, USA.
| | - Deisy Contreras
- Department of Pediatrics, David Geffen Scool of Medicine at UCLAs, University of California, Los Angeles, CA, USA
| | - Hwee Ng
- Department of Pediatrics, David Geffen Scool of Medicine at UCLAs, University of California, Los Angeles, CA, USA
| | - Nicole Tobin
- Department of Pediatrics, David Geffen Scool of Medicine at UCLAs, University of California, Los Angeles, CA, USA
| | - Christina D Chambers
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
- Hebert Wertheim School of Public Health and Longevity Science, University of California, San Diego, La Jolla, CA, USA
| | - Kerri Bertrand
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
- Hebert Wertheim School of Public Health and Longevity Science, University of California, San Diego, La Jolla, CA, USA
| | - Lars Bode
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
- Larsson-RosenquistFoundation Mother-Milk-Infant Center of Research Excellence (MOMI CORE), University of California, San Diego, La Jolla, CA, USA
| | - Grace M Aldrovandi
- Department of Pediatrics, David Geffen Scool of Medicine at UCLAs, University of California, Los Angeles, CA, USA
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8
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Dos Santos PG, Vieira HCVS, Wietholter V, Gallina JP, Andrade TR, Marinowic DR, Zanirati GG, da Costa JC. When to test for COVID-19 using real-time reverse transcriptase polymerase chain reaction: a systematic review. Int J Infect Dis 2022; 123:58-69. [PMID: 35760382 PMCID: PMC9233872 DOI: 10.1016/j.ijid.2022.06.037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 06/18/2022] [Accepted: 06/21/2022] [Indexed: 01/08/2023] Open
Abstract
OBJECTIVES The aim of this study was to evaluate the time in days between symptom onset and first positive real-time reverse transcriptase polymerase chain reaction (RT-PCR) result for COVID-19. METHODS This systematic review was conducted in the MEDLINE (PubMed), Embase, and Scopus databases using the following descriptors: "COVID-19", "SARS-CoV-2", "coronavirus", "RT-PCR", "real time PCR", and "diagnosis". RESULTS The included studies were conducted in 31 different countries and reported on a total of 6831 patients. The median age of the participants was 49.95 years. The three most common symptoms were fever, cough, and dyspnea, which affected 4012 (58.68%), 3192 (46.69%), and 2009 patients (29.38%), respectively. Among the 90 included studies, 13 were prospective cohorts, 15 were retrospective cohorts, 36 were case reports, 20 were case series, and six were cross-sectional studies. The overall mean time between symptom onset and positive test result was 6.72 days. Fourteen articles were analyzed separately for the temporal profile of RT-PCR test results; the best performance was on days 22-24, when 98% of test results were positive. CONCLUSION These findings corroborate the RT-PCR COVID-19 testing practices of some health units. In addition, the most frequently described symptoms of these patients can be considered the initial symptoms of infection and used in decision-making about RT-PCR testing.
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Affiliation(s)
- Paula Gabrielli Dos Santos
- Brain Institute of Rio Grande do Sul (BraIns), Pontifical Catholic University of Rio Grande do Sul (PUCRS), Porto Alegre, Brazil; Graduate Program in Biomedical Gerontology, Institute of Geriatrics and Gerontology, Pontifical Catholic University of Rio Grande do Sul (PUCRS) School of Medicine, Porto Alegre, Brazil
| | - Helena Cristina Valentini Speggiorin Vieira
- Brain Institute of Rio Grande do Sul (BraIns), Pontifical Catholic University of Rio Grande do Sul (PUCRS), Porto Alegre, Brazil; Undergraduate Research Program, School of Medicine and Brain Institute of Rio Grande do Sul (BraIns), Pontifical Catholic University of Rio Grande do Sul (PUCRS), Porto Alegre, Brazil
| | - Vinícius Wietholter
- Brain Institute of Rio Grande do Sul (BraIns), Pontifical Catholic University of Rio Grande do Sul (PUCRS), Porto Alegre, Brazil; Undergraduate Research Program, School of Medicine and Brain Institute of Rio Grande do Sul (BraIns), Pontifical Catholic University of Rio Grande do Sul (PUCRS), Porto Alegre, Brazil
| | - João Pedro Gallina
- Brain Institute of Rio Grande do Sul (BraIns), Pontifical Catholic University of Rio Grande do Sul (PUCRS), Porto Alegre, Brazil; Undergraduate Research Program, School of Medicine and Brain Institute of Rio Grande do Sul (BraIns), Pontifical Catholic University of Rio Grande do Sul (PUCRS), Porto Alegre, Brazil
| | - Thomás Ranquetat Andrade
- Brain Institute of Rio Grande do Sul (BraIns), Pontifical Catholic University of Rio Grande do Sul (PUCRS), Porto Alegre, Brazil; Undergraduate Research Program, School of Medicine and Brain Institute of Rio Grande do Sul (BraIns), Pontifical Catholic University of Rio Grande do Sul (PUCRS), Porto Alegre, Brazil
| | - Daniel Rodrigo Marinowic
- Brain Institute of Rio Grande do Sul (BraIns), Pontifical Catholic University of Rio Grande do Sul (PUCRS), Porto Alegre, Brazil; Graduate Program in Biomedical Gerontology, Institute of Geriatrics and Gerontology, Pontifical Catholic University of Rio Grande do Sul (PUCRS) School of Medicine, Porto Alegre, Brazil; Graduate Program in Pediatrics and Child Health, Pontifical Catholic University of Rio Grande do Sul (PUCRS) School of Medicine, Porto Alegre, Brazil
| | - Gabriele Goulart Zanirati
- Brain Institute of Rio Grande do Sul (BraIns), Pontifical Catholic University of Rio Grande do Sul (PUCRS), Porto Alegre, Brazil; Graduate Program in Pediatrics and Child Health, Pontifical Catholic University of Rio Grande do Sul (PUCRS) School of Medicine, Porto Alegre, Brazil
| | - Jaderson Costa da Costa
- Brain Institute of Rio Grande do Sul (BraIns), Pontifical Catholic University of Rio Grande do Sul (PUCRS), Porto Alegre, Brazil; Graduate Program in Biomedical Gerontology, Institute of Geriatrics and Gerontology, Pontifical Catholic University of Rio Grande do Sul (PUCRS) School of Medicine, Porto Alegre, Brazil; Graduate Program in Pediatrics and Child Health, Pontifical Catholic University of Rio Grande do Sul (PUCRS) School of Medicine, Porto Alegre, Brazil.
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9
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A Pilot Study Evaluating Subgenomic RNAs for Detection of Infectious SARS-CoV-2 in Nasopharyngeal Swabs. ARCHIVES OF CLINICAL INFECTIOUS DISEASES 2022. [DOI: 10.5812/archcid-128040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Background: The prolonged persistence of viral ribonucleic acid (RNA) in coronavirus disease 2019 (COVID-19) patients and the difficulty in differentiating between infectious virus and noninfectious viral RNA have impeded the use of current molecular diagnostic tests as a decision tool in quarantine termination. The performance of new methods to detect surrogate viability markers, such as subgenomic RNAs (sgRNAs), has been discussed, and numerous important questions are still needed to be addressed before broad implementation. Objectives: This study aimed to primarily evaluate the performance of SYBR green quantitative reverse transcription-polymerase chain reaction (RT-qPCR) targeting N and E sgRNAs as a surrogate of viability markers. Methods: This pilot study was carried out to detect genomic RNAs (gRNAs) and sgRNAs using RT-qPCR in cell culture infected with severe acute respiratory syndrome coronavirus 2 and nasopharyngeal swabbing samples from COVID-19 patients, and the results were compared to viral culture as a gold standard method for infectious virus detection. The diagnostic parameters and Cohen’s Kappa correlation index were then analyzed. Results: E subgenomic RNA detection was the most reliable predictor for actively replicating the virus as it showed the highest value of all diagnostic parameters with a good correlation with viral cultivation. The lowest cycle threshold value of gRNAs and sgN detection become undetectable by sgE within the range of 23 - 26. Conclusion: Using a suitable sgRNA type was important for test accuracy. The findings suggested E sgRNA detection as a promising surrogate approach to indicate a truly active viral infection, and when performed with a low-cost molecular test of SYBR green-based assay, it could support huge demands for routine analysis.
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10
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Liu X, Li Y, Wang X, Song Y, Wu L, Yu B, Ma X, Ma P, Liu M, Huang X, Wang X. Rapid and Specific Detection of Active SARS-CoV-2 With CRISPR/Cas12a. Front Microbiol 2022; 12:820698. [PMID: 35154046 PMCID: PMC8832066 DOI: 10.3389/fmicb.2021.820698] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 12/23/2021] [Indexed: 12/18/2022] Open
Abstract
Rapid and sensitive nucleic acid detection of SARS-CoV-2 has contributed to the clinical diagnosis and control of COVID-19. Although detection of virus genomic RNA (gRNA) has been commonly used in clinical diagnosis, SARS-CoV-2 gRNA detection could not discriminate between active infectious virus with remnant viral RNA. In contrast to genomic RNA, subgenomic RNAs (sgRNAs) are only produced when the virus is actively replicating and transcription, detection of sgRNA could be an indication to evaluate infectivity. CRISPR/Cas-based nucleic acid detection methods have been considered potential diagnostic tools due to their intrinsic sensitivity, specificity and simplicity. In this study, to specifically detect active virus replication, we developed a CRISPR-based active SARS-CoV-2 (CRISPR-actCoV) detection strategy by detecting sgRNAs of SARS-CoV-2. CRISPR-actCoV with CRISPR Cas12a-assisted fluorescence reporter system enables detection of sgRNAs at 10 copies in 35 min with high specificity and can be read out with naked eyes. Further, we performed CRISPR-actCoV mediated sgRNA detection in 30 SARS-CoV-2 potentially infected clinical samples, and 21 samples were SARS-CoV-2 sgRNA positive. A quantitative RT-PCR assay was also performed to detect gRNA of SARS-CoV-2 in parallel. Among the 30 clinical samples, 27 samples were gRNA positive. Taken together, CRISPR-actCoV provides an alternative for rapid and accurate detection of active SARS-CoV-2 and has great significance in better response of coronavirus causing epidemic disease.
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Affiliation(s)
- Xinyi Liu
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- Guangzhou Laboratory, Bio-Island, Guangzhou, China
| | - Yanhua Li
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonosis, College of Veterinary Medicine, Yangzhou University, Yangzhou, China
| | - Xin Wang
- School of Life Sciences and Technology, ShanghaiTech University, Shanghai, China
| | - Yifan Song
- School of Life Sciences, Fudan University, Shanghai, China
| | - Lina Wu
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, China
| | - Benyuan Yu
- Animal, Plant and Food Inspection Center of Nanjing Customs District, Nanjing, China
| | - Xiaodong Ma
- Institute for Brain Research and Rehabilitation, Guangdong Key Laboratory of Mental Health and Cognitive Science, Center for Studies of Psychological Application, South China Normal University, Guangzhou, China
| | - Peixiang Ma
- Shanghai Key Laboratory of Orthopedic Implants, Department of Orthopedic Surgery, Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Ming Liu
- State Key Laboratory of Respiratory Disease/National Clinical Research Center for Respiratory Disease/National Center for Respiratory Medicine/Guangzhou Institute of Respiratory Health/The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- *Correspondence: Ming Liu,
| | - Xingxu Huang
- Guangzhou Laboratory, Bio-Island, Guangzhou, China
- School of Life Sciences and Technology, ShanghaiTech University, Shanghai, China
- Xingxu Huang,
| | - Xinjie Wang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- Guangzhou Laboratory, Bio-Island, Guangzhou, China
- Xinjie Wang,
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11
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Van Egeren D, Novokhodko A, Stoddard M, Tran U, Zetter B, Rogers MS, Joseph-McCarthy D, Chakravarty A. Controlling long-term SARS-CoV-2 infections can slow viral evolution and reduce the risk of treatment failure. Sci Rep 2021; 11:22630. [PMID: 34799659 PMCID: PMC8604936 DOI: 10.1038/s41598-021-02148-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 10/27/2021] [Indexed: 12/23/2022] Open
Abstract
The rapid emergence and expansion of novel SARS-CoV-2 variants threatens our ability to achieve herd immunity for COVID-19. These novel SARS-CoV-2 variants often harbor multiple point mutations, conferring one or more evolutionarily advantageous traits, such as increased transmissibility, immune evasion and longer infection duration. In a number of cases, variant emergence has been linked to long-term infections in individuals who were either immunocompromised or treated with convalescent plasma. In this paper, we used a stochastic evolutionary modeling framework to explore the emergence of fitter variants of SARS-CoV-2 during long-term infections. We found that increased viral load and infection duration favor emergence of such variants. While the overall probability of emergence and subsequent transmission from any given infection is low, on a population level these events occur fairly frequently. Targeting these low-probability stochastic events that lead to the establishment of novel advantageous viral variants might allow us to slow the rate at which they emerge in the patient population, and prevent them from spreading deterministically due to natural selection. Our work thus suggests practical ways to achieve control of long-term SARS-CoV-2 infections, which will be critical for slowing the rate of viral evolution.
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Affiliation(s)
- Debra Van Egeren
- Harvard Medical School, Boston, MA, USA
- Dana-Farber Cancer Institute, Boston, MA, USA
- Boston Children's Hospital, Boston, MA, USA
| | | | | | - Uyen Tran
- Fractal Therapeutics, Cambridge, MA, USA
| | - Bruce Zetter
- Harvard Medical School, Boston, MA, USA
- Boston Children's Hospital, Boston, MA, USA
| | - Michael S Rogers
- Harvard Medical School, Boston, MA, USA
- Boston Children's Hospital, Boston, MA, USA
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12
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Immergluck K, Gonzalez MD, Frediani JK, Levy JM, Figueroa J, Wood A, Rogers BB, O'Neal J, Elias-Marcellin R, Suessmith A, Sullivan J, Schinazi RF, Babiker A, Piantadosi A, Vos MB, Martin GS, Lam WA, Waggoner JJ. Correlation of SARS-CoV-2 Subgenomic RNA with Antigen Detection in Nasal Midturbinate Swab Specimens. Emerg Infect Dis 2021; 27:2887-2891. [PMID: 34424838 PMCID: PMC8544990 DOI: 10.3201/eid2711.211135] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Among symptomatic outpatients, subgenomic RNA of severe acute respiratory syndrome coronavirus 2 in nasal midturbinate swab specimens was concordant with antigen detection but remained detectable in 13 (82.1%) of 16 nasopharyngeal swab specimens from antigen-negative persons. Subgenomic RNA in midturbinate swab specimens might be useful for routine diagnostics to identify active virus replication.
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13
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Pérez Lago L, Pérez Latorre L, Herranz M, Tejerina F, Sola-Campoy PJ, Sicilia J, Suárez-González J, Andrés-Zayas C, Chiner-Oms A, Jiménez-Serrano S, García-González N, Comas I, González-Candelas F, Martínez-Laperche C, Catalán P, Muñoz P, García de Viedma D. Complete Analysis of the Epidemiological Scenario around a SARS-CoV-2 Reinfection: Previous Infection Events and Subsequent Transmission. mSphere 2021; 6:e0059621. [PMID: 34494886 PMCID: PMC8550076 DOI: 10.1128/msphere.00596-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 08/12/2021] [Indexed: 11/20/2022] Open
Abstract
The first descriptions of reinfection by SARS-CoV-2 have been recently reported. However, these studies focus exclusively on the reinfected case, without considering the epidemiological context of the event. Our objectives were to perform a complete analysis of the sequential infections and community transmission events around a SARS-CoV-2 reinfection, including the infection events preceding it, the exposure, and subsequent transmissions. Our analysis was supported by host genetics, viral whole-genome sequencing, phylogenomic viral population analysis, and refined epidemiological data obtained from interviews with the involved subjects. The reinfection involved a 53-year-old woman with asthma (Case A), with a first COVID-19 episode in April 2020 and a much more severe second episode 4-1/2 months later, with SARS-CoV-2 seroconversion in August, that required hospital admission. An extended genomic analysis allowed us to demonstrate that the strain involved in Case A's reinfection was circulating in the epidemiological context of Case A and was also transmitted subsequently from Case A to her family context. The reinfection was also supported by a phylogenetic analysis, including 348 strains from Madrid, which revealed that the strain involved in the reinfection was circulating by the time Case A suffered the second episode, August-September 2020, but absent at the time range corresponding to Case A's first episode. IMPORTANCE We present the first complete analysis of the epidemiological scenario around a reinfection by SARS-CoV-2, more severe than the first episode, including three cases preceding the reinfection, the reinfected case per se, and the subsequent transmission to another seven cases.
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Affiliation(s)
- Laura Pérez Lago
- Servicio de Microbiología Clínica y Enfermedades Infecciosas, Gregorio Marañón General University Hospital, Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), Madrid, Spain
| | - Leire Pérez Latorre
- Servicio de Microbiología Clínica y Enfermedades Infecciosas, Gregorio Marañón General University Hospital, Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), Madrid, Spain
| | - Marta Herranz
- Servicio de Microbiología Clínica y Enfermedades Infecciosas, Gregorio Marañón General University Hospital, Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), Madrid, Spain
- CIBER Enfermedades Respiratorias (CIBERES), Madrid, Spain
| | - Francisco Tejerina
- Servicio de Microbiología Clínica y Enfermedades Infecciosas, Gregorio Marañón General University Hospital, Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), Madrid, Spain
| | - Pedro J. Sola-Campoy
- Servicio de Microbiología Clínica y Enfermedades Infecciosas, Gregorio Marañón General University Hospital, Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), Madrid, Spain
| | - Jon Sicilia
- Servicio de Microbiología Clínica y Enfermedades Infecciosas, Gregorio Marañón General University Hospital, Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), Madrid, Spain
| | - Julia Suárez-González
- Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), Madrid, Spain
- Genomics Unit, Gregorio Marañón General University Hospital, Madrid, Spain
| | - Cristina Andrés-Zayas
- Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), Madrid, Spain
- Genomics Unit, Gregorio Marañón General University Hospital, Madrid, Spain
| | | | | | - Neris García-González
- Joint Research Unit Infection and Public Health FISABIO-University of Valencia, Institute for Integrative Systems Biology (I2SysBio), Valencia, Spain
| | - Iñaki Comas
- Instituto de Biomedicina de Valencia-CSIC, Valencia, Spain
- CIBER Salud Pública (CIBERESP), Madrid, Spain
| | - Fernando González-Candelas
- Joint Research Unit Infection and Public Health FISABIO-University of Valencia, Institute for Integrative Systems Biology (I2SysBio), Valencia, Spain
- CIBER Salud Pública (CIBERESP), Madrid, Spain
| | - Carolina Martínez-Laperche
- Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), Madrid, Spain
- Servicio de Oncohematología, Gregorio Marañón General University Hospital, Madrid, Spain
| | - Pilar Catalán
- Servicio de Microbiología Clínica y Enfermedades Infecciosas, Gregorio Marañón General University Hospital, Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), Madrid, Spain
- CIBER Enfermedades Respiratorias (CIBERES), Madrid, Spain
| | - Patricia Muñoz
- Servicio de Microbiología Clínica y Enfermedades Infecciosas, Gregorio Marañón General University Hospital, Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), Madrid, Spain
- CIBER Enfermedades Respiratorias (CIBERES), Madrid, Spain
- Departamento de Medicina, Universidad Complutense, Madrid, Spain
| | - Darío García de Viedma
- Servicio de Microbiología Clínica y Enfermedades Infecciosas, Gregorio Marañón General University Hospital, Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), Madrid, Spain
- CIBER Enfermedades Respiratorias (CIBERES), Madrid, Spain
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14
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Pérez Lago L, Pérez Latorre L, Herranz M, Tejerina F, Sola-Campoy PJ, Sicilia J, Suárez-González J, Andrés-Zayas C, Chiner-Oms A, Jiménez-Serrano S, García-González N, Comas I, González-Candelas F, Martínez-Laperche C, Catalán P, Muñoz P, García de Viedma D. Complete Analysis of the Epidemiological Scenario around a SARS-CoV-2 Reinfection: Previous Infection Events and Subsequent Transmission. mSphere 2021; 6:e0059621. [PMID: 34494886 DOI: 10.21203/rs.3.rs-106167/v1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/25/2023] Open
Abstract
The first descriptions of reinfection by SARS-CoV-2 have been recently reported. However, these studies focus exclusively on the reinfected case, without considering the epidemiological context of the event. Our objectives were to perform a complete analysis of the sequential infections and community transmission events around a SARS-CoV-2 reinfection, including the infection events preceding it, the exposure, and subsequent transmissions. Our analysis was supported by host genetics, viral whole-genome sequencing, phylogenomic viral population analysis, and refined epidemiological data obtained from interviews with the involved subjects. The reinfection involved a 53-year-old woman with asthma (Case A), with a first COVID-19 episode in April 2020 and a much more severe second episode 4-1/2 months later, with SARS-CoV-2 seroconversion in August, that required hospital admission. An extended genomic analysis allowed us to demonstrate that the strain involved in Case A's reinfection was circulating in the epidemiological context of Case A and was also transmitted subsequently from Case A to her family context. The reinfection was also supported by a phylogenetic analysis, including 348 strains from Madrid, which revealed that the strain involved in the reinfection was circulating by the time Case A suffered the second episode, August-September 2020, but absent at the time range corresponding to Case A's first episode. IMPORTANCE We present the first complete analysis of the epidemiological scenario around a reinfection by SARS-CoV-2, more severe than the first episode, including three cases preceding the reinfection, the reinfected case per se, and the subsequent transmission to another seven cases.
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Affiliation(s)
- Laura Pérez Lago
- Servicio de Microbiología Clínica y Enfermedades Infecciosas, Gregorio Marañón General University Hospital, Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), Madrid, Spain
| | - Leire Pérez Latorre
- Servicio de Microbiología Clínica y Enfermedades Infecciosas, Gregorio Marañón General University Hospital, Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), Madrid, Spain
| | - Marta Herranz
- Servicio de Microbiología Clínica y Enfermedades Infecciosas, Gregorio Marañón General University Hospital, Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), Madrid, Spain
- CIBER Enfermedades Respiratorias (CIBERES), Madrid, Spain
| | - Francisco Tejerina
- Servicio de Microbiología Clínica y Enfermedades Infecciosas, Gregorio Marañón General University Hospital, Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), Madrid, Spain
| | - Pedro J Sola-Campoy
- Servicio de Microbiología Clínica y Enfermedades Infecciosas, Gregorio Marañón General University Hospital, Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), Madrid, Spain
| | - Jon Sicilia
- Servicio de Microbiología Clínica y Enfermedades Infecciosas, Gregorio Marañón General University Hospital, Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), Madrid, Spain
| | - Julia Suárez-González
- Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), Madrid, Spain
- Genomics Unit, Gregorio Marañón General University Hospital, Madrid, Spain
| | - Cristina Andrés-Zayas
- Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), Madrid, Spain
- Genomics Unit, Gregorio Marañón General University Hospital, Madrid, Spain
| | | | | | - Neris García-González
- Joint Research Unit Infection and Public Health FISABIO-University of Valencia, Institute for Integrative Systems Biology (I2SysBio), Valencia, Spain
| | - Iñaki Comas
- Instituto de Biomedicina de Valencia-CSIC, Valencia, Spain
- CIBER Salud Pública (CIBERESP), Madrid, Spain
| | - Fernando González-Candelas
- Joint Research Unit Infection and Public Health FISABIO-University of Valencia, Institute for Integrative Systems Biology (I2SysBio), Valencia, Spain
- CIBER Salud Pública (CIBERESP), Madrid, Spain
| | - Carolina Martínez-Laperche
- Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), Madrid, Spain
- Servicio de Oncohematología, Gregorio Marañón General University Hospital, Madrid, Spain
| | - Pilar Catalán
- Servicio de Microbiología Clínica y Enfermedades Infecciosas, Gregorio Marañón General University Hospital, Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), Madrid, Spain
- CIBER Enfermedades Respiratorias (CIBERES), Madrid, Spain
| | - Patricia Muñoz
- Servicio de Microbiología Clínica y Enfermedades Infecciosas, Gregorio Marañón General University Hospital, Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), Madrid, Spain
- CIBER Enfermedades Respiratorias (CIBERES), Madrid, Spain
- Departamento de Medicina, Universidad Complutense, Madrid, Spain
| | - Darío García de Viedma
- Servicio de Microbiología Clínica y Enfermedades Infecciosas, Gregorio Marañón General University Hospital, Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), Madrid, Spain
- CIBER Enfermedades Respiratorias (CIBERES), Madrid, Spain
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15
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Viral culture confirmed SARS-CoV-2 subgenomic RNA value as a good surrogate marker of infectivity. J Clin Microbiol 2021; 60:e0160921. [PMID: 34669457 PMCID: PMC8769718 DOI: 10.1128/jcm.01609-21] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Determining SARS-CoV-2 viral infectivity is crucial for patient clinical assessment and isolation decisions. We assessed subgenomic RNA (sgRNA) as a surrogate marker of SARS-CoV-2 infectivity in SARS-CoV-2-positive reverse transcription PCR (RT-PCR) respiratory samples (n = 105) in comparison with viral culture as the reference standard for virus replication. sgRNA and viral isolation results were concordant in 99/105 cases (94%), indicating highly significant agreement between the two techniques (Cohen’s kappa coefficient 0.88, 95% confidence interval [CI] 0.78 to 0.97, P < 0.001). sgRNA RT-PCR showed a sensitivity of 97% and a positive predictive value of 94% to detect replication-competent virus, further supporting sgRNA as a surrogate marker of SARS-CoV-2 infectivity. sgRNA RT-PCR is an accurate, rapid, and affordable technique that can overcome culture and cycle threshold (CT) value limitations and be routinely implemented in hospital laboratories to detect viral infectivity, which is essential for optimizing patient monitoring, the efficacy of treatments/vaccines, and work reincorporation policies, as well as for safely shortening isolation precautions.
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16
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Feasibility and Effectiveness Assessment of SARS-CoV-2 Antigenic Tests in Mass Screening of a Pediatric Population and Correlation with the Kinetics of Viral Loads. Viruses 2021; 13:v13102071. [PMID: 34696501 PMCID: PMC8537025 DOI: 10.3390/v13102071] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2021] [Revised: 10/01/2021] [Accepted: 10/08/2021] [Indexed: 12/23/2022] Open
Abstract
The gold standard for diagnosis of SARS-CoV-2 infection has been nucleic acid amplification tests (NAAT). However, rapid antigen detection kits (Ag-RDTs), may offer advantages over NAAT in mass screening, generating results in minutes, both as laboratory-based test or point-of-care (POC) use for clinicians, at a lower cost. We assessed two different POC Ag-RDTs in mass screening versus NAAT for SARS-CoV-2 in a cohort of pediatric patients admitted to the Pediatric Emergency Unit of IRCCS-Polyclinic of Sant'Orsola, Bologna (from November 2020 to April 2021). All patients were screened with nasopharyngeal swabs for the detection of SARS-CoV-2-RNA and for antigen tests. Results were obtained from 1146 patients. The COVID-19 Ag FIA kit showed a baseline sensitivity of 53.8% (CI 35.4-71.4%), baseline specificity 99.7% (CI 98.4-100%) and overall accuracy of 80% (95% CI 0.68-0.91); the AFIAS COVID-19 Ag kit, baseline sensitivity of 86.4% (CI 75.0-93.9%), baseline specificity 98.3% (CI 97.1-99.1%) and overall accuracy of 95.3% (95% CI 0.92-0.99). In both tests, some samples showed very low viral load and negative Ag-RDT. This disagreement may reflect the positive inability of Ag-RDTs of detecting antigen in late phase of infection. Among all cases with positive molecular test and negative antigen test, none showed viral loads > 106 copies/mL. Finally, we found one false Ag-RDTs negative result (low cycle thresholds; 9 × 105 copies/mL). Our results suggest that both Ag-RDTs showed good performances in detection of high viral load samples, making it a feasible and effective tool for mass screening in actively infected children.
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17
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Long S. SARS-CoV-2 Subgenomic RNAs: Characterization, Utility, and Perspectives. Viruses 2021; 13:v13101923. [PMID: 34696353 PMCID: PMC8539008 DOI: 10.3390/v13101923] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2021] [Revised: 09/12/2021] [Accepted: 09/16/2021] [Indexed: 12/11/2022] Open
Abstract
SARS-CoV-2, the etiologic agent at the root of the ongoing COVID-19 pandemic, harbors a large RNA genome from which a tiered ensemble of subgenomic RNAs (sgRNAs) is generated. Comprehensive definition and investigation of these RNA products are important for understanding SARS-CoV-2 pathogenesis. This review summarizes the recent progress on SARS-CoV-2 sgRNA identification, characterization, and application as a viral replication marker. The significance of these findings and potential future research areas of interest are discussed.
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Affiliation(s)
- Samuel Long
- Independent Researcher, Clarksburg, MD 20871, USA
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18
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Can Testing Predict SARS-CoV-2 Infectivity? The Potential for Certain Methods to be a Surrogate for Replication-Competent Virus. J Clin Microbiol 2021; 59:e0046921. [PMID: 34346713 PMCID: PMC8525553 DOI: 10.1128/jcm.00469-21] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Since the beginning of the COVID-19 pandemic, molecular methods (e.g., real-time PCR) have been the primary means of diagnosing the disease. It is now well established that molecular tests can continue to detect SARS-CoV-2 genomic RNA for weeks or months following the resolution of clinical illness. This has prompted public health agencies to recommend a symptom- and/or time-based strategy for discontinuation of isolation precautions, which, for hospitalized patients, results in significant use of personal protective equipment. Due to the inability of current molecular diagnostic assays to differentiate between the presence of remnant viral RNA (i.e., noninfectious) and replication-competent (i.e., infectious) virus, there has been interest in determining whether laboratory tests can be used to predict an individual’s likelihood of transmitting the virus to others. This review will highlight what is currently known about the potential for existing assays, such as real-time PCR and antigen tests, to predict active viral infection. In addition, data on the performance of new methods, such as molecular tests targeting viral RNA intermediates (e.g., subgenomic RNA), will be discussed.
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19
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Pérez-Lago L, Aldámiz-Echevarría T, García-Martínez R, Pérez-Latorre L, Herranz M, Sola-Campoy PJ, Suárez-González J, Martínez-Laperche C, Comas I, González-Candelas F, Catalán P, Muñoz P, García de Viedma D. Different Within-Host Viral Evolution Dynamics in Severely Immunosuppressed Cases with Persistent SARS-CoV-2. Biomedicines 2021; 9:808. [PMID: 34356872 PMCID: PMC8301427 DOI: 10.3390/biomedicines9070808] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Revised: 06/23/2021] [Accepted: 07/07/2021] [Indexed: 01/08/2023] Open
Abstract
A successful Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) variant, B.1.1.7, has recently been reported in the UK, causing global alarm. Most likely, the new variant emerged in a persistently infected patient, justifying a special focus on these cases. Our aim in this study was to explore certain clinical profiles involving severe immunosuppression that may help explain the prolonged persistence of viable viruses. We present three severely immunosuppressed cases (A, B, and C) with a history of lymphoma and prolonged SARS-CoV-2 shedding (2, 4, and 6 months), two of whom finally died. Whole-genome sequencing of 9 and 10 specimens from Cases A and B revealed extensive within-patient acquisition of diversity, 12 and 28 new single nucleotide polymorphisms, respectively, which suggests ongoing SARS-CoV-2 replication. This diversity was not observed for Case C after analysing 5 sequential nasopharyngeal specimens and one plasma specimen, and was only observed in one bronchoaspirate specimen, although viral viability was still considered based on constant low Ct values throughout the disease and recovery of the virus in cell cultures. The acquired viral diversity in Cases A and B followed different dynamics. For Case A, new single nucleotide polymorphisms were quickly fixed (13-15 days) after emerging as minority variants, while for Case B, higher diversity was observed at a slower emergence: fixation pace (1-2 months). Slower SARS-CoV-2 evolutionary pace was observed for Case A following the administration of hyperimmune plasma. This work adds knowledge on SARS-CoV-2 prolonged shedding in severely immunocompromised patients and demonstrates viral viability, noteworthy acquired intra-patient diversity, and different SARS-CoV-2 evolutionary dynamics in persistent cases.
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Affiliation(s)
- Laura Pérez-Lago
- Clinical Microbiology and Infectious Diseases Department, Gregorio Marañón General University Hospital, 28007 Madrid, Spain; (L.P.-L.); (T.A.-E.); (L.P.-L.); (M.H.); (P.J.S.-C.); (P.C.); (P.M.)
- Gregorio Marañón Health Research Institute (IiSGM), 28007 Madrid, Spain; (R.G.-M.); (J.S.-G.); (C.M.-L.)
| | - Teresa Aldámiz-Echevarría
- Clinical Microbiology and Infectious Diseases Department, Gregorio Marañón General University Hospital, 28007 Madrid, Spain; (L.P.-L.); (T.A.-E.); (L.P.-L.); (M.H.); (P.J.S.-C.); (P.C.); (P.M.)
- Gregorio Marañón Health Research Institute (IiSGM), 28007 Madrid, Spain; (R.G.-M.); (J.S.-G.); (C.M.-L.)
| | - Rita García-Martínez
- Gregorio Marañón Health Research Institute (IiSGM), 28007 Madrid, Spain; (R.G.-M.); (J.S.-G.); (C.M.-L.)
- Internal Medicine Department, Gregorio Marañón General University Hospital, 28007 Madrid, Spain
| | - Leire Pérez-Latorre
- Clinical Microbiology and Infectious Diseases Department, Gregorio Marañón General University Hospital, 28007 Madrid, Spain; (L.P.-L.); (T.A.-E.); (L.P.-L.); (M.H.); (P.J.S.-C.); (P.C.); (P.M.)
- Gregorio Marañón Health Research Institute (IiSGM), 28007 Madrid, Spain; (R.G.-M.); (J.S.-G.); (C.M.-L.)
| | - Marta Herranz
- Clinical Microbiology and Infectious Diseases Department, Gregorio Marañón General University Hospital, 28007 Madrid, Spain; (L.P.-L.); (T.A.-E.); (L.P.-L.); (M.H.); (P.J.S.-C.); (P.C.); (P.M.)
- Gregorio Marañón Health Research Institute (IiSGM), 28007 Madrid, Spain; (R.G.-M.); (J.S.-G.); (C.M.-L.)
- CIBER Respiratory Diseases (CIBERES), 28029 Madrid, Spain
| | - Pedro J. Sola-Campoy
- Clinical Microbiology and Infectious Diseases Department, Gregorio Marañón General University Hospital, 28007 Madrid, Spain; (L.P.-L.); (T.A.-E.); (L.P.-L.); (M.H.); (P.J.S.-C.); (P.C.); (P.M.)
- Gregorio Marañón Health Research Institute (IiSGM), 28007 Madrid, Spain; (R.G.-M.); (J.S.-G.); (C.M.-L.)
| | - Julia Suárez-González
- Gregorio Marañón Health Research Institute (IiSGM), 28007 Madrid, Spain; (R.G.-M.); (J.S.-G.); (C.M.-L.)
- Genomics Unit, Gregorio Marañón General University Hospital, 28007 Madrid, Spain
| | - Carolina Martínez-Laperche
- Gregorio Marañón Health Research Institute (IiSGM), 28007 Madrid, Spain; (R.G.-M.); (J.S.-G.); (C.M.-L.)
- Oncohematology Service, Gregorio Marañón General University Hospital, 28007 Madrid, Spain
| | - Iñaki Comas
- Tuberculosis Genomics Unit, Instituto de Biomedicina de Valencia-CSIC, 46010 Valencia, Spain;
- CIBER Salud Pública (CIBERESP), 28029 Madrid, Spain;
| | - Fernando González-Candelas
- CIBER Salud Pública (CIBERESP), 28029 Madrid, Spain;
- Joint Research Unit “Infection and Public Health”, Institute for Integrative Systems Biology (I2SysBio), FISABIO-University of Valencia, 46980 Valencia, Spain
| | - Pilar Catalán
- Clinical Microbiology and Infectious Diseases Department, Gregorio Marañón General University Hospital, 28007 Madrid, Spain; (L.P.-L.); (T.A.-E.); (L.P.-L.); (M.H.); (P.J.S.-C.); (P.C.); (P.M.)
- Gregorio Marañón Health Research Institute (IiSGM), 28007 Madrid, Spain; (R.G.-M.); (J.S.-G.); (C.M.-L.)
- CIBER Respiratory Diseases (CIBERES), 28029 Madrid, Spain
| | - Patricia Muñoz
- Clinical Microbiology and Infectious Diseases Department, Gregorio Marañón General University Hospital, 28007 Madrid, Spain; (L.P.-L.); (T.A.-E.); (L.P.-L.); (M.H.); (P.J.S.-C.); (P.C.); (P.M.)
- Gregorio Marañón Health Research Institute (IiSGM), 28007 Madrid, Spain; (R.G.-M.); (J.S.-G.); (C.M.-L.)
- CIBER Respiratory Diseases (CIBERES), 28029 Madrid, Spain
- Departamento de Medicina, Universidad Complutense, 28040 Madrid, Spain
| | - Darío García de Viedma
- Clinical Microbiology and Infectious Diseases Department, Gregorio Marañón General University Hospital, 28007 Madrid, Spain; (L.P.-L.); (T.A.-E.); (L.P.-L.); (M.H.); (P.J.S.-C.); (P.C.); (P.M.)
- Gregorio Marañón Health Research Institute (IiSGM), 28007 Madrid, Spain; (R.G.-M.); (J.S.-G.); (C.M.-L.)
- CIBER Respiratory Diseases (CIBERES), 28029 Madrid, Spain
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20
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Bruno A, de Mora D, Freire-Paspuel B, Rodriguez AS, Paredes-Espinosa MB, Olmedo M, Sanchez M, Romero J, Paez M, Gonzalez M, Orlando A, Garcia-Bereguiain MA. Analytical and clinical evaluation of a heat shock SARS-CoV-2 detection method without RNA extraction for N and E genes RT-qPCR. Int J Infect Dis 2021; 109:315-320. [PMID: 34166793 PMCID: PMC8215877 DOI: 10.1016/j.ijid.2021.06.038] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Revised: 06/13/2021] [Accepted: 06/15/2021] [Indexed: 12/28/2022] Open
Abstract
Background The COVID-19 pandemic has caused significant supply shortages worldwide for SARS-CoV-2 molecular diagnosis, like RNA extraction kits. Objective The aim of our study was to evaluate the clinical performance and analytical sensitivity of a simple SARS-CoV-2 diagnosis protocol based on heat shock without RNA extraction using both "CDC" (N gene) and "Charite" (E gene) RT-qPCR protocols. Results 1,036 nasopharyngeal samples, 543 of them SARS-CoV-2 positive, were analyzed. The heat shock method correctly identified 68.8% (232/337) and 89.4% (202/226) of SARS-CoV-2 positive samples for N gene and E gene, respectively. Analytical sensitivity was assessed for heat shock method using the CDC RT-qPCR protocol, obtaining sensitivity values of 98.6%, 93.3% and 84.8% for limit of detection of 100.000, 50.000 and 20.000 viral RNA copies/mL of sample. Conclusions Our findings show that a simple heat shock SARS-CoV-2 RT-qPCR diagnosis method without RNA extraction is a reliable alternative for potentially infectious SARS-CoV-2 positive patients at the time of testing. This affordable protocol can help overcome the cost and supply shortages for SARS-CoV-2 diagnosis, especially in developing countries. In Ecuador, it has been used already by laboratories in the public health system for more than 100.000 specimens.
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Affiliation(s)
- Alfredo Bruno
- Instituto Nacional de Salud Pública e Investigación "Leopoldo Izquieta Pérez", Guayaquil, Ecuador; Universidad Agraria del Ecuador, Guayaquil, Ecuador
| | - Domenica de Mora
- Instituto Nacional de Salud Pública e Investigación "Leopoldo Izquieta Pérez", Guayaquil, Ecuador
| | | | - Angel S Rodriguez
- One Health Research Group, Universidad de Las Americas, Quito, Ecuador
| | | | - Maritza Olmedo
- Instituto Nacional de Salud Pública e Investigación "Leopoldo Izquieta Pérez", Guayaquil, Ecuador
| | - Martha Sanchez
- Instituto Nacional de Salud Pública e Investigación "Leopoldo Izquieta Pérez", Guayaquil, Ecuador
| | - Jennifer Romero
- Instituto Nacional de Salud Pública e Investigación "Leopoldo Izquieta Pérez", Guayaquil, Ecuador
| | - Michelle Paez
- Instituto Nacional de Salud Pública e Investigación "Leopoldo Izquieta Pérez", Guayaquil, Ecuador
| | - Manuel Gonzalez
- Instituto Nacional de Salud Pública e Investigación "Leopoldo Izquieta Pérez", Guayaquil, Ecuador; Universidad de Guayaquil, Guayaquil, Ecuador
| | - Alberto Orlando
- Instituto Nacional de Salud Pública e Investigación "Leopoldo Izquieta Pérez", Guayaquil, Ecuador; Universidad Agraria del Ecuador, Guayaquil, Ecuador
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21
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Krogstad P, Contreras D, Ng H, Tobin N, Chambers CD, Bertrand K, Bode L, Aldrovandi G. No Evidence of Infectious SARS-CoV-2 in Human Milk: Analysis of a Cohort of 110 Lactating Women. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2021:2021.04.05.21254897. [PMID: 33851178 PMCID: PMC8043475 DOI: 10.1101/2021.04.05.21254897] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
BACKGROUND SARS-CoV-2 infections of infants and toddlers are usually mild but can result in life-threatening disease. SARS-CoV-2 RNA been detected in the breast milk of lactating women, but the potential role of breastfeeding in transmission to infants has remained uncertain. METHODS Breast milk specimens were examined for the presence of the virus by RT-PCR and/or culture. Specimens that contained viral RNA (vRNA) were examined for the presence of subgenomic coronavirus RNA (sgRNA), a putative marker of infectivity. Culture methods were used to determine the thermal stability of SARS-CoV-2 in human milk. RESULTS Breast milk samples from 110 women (65 confirmed with a SARS-CoV-2 diagnostic test, 36 with symptoms but without tests, and 9 with symptoms but a negative SARS-CoV-2 diagnostic test) were tested by RT-PCR (285 samples) and/or viral culture (160 samples). Although vRNA of SARS-CoV-2 was detected in the milk of 7 of 110 (6%) women with either a confirmed infection or symptomatic illness, and in 6 of 65 (9%) of women with a positive SARS-CoV-2 diagnostic test, virus was not detected in any culture. None of the 7 milk specimens with detectable vRNA contained sgRNA. Notably, when artificially added to human milk in control experiments, infectious SARS-CoV-2 could be cultured despite several freeze-thaw cycles, as occurs in the storage and usage of human milk. CONCLUSIONS SARS-CoV-2 RNA can be found infrequently in the breastmilk of women with recent infection, but we found no evidence that breastmilk contains infectious virus or that breastfeeding represents a risk factor for transmission of infection to infants. KEY POINTS Question: SARS-CoV-2 RNA has been detected in a small number of human milk samples collected from recently infected women. The role of breastfeeding in transmission of the virus to infants has remained uncertain due to the small number of specimens analyzed in any study published thus far.Findings: In a total study group of 110 women, SARS-CoV-2 RNA was detected in milk from 6 of 65 women (9.2%) with recent confirmed infection. Neither infectious virus nor subgenomic RNA (a marker of virus infectivity) were detected in any of the samples.Meaning: We found no evidence that infectious SARS-CoV-2 is present milk from recently infected women, even if SARS-CoV-2 PCR tests are positive, providing reassurance of the safety of breastfeeding.
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Affiliation(s)
- Paul Krogstad
- Department of Pediatrics, David Geffen School of Medicine at UCLA, University of California, Los Angeles CA 90095
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine at UCLA, University of California, Los Angeles CA 90095
| | - Deisy Contreras
- Department of Pediatrics, David Geffen School of Medicine at UCLA, University of California, Los Angeles CA 90095
| | - Hwee Ng
- Department of Pediatrics, David Geffen School of Medicine at UCLA, University of California, Los Angeles CA 90095
| | - Nicole Tobin
- Department of Pediatrics, David Geffen School of Medicine at UCLA, University of California, Los Angeles CA 90095
| | - Christina D. Chambers
- Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093
- Hebert Wertheim School of Public Health and Longevity Science
| | - Kerri Bertrand
- Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093
- Hebert Wertheim School of Public Health and Longevity Science
| | - Lars Bode
- Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093
- Larsson-Rosenquist Foundation Mother-Milk-Infant Center of Research Excellence (MOMI CORE)
| | - Grace Aldrovandi
- Department of Pediatrics, David Geffen School of Medicine at UCLA, University of California, Los Angeles CA 90095
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22
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Menchinelli G, Bordi L, Liotti FM, Palucci I, Capobianchi MR, Sberna G, Lalle E, Romano L, De Angelis G, Marchetti S, Sanguinetti M, Cattani P, Posteraro B. Lumipulse G SARS-CoV-2 Ag assay evaluation using clinical samples from different testing groups. Clin Chem Lab Med 2021; 59:1468-1476. [PMID: 33823089 DOI: 10.1515/cclm-2021-0182] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Accepted: 03/29/2021] [Indexed: 12/27/2022]
Abstract
OBJECTIVES Compared to RT-PCR, lower performance of antigen detection assays, including the Lumipulse G SARS-CoV-2 Ag assay, may depend on specific testing scenarios. METHODS We tested 594 nasopharyngeal swab samples from individuals with COVID-19 (RT-PCR cycle threshold [Ct] values ≤ 40) or non-COVID-19 (Ct values >40) diagnoses. RT-PCR positive samples were assigned to diagnostic, screening, or monitoring groups of testing. RESULTS With a limit of detection of 1.2 × 104 SARS-CoV-2 RNA copies/mL, Lumipulse showed positive percent agreement (PPA) of 79.9% (155/194) and negative percent agreement of 99.3% (397/400), whereas PPAs were 100% for samples with Ct values of <18 or 18-<25 and 92.5% for samples with Ct values of 25-<30. By three groups, Lumipulse showed PPA of 87.0% (60/69), 81.1% (43/53), or 72.2% (52/72), respectively, whereas PPA was 100% for samples with Ct values of <18 or 18-<25, and was 94.4, 80.0, or 100% for samples with Ct values of 25-<30, respectively. Additional testing of RT-PCR positive samples for SARS-CoV-2 subgenomic RNA showed that, by three groups, PPA was 63.8% (44/69), 62.3% (33/53), or 33.3% (24/72), respectively. PPAs dropped to 55.6, 20.0, or 41.7% for samples with Ct values of 25-<30, respectively. All 101 samples with a subgenomic RNA positive result had a Lumipulse assay's antigen positive result, whereas only 54 (58.1%) of remaining 93 samples had a Lumipulse assay's antigen positive result. CONCLUSIONS Lumipulse assay was highly sensitive in samples with low RT-PCR Ct values, implying repeated testing to reduce consequences of false-negative results.
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Affiliation(s)
- Giulia Menchinelli
- Dipartimento di Scienze Biotecnologiche di Base, Cliniche Intensivologiche e Perioperatorie, Università Cattolica del Sacro Cuore, Rome, Italy.,Dipartimento di Scienze di Laboratorio e Infettivologiche, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - Licia Bordi
- Istituto Nazionale per le Malattie Infettive (INMI) Lazzaro Spallanzani IRCCS, Rome, Italy
| | - Flora Marzia Liotti
- Dipartimento di Scienze Biotecnologiche di Base, Cliniche Intensivologiche e Perioperatorie, Università Cattolica del Sacro Cuore, Rome, Italy.,Dipartimento di Scienze di Laboratorio e Infettivologiche, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - Ivana Palucci
- Dipartimento di Scienze Biotecnologiche di Base, Cliniche Intensivologiche e Perioperatorie, Università Cattolica del Sacro Cuore, Rome, Italy.,Dipartimento di Scienze di Laboratorio e Infettivologiche, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | | | - Giuseppe Sberna
- Istituto Nazionale per le Malattie Infettive (INMI) Lazzaro Spallanzani IRCCS, Rome, Italy
| | - Eleonora Lalle
- Istituto Nazionale per le Malattie Infettive (INMI) Lazzaro Spallanzani IRCCS, Rome, Italy
| | - Lucio Romano
- Dipartimento di Scienze di Laboratorio e Infettivologiche, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - Giulia De Angelis
- Dipartimento di Scienze Biotecnologiche di Base, Cliniche Intensivologiche e Perioperatorie, Università Cattolica del Sacro Cuore, Rome, Italy.,Dipartimento di Scienze di Laboratorio e Infettivologiche, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - Simona Marchetti
- Dipartimento di Scienze di Laboratorio e Infettivologiche, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - Maurizio Sanguinetti
- Dipartimento di Scienze Biotecnologiche di Base, Cliniche Intensivologiche e Perioperatorie, Università Cattolica del Sacro Cuore, Rome, Italy.,Dipartimento di Scienze di Laboratorio e Infettivologiche, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - Paola Cattani
- Dipartimento di Scienze Biotecnologiche di Base, Cliniche Intensivologiche e Perioperatorie, Università Cattolica del Sacro Cuore, Rome, Italy.,Dipartimento di Scienze di Laboratorio e Infettivologiche, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - Brunella Posteraro
- Dipartimento di Scienze Biotecnologiche di Base, Cliniche Intensivologiche e Perioperatorie, Università Cattolica del Sacro Cuore, Rome, Italy.,Dipartimento di Scienze Mediche e Chirurgiche, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
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23
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Beran A, Zink E, Mhanna M, Abugharbyeh A, Hanrahan J, Duggan J, Assaly R. Transmissibility and viral replication of SARS-COV-2 in immunocompromised patients. J Med Virol 2021; 93:4156-4160. [PMID: 33782995 PMCID: PMC8250487 DOI: 10.1002/jmv.26970] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 03/17/2021] [Accepted: 03/24/2021] [Indexed: 01/01/2023]
Affiliation(s)
- Azizullah Beran
- Department of Internal Medicine, University of Toledo, Toledo, Ohio, USA
| | - Evan Zink
- Department of Infectious Diseases, University of Toledo, Toledo, Ohio, USA
| | - Mohammed Mhanna
- Department of Internal Medicine, University of Toledo, Toledo, Ohio, USA
| | - Aya Abugharbyeh
- Department of Internal Medicine, University of Toledo, Toledo, Ohio, USA
| | - Jennifer Hanrahan
- Department of Infectious Diseases, University of Toledo, Toledo, Ohio, USA
| | - Joan Duggan
- Department of Infectious Diseases, University of Toledo, Toledo, Ohio, USA
| | - Ragheb Assaly
- Department of Internal Medicine, University of Toledo, Toledo, Ohio, USA.,Department of Pulmonary and Critical Care, University of Toledo, Toledo, Ohio, USA
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24
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Frankel AE, Reddy R, DeSuza KR, Deeb K, Carlin AF, Smith D, Xie Y, Naik E, Silver RT, Hasselbalch HC. Response to pegylated interferon in a COVID-19-positive elderly woman with primary myelofibrosis treated with ruxolitinib. Clin Case Rep 2021; 9:2228-2235. [PMID: 33936671 PMCID: PMC8077319 DOI: 10.1002/ccr3.3997] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 01/28/2021] [Accepted: 02/07/2021] [Indexed: 01/08/2023] Open
Abstract
An 83-year-old female had asymptomatic SARS-CoV-2 infection while taking ruxolitinib. She remained RT-PCR positive for viral RNA for >120 days, and Pegylated interferon for 4 weeks led to viral RNA clearance. The observations support combination therapy of ruxolitinib + interferon for COVID-19.
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Affiliation(s)
- Arthur E. Frankel
- Department of MedicineWest Palm Beach VA Medical CenterWest Palm BeachFLUSA
| | - Renuka Reddy
- Department of MedicineWest Palm Beach VA Medical CenterWest Palm BeachFLUSA
| | - Kayla R. DeSuza
- Department of MedicineWest Palm Beach VA Medical CenterWest Palm BeachFLUSA
| | - Khaled Deeb
- Department of MedicineWest Palm Beach VA Medical CenterWest Palm BeachFLUSA
| | - Aaron F. Carlin
- Division of Infectious DiseaseUCSD Medical SchoolSan DiegoCAUSA
| | - Davey Smith
- Division of Infectious DiseaseUCSD Medical SchoolSan DiegoCAUSA
| | - Yushuang Xie
- Department of MedicineWest Palm Beach VA Medical CenterWest Palm BeachFLUSA
| | - Eknath Naik
- Department of MedicineWest Palm Beach VA Medical CenterWest Palm BeachFLUSA
| | - Richard T. Silver
- Division of Hematology and Medical OncologyWeill Cornell MedicineNew YorkNYUSA
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25
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Mukherjee A, Anand T, Agarwal A, Singh H, Chatterjee P, Narayan J, Rana S, Gupta N, Bhargava B, Panda S. SARS-CoV-2 re-infection: development of an epidemiological definition from India. Epidemiol Infect 2021; 149:e82. [PMID: 33766185 PMCID: PMC8027559 DOI: 10.1017/s0950268821000662] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Revised: 03/20/2021] [Accepted: 03/23/2021] [Indexed: 12/22/2022] Open
Abstract
The current investigation was conducted with the objective to develop an epidemiological case definition of possible severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) re-infection and assess its magnitude in India. The epidemiological case definition for SARS-CoV-2 re-infection was developed from literature review of data on viral kinetics. For achieving second objective, the individuals who satisfied the developed case definition for SARS-CoV-2 re-infection were contacted telephonically. Taking available evidence into consideration, re-infection with SARS-CoV-2 in our study was defined as any individual who tested positive for SARS-CoV-2 on two separate occasions by either molecular tests or rapid antigen test at an interval of at least 102 days with one negative molecular test in between. In this archive based, telephonic survey, 58 out of 1300 individuals (4.5%) fulfilled the above-mentioned definition; 38 individuals could be contacted with healthcare workers (HCWs) accounting for 31.6% of the cases. A large proportion of participants was asymptomatic and had higher Ct value during the first episode. While SARS-CoV-2 re-infection is still a rare phenomenon, there is a need for epidemiological definition of re-infection for establishing surveillance systems and this study contributes to such a goal.Severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) re-infection is an emerging concern and there is a need to define it. Therefore, working epidemiological case definition for re-infection was developed and its magnitude was explored via archive-based, telephonic survey. Re-infection with SARS-CoV-2 was defined as two positive tests at an interval of at least 102 days with one interim negative test. Thirty-eight of the 58 eligible patients could be contacted with 12 (31.6%) being HCWs. Majority of the participants were asymptomatic and had higher Ct value during their first episode. To conclude, a working epidemiological case definition of SARS-CoV-2 re-infection is important to strengthen surveillance. The present investigation contributes to this goal and records reinfection in 4.5% of SARS-CoV-2 infected individuals in India.
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Affiliation(s)
- Aparna Mukherjee
- Division of Epidemiology & Communicable Diseases, ICMR Headquarters, Delhi, India
| | - Tanu Anand
- Division of Epidemiology & Communicable Diseases, ICMR Headquarters, Delhi, India
| | - Anup Agarwal
- Division of Epidemiology & Communicable Diseases, ICMR Headquarters, Delhi, India
| | - Harpreet Singh
- Division of Information, Systems and Research Management, ICMR Headquarters, Delhi, India
| | - Pranab Chatterjee
- Department of International Health, Johns Hopkins Bloomberg School of Public Health, Johns Hopkins University, Baltimore, USA
| | - Jitendra Narayan
- Division of Epidemiology & Communicable Diseases, ICMR Headquarters, Delhi, India
| | - Salaj Rana
- Division of Epidemiology & Communicable Diseases, ICMR Headquarters, Delhi, India
| | - Nivedita Gupta
- Division of Epidemiology & Communicable Diseases, ICMR Headquarters, Delhi, India
| | | | - Samiran Panda
- Division of Epidemiology & Communicable Diseases, ICMR Headquarters, Delhi, India
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