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Bell C, Goss M, Norton D, Barlow S, Temte E, He C, Hamer C, Walters S, Sabry A, Johnson K, Chen G, Uzicanin A, Temte J. Descriptive Epidemiology of Pathogens Associated with Acute Respiratory Infection in a Community-Based Study of K-12 School Children (2015-2023). Pathogens 2024; 13:340. [PMID: 38668295 PMCID: PMC11053468 DOI: 10.3390/pathogens13040340] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Revised: 04/10/2024] [Accepted: 04/17/2024] [Indexed: 04/29/2024] Open
Abstract
School-based outbreaks often precede increased incidence of acute respiratory infections in the greater community. We conducted acute respiratory infection surveillance among children to elucidate commonly detected pathogens in school settings and their unique characteristics and epidemiological patterns. The ORegon CHild Absenteeism due to Respiratory Disease Study (ORCHARDS) is a longitudinal, laboratory-supported, school-based, acute respiratory illness (ARI) surveillance study designed to evaluate the utility of cause-specific student absenteeism monitoring for early detection of increased activity of influenza and other respiratory viruses in schools from kindergarten through 12th grade. Eligible participants with ARIs provided demographic, epidemiologic, and symptom data, along with a nasal swab or oropharyngeal specimen. Multipathogen testing using reverse-transcription polymerase chain reaction (RT-PCR) was performed on all specimens for 18 respiratory viruses and 2 atypical bacterial pathogens (Chlamydia pneumoniae and Mycoplasma pneumoniae). Between 5 January 2015 and 9 June 2023, 3498 children participated. Pathogens were detected in 2455 of 3498 (70%) specimens. Rhinovirus/enteroviruses (36%) and influenza viruses A/B (35%) were most commonly identified in positive specimens. Rhinovirus/enteroviruses and parainfluenza viruses occurred early in the academic year, followed by seasonal coronaviruses, RSV, influenza viruses A/B, and human metapneumovirus. Since its emergence in 2020, SARS-CoV-2 was detected year-round and had a higher median age than the other pathogens. A better understanding of the etiologies, presentations, and patterns of pediatric acute respiratory infections can help inform medical and public health system responses.
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Affiliation(s)
- Cristalyne Bell
- Department of Family Medicine and Community Health, School of Medicine and Public Health, University of Wisconsin, Madison, WI 53706, USA; (C.B.); (S.B.); (E.T.); (C.H.); (C.H.); (S.W.); (A.S.); (K.J.); (J.T.)
| | - Maureen Goss
- Department of Family Medicine and Community Health, School of Medicine and Public Health, University of Wisconsin, Madison, WI 53706, USA; (C.B.); (S.B.); (E.T.); (C.H.); (C.H.); (S.W.); (A.S.); (K.J.); (J.T.)
| | - Derek Norton
- Department of Biostatistics and Medical Informatics, School of Medicine and Public Health, University of Wisconsin, Madison, WI 53706, USA; (D.N.); (G.C.)
| | - Shari Barlow
- Department of Family Medicine and Community Health, School of Medicine and Public Health, University of Wisconsin, Madison, WI 53706, USA; (C.B.); (S.B.); (E.T.); (C.H.); (C.H.); (S.W.); (A.S.); (K.J.); (J.T.)
| | - Emily Temte
- Department of Family Medicine and Community Health, School of Medicine and Public Health, University of Wisconsin, Madison, WI 53706, USA; (C.B.); (S.B.); (E.T.); (C.H.); (C.H.); (S.W.); (A.S.); (K.J.); (J.T.)
| | - Cecilia He
- Department of Family Medicine and Community Health, School of Medicine and Public Health, University of Wisconsin, Madison, WI 53706, USA; (C.B.); (S.B.); (E.T.); (C.H.); (C.H.); (S.W.); (A.S.); (K.J.); (J.T.)
| | - Caroline Hamer
- Department of Family Medicine and Community Health, School of Medicine and Public Health, University of Wisconsin, Madison, WI 53706, USA; (C.B.); (S.B.); (E.T.); (C.H.); (C.H.); (S.W.); (A.S.); (K.J.); (J.T.)
| | - Sarah Walters
- Department of Family Medicine and Community Health, School of Medicine and Public Health, University of Wisconsin, Madison, WI 53706, USA; (C.B.); (S.B.); (E.T.); (C.H.); (C.H.); (S.W.); (A.S.); (K.J.); (J.T.)
| | - Alea Sabry
- Department of Family Medicine and Community Health, School of Medicine and Public Health, University of Wisconsin, Madison, WI 53706, USA; (C.B.); (S.B.); (E.T.); (C.H.); (C.H.); (S.W.); (A.S.); (K.J.); (J.T.)
| | - Kelly Johnson
- Department of Family Medicine and Community Health, School of Medicine and Public Health, University of Wisconsin, Madison, WI 53706, USA; (C.B.); (S.B.); (E.T.); (C.H.); (C.H.); (S.W.); (A.S.); (K.J.); (J.T.)
| | - Guanhua Chen
- Department of Biostatistics and Medical Informatics, School of Medicine and Public Health, University of Wisconsin, Madison, WI 53706, USA; (D.N.); (G.C.)
| | - Amra Uzicanin
- Centers for Disease Control and Prevention, Atlanta, GA 30329, USA;
| | - Jonathan Temte
- Department of Family Medicine and Community Health, School of Medicine and Public Health, University of Wisconsin, Madison, WI 53706, USA; (C.B.); (S.B.); (E.T.); (C.H.); (C.H.); (S.W.); (A.S.); (K.J.); (J.T.)
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Temte JL, Bell C, Goss MD, Reisdorf E, Tamerius J, Reddy S, Griesser R, Barlow S, Temte E, Wedig M, Shult PA. Adequacy of using a single nasal swab for rapid influenza diagnostic testing, PCR, and whole genome sequencing. PLOS GLOBAL PUBLIC HEALTH 2023; 3:e0001422. [PMID: 37224148 DOI: 10.1371/journal.pgph.0001422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 04/24/2023] [Indexed: 05/26/2023]
Abstract
Rapid influenza diagnostic tests (RIDT) demonstrate varying sensitivities, often necessitating reverse transcriptase polymerase chain reaction (RT-PCR) to confirm results. The two methods generally require separate specimens. Using the same anterior nasal swab for both RIDT and molecular confirmation would reduce cost and waste and increase patient comfort. The aim of this study was to determine if RIDT residual nasal swab (rNS) specimens are adequate for RT-PCR and whole genome sequencing (WGS). We performed RT-PCR and WGS on paired rNS and nasopharyngeal or oropharyngeal (NP/OP) swab specimens that were collected from primary care patients across all ages. We randomly selected 199 and 40 paired specimens for RT-PCR and WGS, respectively, from the 962 paired surveillance specimens collected during the 2014-2015 influenza season. Sensitivity and specificity for rNS specimens were 81.3% and 96.7%, respectively, as compared to NP/OP specimens. The mean cycle threshold (Ct) value for the NP/OP specimen was significantly lower when the paired specimens were both positive than when the NP/OP swab was positive and the nasal swab was negative (25.5 vs 29.5; p<0.001). Genomic information was extracted from all 40 rNS specimens and 37 of the 40 NP/OP specimens. Complete WGS reads were available for 67.5% (14 influenza A; 13 influenza B) of the rNS specimens and 59.5% (14 influenza A; 8 influenza B) of the NP/OP specimens. It is feasible to use a single anterior nasal swab for RIDT followed by RT-PCR and/or WGS. This approach may be appropriate in situations where training and supplies are limited. Additional studies are needed to determine if residual nasal swabs from other rapid diagnostic tests produce similar results.
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Affiliation(s)
- Jonathan L Temte
- Department of Family Medicine and Community Health, School of Medicine and Public Health, University of Wisconsin, Madison, Wisconsin, United States of America
| | - Cristalyne Bell
- Department of Family Medicine and Community Health, School of Medicine and Public Health, University of Wisconsin, Madison, Wisconsin, United States of America
| | - Maureen D Goss
- Department of Family Medicine and Community Health, School of Medicine and Public Health, University of Wisconsin, Madison, Wisconsin, United States of America
| | - Erik Reisdorf
- Wisconsin State Laboratory of Hygiene, Madison, Wisconsin, United States of America
| | - John Tamerius
- Quidel Corporation, San Diego, California, United States of America
| | - Sushruth Reddy
- Quidel Corporation, San Diego, California, United States of America
| | - Richard Griesser
- Wisconsin State Laboratory of Hygiene, Madison, Wisconsin, United States of America
| | - Shari Barlow
- Department of Family Medicine and Community Health, School of Medicine and Public Health, University of Wisconsin, Madison, Wisconsin, United States of America
| | - Emily Temte
- Department of Family Medicine and Community Health, School of Medicine and Public Health, University of Wisconsin, Madison, Wisconsin, United States of America
| | - Mary Wedig
- Wisconsin State Laboratory of Hygiene, Madison, Wisconsin, United States of America
| | - Peter A Shult
- Wisconsin State Laboratory of Hygiene, Madison, Wisconsin, United States of America
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Maidana-Kulesza MN, Poma HR, Sanguino-Jorquera DG, Reyes SI, Del Milagro Said-Adamo M, Mainardi-Remis JM, Gutiérrez-Cacciabue D, Cristóbal HA, Cruz MC, Aparicio González M, Rajal VB. Tracking SARS-CoV-2 in rivers as a tool for epidemiological surveillance. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022. [PMID: 35908692 DOI: 10.1101/2021.06.17.21259122] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
The aim of this work was to evaluate if rivers could be used for SARS-CoV-2 surveillance. Five sampling points from three rivers (AR-1 and AR-2 in Arenales River, MR-1 and MR-2 in Mojotoro River, and CR in La Caldera River) from Salta (Argentina), two of them receiving discharges from wastewater plants (WWTP), were monitored from July to December 2020. Fifteen water samples from each point (75 in total) were collected and characterized physico-chemically and microbiologically and SARS-CoV-2 was quantified by RT-qPCR. Also, two targets linked to human contributions, human polyomavirus (HPyV) and RNase P, were quantified and used to normalize SARS-CoV-2 concentration, which was compared to reported COVID-19 cases. Statistical analyses allowed us to verify the correlation between SARS-CoV-2 and the concentration of fecal indicator bacteria (FIB), as well as to find similarities and differences between sampling points. La Caldera River showed the best water quality; FIBs were within acceptable limits for recreational activities. Mojotoro River's water quality was not affected by the northern WWTP of the city. Instead, Arenales River presented the poorest water quality; at AR-2 was negatively affected by the discharges of the southern WWTP, which contributed to significant increase of fecal contamination. SARS-CoV-2 was found in about half of samples in low concentrations in La Caldera and Mojotoro Rivers, while it was high and persistent in Arenales River. No human tracers were detected in CR, only HPyV was found in MR-1, MR-2 and AR-1, and both were quantified in AR-2. The experimental and normalized viral concentrations strongly correlated with reported COVID-19 cases; thus, Arenales River at AR-2 reflected the epidemiological situation of the city. This is the first study showing the dynamic of SARS-CoV-2 concentration in an urban river highly impacted by wastewater and proved that can be used for SARS-CoV-2 surveillance to support health authorities.
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Affiliation(s)
- María Noel Maidana-Kulesza
- Laboratorio de Aguas y Suelos, Instituto de Investigaciones para la Industria Química (INIQUI), Universidad Nacional de Salta (UNSa) - Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Av. Bolivia 5150, Salta 4400, Argentina
| | - Hugo Ramiro Poma
- Laboratorio de Aguas y Suelos, Instituto de Investigaciones para la Industria Química (INIQUI), Universidad Nacional de Salta (UNSa) - Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Av. Bolivia 5150, Salta 4400, Argentina
| | - Diego Gastón Sanguino-Jorquera
- Laboratorio de Aguas y Suelos, Instituto de Investigaciones para la Industria Química (INIQUI), Universidad Nacional de Salta (UNSa) - Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Av. Bolivia 5150, Salta 4400, Argentina
| | - Sarita Isabel Reyes
- Laboratorio de Aguas y Suelos, Instituto de Investigaciones para la Industria Química (INIQUI), Universidad Nacional de Salta (UNSa) - Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Av. Bolivia 5150, Salta 4400, Argentina
| | - María Del Milagro Said-Adamo
- Laboratorio de Aguas y Suelos, Instituto de Investigaciones para la Industria Química (INIQUI), Universidad Nacional de Salta (UNSa) - Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Av. Bolivia 5150, Salta 4400, Argentina; Facultad de Ciencias Naturales, UNSa, Av. Bolivia 5150, Salta 4400, Argentina
| | - Juan Martín Mainardi-Remis
- Laboratorio de Aguas y Suelos, Instituto de Investigaciones para la Industria Química (INIQUI), Universidad Nacional de Salta (UNSa) - Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Av. Bolivia 5150, Salta 4400, Argentina; Facultad de Ingeniería, UNSa, Av. Bolivia 5150, Salta 4400, Argentina
| | - Dolores Gutiérrez-Cacciabue
- Laboratorio de Aguas y Suelos, Instituto de Investigaciones para la Industria Química (INIQUI), Universidad Nacional de Salta (UNSa) - Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Av. Bolivia 5150, Salta 4400, Argentina; Facultad de Ingeniería, UNSa, Av. Bolivia 5150, Salta 4400, Argentina
| | - Héctor Antonio Cristóbal
- Laboratorio de Aguas y Suelos, Instituto de Investigaciones para la Industria Química (INIQUI), Universidad Nacional de Salta (UNSa) - Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Av. Bolivia 5150, Salta 4400, Argentina; Facultad de Ciencias Naturales, UNSa, Av. Bolivia 5150, Salta 4400, Argentina
| | - Mercedes Cecilia Cruz
- Laboratorio de Aguas y Suelos, Instituto de Investigaciones para la Industria Química (INIQUI), Universidad Nacional de Salta (UNSa) - Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Av. Bolivia 5150, Salta 4400, Argentina
| | - Mónica Aparicio González
- Laboratorio de Aguas y Suelos, Instituto de Investigaciones para la Industria Química (INIQUI), Universidad Nacional de Salta (UNSa) - Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Av. Bolivia 5150, Salta 4400, Argentina
| | - Verónica Beatriz Rajal
- Laboratorio de Aguas y Suelos, Instituto de Investigaciones para la Industria Química (INIQUI), Universidad Nacional de Salta (UNSa) - Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Av. Bolivia 5150, Salta 4400, Argentina; Facultad de Ingeniería, UNSa, Av. Bolivia 5150, Salta 4400, Argentina; Singapore Centre for Environmental Life Science Engineering (SCELSE), Nanyang Technological University, Singapore.
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Maidana-Kulesza MN, Poma HR, Sanguino-Jorquera DG, Reyes SI, Del Milagro Said-Adamo M, Mainardi-Remis JM, Gutiérrez-Cacciabue D, Cristóbal HA, Cruz MC, Aparicio González M, Rajal VB. Tracking SARS-CoV-2 in rivers as a tool for epidemiological surveillance. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 848:157707. [PMID: 35908692 PMCID: PMC9334864 DOI: 10.1016/j.scitotenv.2022.157707] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2021] [Revised: 07/04/2022] [Accepted: 07/26/2022] [Indexed: 05/22/2023]
Abstract
The aim of this work was to evaluate if rivers could be used for SARS-CoV-2 surveillance. Five sampling points from three rivers (AR-1 and AR-2 in Arenales River, MR-1 and MR-2 in Mojotoro River, and CR in La Caldera River) from Salta (Argentina), two of them receiving discharges from wastewater plants (WWTP), were monitored from July to December 2020. Fifteen water samples from each point (75 in total) were collected and characterized physico-chemically and microbiologically and SARS-CoV-2 was quantified by RT-qPCR. Also, two targets linked to human contributions, human polyomavirus (HPyV) and RNase P, were quantified and used to normalize SARS-CoV-2 concentration, which was compared to reported COVID-19 cases. Statistical analyses allowed us to verify the correlation between SARS-CoV-2 and the concentration of fecal indicator bacteria (FIB), as well as to find similarities and differences between sampling points. La Caldera River showed the best water quality; FIBs were within acceptable limits for recreational activities. Mojotoro River's water quality was not affected by the northern WWTP of the city. Instead, Arenales River presented the poorest water quality; at AR-2 was negatively affected by the discharges of the southern WWTP, which contributed to significant increase of fecal contamination. SARS-CoV-2 was found in about half of samples in low concentrations in La Caldera and Mojotoro Rivers, while it was high and persistent in Arenales River. No human tracers were detected in CR, only HPyV was found in MR-1, MR-2 and AR-1, and both were quantified in AR-2. The experimental and normalized viral concentrations strongly correlated with reported COVID-19 cases; thus, Arenales River at AR-2 reflected the epidemiological situation of the city. This is the first study showing the dynamic of SARS-CoV-2 concentration in an urban river highly impacted by wastewater and proved that can be used for SARS-CoV-2 surveillance to support health authorities.
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Affiliation(s)
- María Noel Maidana-Kulesza
- Laboratorio de Aguas y Suelos, Instituto de Investigaciones para la Industria Química (INIQUI), Universidad Nacional de Salta (UNSa) - Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Av. Bolivia 5150, Salta 4400, Argentina
| | - Hugo Ramiro Poma
- Laboratorio de Aguas y Suelos, Instituto de Investigaciones para la Industria Química (INIQUI), Universidad Nacional de Salta (UNSa) - Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Av. Bolivia 5150, Salta 4400, Argentina
| | - Diego Gastón Sanguino-Jorquera
- Laboratorio de Aguas y Suelos, Instituto de Investigaciones para la Industria Química (INIQUI), Universidad Nacional de Salta (UNSa) - Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Av. Bolivia 5150, Salta 4400, Argentina
| | - Sarita Isabel Reyes
- Laboratorio de Aguas y Suelos, Instituto de Investigaciones para la Industria Química (INIQUI), Universidad Nacional de Salta (UNSa) - Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Av. Bolivia 5150, Salta 4400, Argentina
| | - María Del Milagro Said-Adamo
- Laboratorio de Aguas y Suelos, Instituto de Investigaciones para la Industria Química (INIQUI), Universidad Nacional de Salta (UNSa) - Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Av. Bolivia 5150, Salta 4400, Argentina; Facultad de Ciencias Naturales, UNSa, Av. Bolivia 5150, Salta 4400, Argentina
| | - Juan Martín Mainardi-Remis
- Laboratorio de Aguas y Suelos, Instituto de Investigaciones para la Industria Química (INIQUI), Universidad Nacional de Salta (UNSa) - Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Av. Bolivia 5150, Salta 4400, Argentina; Facultad de Ingeniería, UNSa, Av. Bolivia 5150, Salta 4400, Argentina
| | - Dolores Gutiérrez-Cacciabue
- Laboratorio de Aguas y Suelos, Instituto de Investigaciones para la Industria Química (INIQUI), Universidad Nacional de Salta (UNSa) - Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Av. Bolivia 5150, Salta 4400, Argentina; Facultad de Ingeniería, UNSa, Av. Bolivia 5150, Salta 4400, Argentina
| | - Héctor Antonio Cristóbal
- Laboratorio de Aguas y Suelos, Instituto de Investigaciones para la Industria Química (INIQUI), Universidad Nacional de Salta (UNSa) - Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Av. Bolivia 5150, Salta 4400, Argentina; Facultad de Ciencias Naturales, UNSa, Av. Bolivia 5150, Salta 4400, Argentina
| | - Mercedes Cecilia Cruz
- Laboratorio de Aguas y Suelos, Instituto de Investigaciones para la Industria Química (INIQUI), Universidad Nacional de Salta (UNSa) - Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Av. Bolivia 5150, Salta 4400, Argentina
| | - Mónica Aparicio González
- Laboratorio de Aguas y Suelos, Instituto de Investigaciones para la Industria Química (INIQUI), Universidad Nacional de Salta (UNSa) - Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Av. Bolivia 5150, Salta 4400, Argentina
| | - Verónica Beatriz Rajal
- Laboratorio de Aguas y Suelos, Instituto de Investigaciones para la Industria Química (INIQUI), Universidad Nacional de Salta (UNSa) - Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Av. Bolivia 5150, Salta 4400, Argentina; Facultad de Ingeniería, UNSa, Av. Bolivia 5150, Salta 4400, Argentina; Singapore Centre for Environmental Life Science Engineering (SCELSE), Nanyang Technological University, Singapore.
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Temte JL, Barlow S, Temte E, Goss M, Bateman A, Florek K, Uzicanin A. Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Codetection With Influenza A and Other Respiratory Viruses Among School-Aged Children and Their Household Members-12 March 2020 to 22 February 2022, Dane County, Wisconsin. Clin Infect Dis 2022; 75:S205-S215. [PMID: 35737942 PMCID: PMC9278263 DOI: 10.1093/cid/ciac487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
BACKGROUND Concurrent detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and another respiratory virus in individuals can document contemporaneous circulation. We used an ongoing, community-based study of school-aged children and their households to evaluate SARS-CoV-2 codetections with other respiratory viruses in a non-medically attended population over a 2-year period. METHODS Household enrollment was predicated on an acute respiratory illness in a child residing in that household who was also a kindergarten through 12th-grade student in the participating school district. Demographic, symptom, and household composition data and self-collected nasal specimens were obtained on the recruitment day, and 7 and 14 days later, from the index child and all other household members. All specimens were tested for SARS-CoV-2 and influenza A/B by reverse-transcription polymerase chain reaction. Day 0 specimens from the index children were simultaneously tested for 16 pathogens using a commercial respiratory pathogen panel (RPP). To assess viral codetections involving SARS-CoV-2, all household specimens were tested via RPP if the index child's day 0 specimen tested positive to any of the 16 pathogen targets in RPP and any household member tested positive for SARS-CoV-2. RESULTS Of 2109 participants (497 index children in 497 households with 1612 additional household members), 2 (0.1%) were positive for both SARS-CoV-2 and influenza A; an additional 11 (0.5%) were positive for SARS-CoV-2 and another RPP-covered respiratory virus. Codetections predominantly affected school-aged children (12 of 13 total) and were noted in 11 of 497 households. CONCLUSIONS SARS-CoV-2 codetections with other respiratory viruses were uncommon and predominated in school-aged children.
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Affiliation(s)
- Jonathan L Temte
- Alternate corresponding author: Jonathan L. Temte, MD/PhD University of Wisconsin-Madison Dept of Family Medicine and Community Health 1100 Delaplaine Court Madison, WI 53515
| | - Shari Barlow
- Department of Family Medicine and Community Health. University of Wisconsin School of Medicine and Public Health. Madison, WI
| | - Emily Temte
- Department of Family Medicine and Community Health. University of Wisconsin School of Medicine and Public Health. Madison, WI
| | - Maureen Goss
- Corresponding author: Maureen Goss, MPH University of Wisconsin-Madison Dept of Family Medicine and Community Health 1100 Delaplaine Court Madison, WI 53715
| | | | | | - Amra Uzicanin
- U.S. Centers for Disease Control and Prevention. Atlanta, GA
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Requirements and study designs for US regulatory approval of influenza home tests. J Clin Microbiol 2021; 60:e0188421. [PMID: 34911365 PMCID: PMC9116184 DOI: 10.1128/jcm.01884-21] [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] [Indexed: 11/20/2022] Open
Abstract
Home testing for infectious disease has come to the forefront during the COVID-19 pandemic. There is now considerable commercial interest in developing complete home tests for a variety of viral and bacterial pathogens. However, the regulatory science around home infectious disease test approval, and procedures test manufacturers and laboratory professionals will need to follow, have not yet been formalized by US FDA, with the exception of EUA guidance for COVID-19 tests. We describe the state of home-based testing for influenza with a focus on sample-to-result home tests, discuss the various regulatory pathways by which these products can reach populations, and provide recommendations for study designs, patient samples, and other important features necessary to gain market access. These recommendations have potential application for home use tests being developed for other viral respiratory infections, such as COVID-19, as guidance moves from EUA designation into 510(k) requirements.
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Prospective Study of the Performance of Parent-Collected Nasal and Saliva Swab Samples, Compared with Nurse-Collected Swab Samples, for the Molecular Detection of Respiratory Microorganisms. Microbiol Spectr 2021; 9:e0016421. [PMID: 34756077 PMCID: PMC8579848 DOI: 10.1128/spectrum.00164-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Respiratory tract infections (RTIs) are ubiquitous among children in the community. A prospective observational study was performed to evaluate the diagnostic performance and quality of at-home parent-collected (PC) nasal and saliva swab samples, compared to nurse-collected (NC) swab samples, from children with RTI symptoms. Children with RTI symptoms were swabbed at home on the same day by a parent and a nurse. We compared the performance of PC swab samples as the test with NC swab samples as the reference for the detection of respiratory pathogen gene targets by reverse transcriptase PCR, with quality assessment using a human gene. PC and NC paired nasal and saliva swab samples were collected from 91 and 92 children, respectively. Performance and interrater agreement (Cohen's κ) of PC versus NC nasal swab samples for viruses combined showed sensitivity of 91.6% (95% confidence interval [CI], 85.47 to 95.73%) and κ of 0.84 (95% CI, 0.79 to 0.88), respectively; the respective values for bacteria combined were 91.4% (95% CI, 86.85 to 94.87%) and κ of 0.85 (95% CI, 0.80 to 0.89). In saliva samples, viral and bacterial sensitivities were lower at 69.0% (95% CI, 57.47 to 79.76%) and 78.1% (95% CI, 71.60 to 83.76%), as were κ values at 0.64 (95% CI, 0.53 to 0.72) and 0.70 (95% CI, 0.65 to 0.76), respectively. Quality assessment for human biological material (18S rRNA) indicated perfect interrater agreement. At-home PC nasal swab samples performed comparably to NC swab samples, whereas PC saliva swab samples lacked sensitivity for the detection of respiratory microbes. IMPORTANCE RTIs are ubiquitous among children. Diagnosis involves a swab sample being taken by a health professional, which places a considerable burden on community health care systems, given the number of cases involved. The coronavirus disease 2019 (COVID-19) pandemic has seen an increase in the at-home self-collection of upper respiratory tract swab samples without the involvement of health professionals. It is advised that parents conduct or supervise swabbing of children. Surprisingly, few studies have addressed the quality of PC swab samples for subsequent identification of respiratory pathogens. We compared NC and PC nasal and saliva swab samples taken from the same child with RTI symptoms, for detection of respiratory pathogens. The PC nasal swab samples performed comparably to NC samples, whereas saliva swab samples lacked sensitivity for the detection of respiratory microbes. Collection of swab samples by parents would greatly reduce the burden on community nurses without reducing the effectiveness of diagnoses.
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Temte JL, Barlow S, Temte E, Goss M, Florek K, Braun KM, Friedrich TC, Reisdorf E, Bateman AC, Uzicanin A. Evidence of Early Household Transmission of SARS-CoV-2 Involving a School-aged Child. WMJ : OFFICIAL PUBLICATION OF THE STATE MEDICAL SOCIETY OF WISCONSIN 2021; 120:233-236. [PMID: 34710308 PMCID: PMC8721881] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
INTRODUCTION Little is known about the role of school-aged children and household transmission at the start of the SARS-CoV-2 pandemic. To evaluate for SARS-CoV-2 in school-aged children and assess household transmission, we performed reverse transcription polymerase chain reaction on 670 archived specimens that were collected between September 1, 2019 and June 30, 2020 as part of a community-based study. CASE PRESENTATION A single SARS-CoV-2 case was detected in an 11-year-old girl on March 18, 2020, resulting in very low prevalence (0.15% [95% CI, 0.03-0.84]) in this population. This case was associated with SARS-CoV-2 detection in all other household members. Symptoms were reported as mild to moderate. Whole genome sequencing supported household transmission of near-identical viruses within the 19B clade. DISCUSSION This case represents the earliest known household cluster of SARS-CoV2 in Wisconsin. CONCLUSION This case suggests that household transmission associated with school-aged children may have contributed to wide seeding across populations.
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Affiliation(s)
- Jonathan L Temte
- University of Wisconsin School of Medicine and Public Health, Department of Family Medicine and Community Health, Madison, Wisconsin,
| | - Shari Barlow
- University of Wisconsin School of Medicine and Public Health, Department of Family Medicine and Community Health, Madison, Wisconsin
| | - Emily Temte
- University of Wisconsin School of Medicine and Public Health, Department of Family Medicine and Community Health, Madison, Wisconsin
| | - Maureen Goss
- University of Wisconsin School of Medicine and Public Health, Department of Family Medicine and Community Health, Madison, Wisconsin
| | - Kelsey Florek
- Wisconsin State Laboratory of Hygiene, Madison, Wisconsin
| | - Katarina M Braun
- University of Wisconsin School of Veterinary Medicine, Department of Pathobiological Sciences, Madison, Wisconsin
| | - Thomas C Friedrich
- University of Wisconsin School of Veterinary Medicine, Department of Pathobiological Sciences, Madison, Wisconsin
| | - Erik Reisdorf
- Wisconsin State Laboratory of Hygiene, Madison, Wisconsin
| | | | - Amra Uzicanin
- US Centers for Disease Control and Prevention, Atlanta, Georgia
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Gable P, Huang JY, Gilbert SE, Bollinger S, Lyons AK, Sabour S, Surie D, Biedron C, Haney T, Beshearse E, Gregory CJ, Seely KA, Clemmons NS, Patil N, Kothari A, Gulley T, Garner K, Anderson K, Thornburg NJ, Halpin AL, McDonald LC, Kutty PK, Brown AC. A Comparison of Less Invasive Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Diagnostic Specimens in Nursing Home Residents-Arkansas, June-August 2020. Clin Infect Dis 2021; 73:S58-S64. [PMID: 33909063 PMCID: PMC8135387 DOI: 10.1093/cid/ciab310] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Background SARS-CoV-2 testing remains essential for early identification and clinical management of cases. We compared the diagnostic performance of three specimen types for characterizing SARS-CoV-2 in infected nursing home residents. Methods A convenience sample of 17 residents were enrolled within 15 days of first positive SARS-CoV-2 result by real-time reverse transcription polymerase chain reaction (RT-PCR) and prospectively followed for 42 days. Anterior nasal swabs (AN), oropharyngeal swabs (OP), and saliva specimens (SA) were collected on the day of enrollment, every 3 days for the first 21 days, then weekly for 21 days. Specimens were tested for presence of SARS-CoV-2 RNA using RT-PCR and replication-competent virus by viral culture. Results Comparing the three specimen types collected from each participant at each time point, the concordance of paired RT-PCR results ranged from 80–88%. After the first positive result, SA and OP were RT-PCR–positive for ≤48 days; AN were RT-PCR–positive for ≤33 days. AN had the highest percentage of RT-PCR–positive results (81%; 21/26) when collected ≤10 days of participants’ first positive result. Eleven specimens were positive by viral culture: nine AN collected ≤19 days following first positive result and two OP collected ≤5 days following first positive result. Conclusions AN, OP, and SA were effective methods for repeated testing in this population. More AN than OP were positive by viral culture. SA and OP remained RT-PCR–positive longer than AN, which could lead to unnecessary interventions if RT-PCR detection occurred after viral shedding has likely ceased.
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Affiliation(s)
- Paige Gable
- COVID-19 Response Team, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Jennifer Y Huang
- COVID-19 Response Team, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Sarah E Gilbert
- COVID-19 Response Team, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Susan Bollinger
- COVID-19 Response Team, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Amanda K Lyons
- COVID-19 Response Team, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Sarah Sabour
- COVID-19 Response Team, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Diya Surie
- COVID-19 Response Team, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Caitlin Biedron
- COVID-19 Response Team, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Tafarra Haney
- Arkansas Department of Health, Little Rock, Arkansas, USA
| | - Elizabeth Beshearse
- COVID-19 Response Team, Centers for Disease Control and Prevention, Atlanta, Georgia, USA.,Epidemic Intelligence Service, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Christopher J Gregory
- COVID-19 Response Team, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | | | - Nakia S Clemmons
- COVID-19 Response Team, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Naveen Patil
- Arkansas Department of Health, Little Rock, Arkansas, USA
| | - Atul Kothari
- Arkansas Department of Health, Little Rock, Arkansas, USA
| | - Trent Gulley
- Arkansas Department of Health, Little Rock, Arkansas, USA
| | - Kelley Garner
- Arkansas Department of Health, Little Rock, Arkansas, USA
| | - Karen Anderson
- COVID-19 Response Team, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Natalie J Thornburg
- COVID-19 Response Team, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Alison L Halpin
- COVID-19 Response Team, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - L Clifford McDonald
- COVID-19 Response Team, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Preeta K Kutty
- COVID-19 Response Team, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Allison C Brown
- COVID-19 Response Team, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
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Kagan RM, Rogers AA, Borillo GA, Clarke NJ, Marlowe EM. Performance of Unobserved Self-Collected Nasal Swabs for Detection of SARS-CoV-2 by RT-PCR Utilizing a Remote Specimen Collection Strategy. Open Forum Infect Dis 2021; 8:ofab039. [PMID: 33954224 PMCID: PMC7928651 DOI: 10.1093/ofid/ofab039] [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: 01/22/2021] [Accepted: 01/25/2021] [Indexed: 12/23/2022] Open
Abstract
Background The use of a remote specimen collection strategy employing a kit designed for unobserved self-collection for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) reverse transcription polymerase chain reaction (RT-PCR) can decrease the use of personal protective equipment (PPE) and exposure risk. To assess the impact of unobserved specimen self-collection on test performance, we examined results from a SARS-CoV-2 qualitative RT-PCR test for self-collected specimens from participants in a return-to-work screening program and assessed the impact of a pooled testing strategy in this cohort. Methods Self-collected anterior nasal swabs from employee return-to-work programs were tested using the Quest Diagnostics Emergency Use Authorization SARS-CoV-2 RT-PCR. The cycle threshold (Ct) values for the N1 and N3 N-gene targets and a human RNase P (RP) gene control target were tabulated. For comparison, we utilized Ct values from a cohort of health care provider–collected specimens from patients with and without coronavirus disease 2019 symptoms. Results Among 47 923 participants, 1.8% were positive. RP failed to amplify for 13/115 435 (0.011%) specimens. The median (interquartile range) Cts were 32.7 (25.0–35.7) for N1 and 31.3 (23.8–34.2) for N3. Median Ct values in the self-collected cohort were significantly higher than those of symptomatic but not asymptomatic patients. Based on Ct values, pooled testing with 4 specimens would have yielded inconclusive results in 67/1268 (5.2%) specimens but only a single false-negative result. Conclusions Unobserved self-collection of nasal swabs provides adequate sampling for SARS-CoV-2 RT-PCR testing. These findings alleviate concerns of increased false negatives in this context. Specimen pooling could be used for this population, as the likelihood of false-negative results is very low when using a sensitive, dual-target methodology.
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Affiliation(s)
- Ron M Kagan
- Quest Diagnostics Infectious Disease, San Juan Capistrano, California, USA
| | - Amy A Rogers
- Quest Diagnostics Infectious Disease, San Juan Capistrano, California, USA
| | | | - Nigel J Clarke
- Quest Diagnostics Nichols Institute, San Juan Capistrano, California, USA
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