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Thampi N, Guzman-Cottrill J, Bartlett AH, Berg W, Cantey JB, Kitt E, Ravin K, Zangwill KM, Elward A. SHEA NICU white paper series: Practical approaches for the prevention of viral respiratory infections. Infect Control Hosp Epidemiol 2024; 45:267-276. [PMID: 37877172 DOI: 10.1017/ice.2023.120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2023]
Abstract
This white paper provides clinicians and hospital leaders with practical guidance on the prevention and control of viral respiratory infections in the neonatal intensive care unit (NICU). This document serves as a companion to Centers for Disease Control and Prevention Healthcare Infection Control Practices Advisory Committee (HICPAC)'s "Prophylaxis and Screening for Prevention of Viral Respiratory Infections in Neonatal Intensive Care Unit Patients: A Systematic Review." It provides practical, expert opinion and/or evidence-based answers to frequently asked questions about viral respiratory detection and prevention in the NICU. It was developed by a writing panel of pediatric and pathogen-specific experts who collaborated with members of the HICPAC systematic review writing panel and the SHEA Pediatric Leadership Council to identify questions that should be addressed. The document has been endorsed by SHEA, the American Hospital Association (AHA), The Joint Commission, the Pediatric Infectious Diseases Society (PIDS), the Association for Professionals in Infection Control and Epidemiology (APIC), the Infectious Diseases Society of America (IDSA), and the National Association of Neonatal Nurses (NANN).
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Affiliation(s)
- Nisha Thampi
- Children's Hospital of Eastern Ontario, Ottawa, Ontario, Canada
| | | | - Allison H Bartlett
- University of Chicago and Comer Children's Hospital, Chicago, Illinois, USA
| | - Wendy Berg
- Children's Minnesota, St. Paul, Minnesota, USA
| | - Joseph B Cantey
- The University of Texas Health Science Center, San Antonio, Texas, USA
| | - Eimear Kitt
- Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Karen Ravin
- Nemours Children's Health, Wilmington, Delaware, USA
| | | | - Alexis Elward
- Washington University School of Medicine, St. Louis, Missouri, USA
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Gill CJ, Mwananyanda L, MacLeod WB, Kwenda G, Pieciak R, Mupila Z, Murphy C, Chikoti C, Forman L, Berklein F, Lapidot R, Chimoga C, Ngoma B, Larson A, Lungu J, Nakazwe R, Nzara D, Pemba L, Yankonde B, Chirwa A, Mwale M, Thea DM. Infant deaths from respiratory syncytial virus in Lusaka, Zambia from the ZPRIME study: a 3-year, systematic, post-mortem surveillance project. Lancet Glob Health 2022; 10:e269-e277. [PMID: 35063114 PMCID: PMC8789563 DOI: 10.1016/s2214-109x(21)00518-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 10/22/2021] [Accepted: 10/25/2021] [Indexed: 12/13/2022]
Abstract
Background Respiratory syncytial virus (RSV) is the leading cause of acute lower respiratory tract infections and a key driver of childhood mortality. Previous RSV burden of disease estimates used hospital-based surveillance data and modelled, rather than directly measured, community deaths. Given this uncertainty, we conducted a 3-year post-mortem prevalence study among young infants at a busy morgue in Lusaka, Zambia—the Zambia Pertussis RSV Infant Mortality Estimation (ZPRIME) study. Methods Infants were eligible for inclusion if they were aged between 4 days and less than 6 months and were enrolled within 48 h of death. Enrolment occurred mainly at the University Teaching Hospital of the University of Zambia Medical School (Lusaka, Zambia), the largest teaching hospital in Zambia. We extracted demographic and clinical data from medical charts and official death certificates, and we conducted verbal autopsies with the guardian or next of kin. RSV was identified using reverse transcriptase quantitative PCR and stratified by age, time of year, and setting (community vs facility deaths). By combining the PCR prevalence data with syndromic presentation, we estimated the proportion of all infant deaths that were due to RSV. Findings The ZPRIME study ran from Aug 31, 2017, to Aug 31, 2020, except for from April 1 to May 6, 2020, during which data were not collected due to restrictions on human research at this time (linked to COVID-19). We enrolled 2286 deceased infants, representing 79% of total infant deaths in Lusaka. RSV was detected in 162 (7%) of 2286 deceased infants. RSV was detected in 102 (9%) of 1176 community deaths, compared with 10 (4%) of 236 early facility deaths (<48 h from admission) and 36 (5%) of 737 late facility deaths (≥48 h from admission). RSV deaths were concentrated in infants younger than 3 months (116 [72%] of 162 infants), and were clustered in the first half of each year and in the poorest and most densely populated Lusaka townships. RSV caused at least 2·8% (95% CI 1·0–4·6) of all infant deaths and 4·7% (1·3–8·1) of community deaths. Interpretation RSV was a major seasonal cause of overall infant mortality, particularly among infants younger than 3 months of age. Because most RSV deaths occurred in the community and would have been missed through hospital-based surveillance, the global burden of fatal RSV has probably been underestimated. Funding Bill & Melinda Gates Foundation.
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Affiliation(s)
- Christopher J Gill
- Department of Global Health, Boston University School of Public Health, Boston, MA, USA.
| | - Lawrence Mwananyanda
- Department of Global Health, Boston University School of Public Health, Boston, MA, USA; Right to Care Zambia, Lusaka, Zambia
| | - William B MacLeod
- Department of Global Health, Boston University School of Public Health, Boston, MA, USA
| | - Geoffrey Kwenda
- Department of Biomedical Sciences, School of Health Sciences, University of Zambia, Lusaka, Zambia
| | - Rachel Pieciak
- Department of Global Health, Boston University School of Public Health, Boston, MA, USA
| | | | | | | | - Leah Forman
- Biostatistics and Epidemiology Data Analytics Center, Boston University School of Public Health, Boston, MA, USA
| | - Flora Berklein
- Biostatistics and Epidemiology Data Analytics Center, Boston University School of Public Health, Boston, MA, USA
| | - Rotem Lapidot
- Department of Pediatrics, Boston University School of Medicine, Boston, MA, USA
| | | | | | - Anna Larson
- Department of Global Health, Boston University School of Public Health, Boston, MA, USA
| | | | | | | | | | | | - Angel Chirwa
- Department of Psychiatry, University Teaching Hospital, University of Zambia School of Medicine, Lusaka, Zambia
| | | | - Donald M Thea
- Department of Global Health, Boston University School of Public Health, Boston, MA, USA
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Nagasawa K, Ishiwada N. Disease burden of respiratory syncytial virus infection in the pediatric population in Japan. J Infect Chemother 2021; 28:146-157. [PMID: 34952776 DOI: 10.1016/j.jiac.2021.11.007] [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] [Received: 06/07/2021] [Revised: 09/22/2021] [Accepted: 11/11/2021] [Indexed: 11/18/2022]
Abstract
INTRODUCTION Respiratory syncytial virus (RSV) is one of the most common causes of lower respiratory tract infections in children aged <5 years and is associated with long-term respiratory morbidities such as recurrent wheezing and asthma, decreased lung function, and allergic sensitization. The objective of this review was to evaluate the epidemiology and burden of RSV infection in the pediatric population in Japan. METHODS Studies indexed in PubMed and ICHUSHI databases during January 2010-December 2020 were manually reviewed. Data on proportion of RSV infections, seasonality, length of stay (LoS), mortality, medical expenses, and palivizumab use were extracted from the selected articles. RESULTS Ninety-three articles were included (PubMed, 64; ICHUSHI, 29). The proportion of patients/samples with an RSV infection was 5.5%-66.7%, and 6.0%-29.9% in the inpatient and outpatient departments, respectively. RSV infections generally occurred during autumn/winter; however, recently the peak has shifted to summer. The LoS was variable and depended on factors such as age, infection severity, wheezing, and RSV subgroups. Mortality rates varied from <1% to 19% depending on the infection severity. The average daily hospitalization and intensive care unit cost was JPY 34,548 while intensive care unit incurred an additional cost of JPY 541,293. Palivizumab was indicated for high-risk infants and 0%-3% of patients required hospitalization despite palivizumab use. CONCLUSIONS RSV imposes a significant burden on the Japanese healthcare system, suggesting a need to create awareness among caregivers of children, pregnant women and healthcare professionals to ensure early recognition of infection and adequate treatment or prophylaxis.
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Affiliation(s)
- Koo Nagasawa
- Division of Infectious Diseases, Chiba Children's Hospital, 579-1, Heta-cho, Midori-ku, Chiba 266-0007, Japan; Laboratory of Cancer Genetics, Chiba Cancer Center Research Institute, 666-2, Nitona-cho, Chuo-ku, Chiba 260-8717, Japan.
| | - Naruhiko Ishiwada
- Department of Infectious Diseases, Medical Mycology Research Center, Chiba University, 1-8-1, Inohana, Chuo-ku, Chiba-shi, Chiba 260-8673, Japan
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Simmonds P, Williams S, Harvala H. Understanding the outcomes of COVID-19 - does the current model of an acute respiratory infection really fit? J Gen Virol 2021; 102:001545. [PMID: 33331810 PMCID: PMC8222868 DOI: 10.1099/jgv.0.001545] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Accepted: 12/01/2020] [Indexed: 12/11/2022] Open
Abstract
Although coronavirus disease 2019 (COVID-19) is regarded as an acute, resolving infection followed by the development of protective immunity, recent systematic literature review documents evidence for often highly prolonged shedding of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in respiratory and faecal samples, periodic recurrence of PCR positivity in a substantial proportion of individuals and increasingly documented instances of reinfection associated with a lack of protective immunity. This pattern of infection is quite distinct from the acute/resolving nature of other human pathogenic respiratory viruses, such as influenza A virus and respiratory syncytial virus. Prolonged shedding of SARS-CoV-2 furthermore occurs irrespective of disease severity or development of virus-neutralizing antibodies. SARS-CoV-2 possesses an intensely structured RNA genome, an attribute shared with other human and veterinary coronaviruses and with other mammalian RNA viruses such as hepatitis C virus. These are capable of long-term persistence, possibly through poorly understood RNA structure-mediated effects on innate and adaptive host immune responses. The assumption that resolution of COVID-19 and the appearance of anti-SARS-CoV-2 IgG antibodies represents virus clearance and protection from reinfection, implicit for example in the susceptible-infected-recovered (SIR) model used for epidemic prediction, should be rigorously re-evaluated.
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Affiliation(s)
- Peter Simmonds
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Sarah Williams
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Heli Harvala
- National Microbiology Services, NHS Blood and Transplant, London, UK
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Abstract
Infections caused by respiratory viruses in neonates during their stay in the neonatal intensive care unit (NICU) are more frequent than generally suspected. Respiratory syncytial virus (RSV), a highly contagious pathogen, is the most common etiologic agent, and it carries a high risk of nosocomial spread. During the RSV season, overcrowding of the NICU, shortage of staff, and unrestricted visitors are factors predisposing outbreaks. Since signs and symptoms of RSV infections are no specific, a high index of suspicion is essential to prevent or limit epidemics. The etiologic agent should be confirmed and polymerase chain reaction (PCR) is the gold-standard test. Shedding of the virus by infected preterm infants is prolonged and RSV lasts for several hours on countertops and other surfaces. The first case should be isolated and strict cohorting must be instituted. Compliance with hand washing must be warranted. Wearing gowns and gloves may help. The severity of nosocomial RSV infections tends to be higher than that of those community acquired. There is no uniform recommendation to start palivizumab during hospital stay of premature and high-risk infants. The use of this monoclonal antibody to stop or limit the spread of outbreaks is controversial. It is recommended by some professional organizations and not by others but its use during large outbreaks in infants at risk who share the room with infected neonates is not uncommon. KEY POINTS: · During peak community epidemic, NICU outbreaks of RSV infections are not uncommon.. · High index of suspicion is essential as initial signs are nonspecific in preterm neonates.. · Isolation and cohorting, strict hand washing, gowns, gloves, and eventually palivizumab are main tools for management..
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Affiliation(s)
- Nestor E Vain
- FUNDASAMIN, Foundation for Maternal Infant Health, Buenos Aires, Argentina.,Newborn Medicine, Hospitals Sanatorio Trinidad Palermo, San Isidro and Ramos Mejía, Buenos Aires, Argentina.,Department of Pediatrics, School of Medicine, University of Buenos Aires, Buenos Aires, Argentina
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Ganzenmueller T, Kaiser R, Baier C, Wehrhane M, Hilfrich B, Witthuhn J, Flucht S, Heim A. Comparison of the performance of the Panther Fusion respiratory virus panel to R-Gene and laboratory developed tests for diagnostic and hygiene screening specimens from the upper and lower respiratory tract. J Med Microbiol 2020; 69:427-435. [DOI: 10.1099/jmm.0.001133] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Introduction. Diagnosis of acute respiratory infections (ARIs) can be facilitated by the Panther Fusion (PF) automatic, random access PCR system for the detection of influenzavirus A (Flu A) and B (Flu B), parainfluenzavirus (Paraflu), respiratory syncytial virus (RSV), human metapneumovirus (hMPV), rhinovirus (RV) and human adenovirus (AdV) in nasopharyngeal swabs.
Aim. To evaluate the performance of PF in comparison with established methods, including subsets of (1) lower respiratory tract (LRT) specimens and (2) upper respiratory tract (URT) hygiene screening specimens of patients without ARI symptoms.
Methodology. The performance characteristics of PF were compared with bioMérieux R-Gene and laboratory-developed PCR tests (LDTs). Overall, 1544 specimens with 6658 individual diagnostic requests were analysed.
Results. The overall concordances of PF and LDTs for Flu A, Flu B and AdV were 98.4, 99.9 and 96.1%, respectively; by re-testing of discrepant specimens concordances increased to 99.4, 99.9 and 98.0%, respectively. Initial concordances of PF and R-Gene assays for RSV, Paraflu, hMPV and RV were 98.4, 96.3, 99.3 and 96.0%, respectively, and retest concordances were 99.7, 97.9, 99.9 and 98.9%, respectively. No differences to the overall performance were found for the subgroups of LRT and hygiene screening specimens. PCR cycle threshold (Ct) values correlated very well between methods, indicating that a semi-quantitative diagnostic approach using Ct values (e.g. highly vs. weakly positive) could augment the diagnostic information.
Conclusion. PF performed similar to R-Gene and LDTs not only for its intended use but also for LRT and hygiene screening specimens with shorter hands-on and turnaround times.
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Affiliation(s)
- Tina Ganzenmueller
- Institute for Medical Virology, University Hospital Tuebingen, Tuebingen, Germany
- Institute for Virology, Hannover Medical School, Hannover, Germany
| | - Rolf Kaiser
- Institute for Virology, University Hospital Cologne, Cologne, Germany
| | - Claas Baier
- Institute for Medical Microbiology and Hospital Epidemiology, Hannover Medical School, Hannover, Germany
| | - Marlies Wehrhane
- Institute for Virology, Hannover Medical School, Hannover, Germany
| | | | - Jenny Witthuhn
- Institute for Virology, Hannover Medical School, Hannover, Germany
| | - Sandra Flucht
- Institute for Virology, Hannover Medical School, Hannover, Germany
| | - Albert Heim
- Institute for Virology, Hannover Medical School, Hannover, Germany
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González-Parra G, Dobrovolny HM. The rate of viral transfer between upper and lower respiratory tracts determines RSV illness duration. J Math Biol 2019; 79:467-483. [PMID: 31011792 DOI: 10.1007/s00285-019-01364-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Revised: 04/11/2019] [Indexed: 12/26/2022]
Abstract
Respiratory syncytial virus can lead to serious lower respiratory infection (LRI), particularly in children and the elderly. LRI can cause longer infections, lingering respiratory problems, and higher incidence of hospitalization. In this paper, we use a simplified ordinary differential equation model of viral dynamics to study the role of transport mechanisms in the occurrence of LRI. Our model uses two compartments to simulate the upper respiratory tract and the lower respiratory tract (LRT) and assumes two distinct types of viral transfer between the two compartments: diffusion and advection. We find that a range of diffusion and advection values lead to long-lasting infections in the LRT, elucidating a possible mechanism for the severe LRI infections observed in humans.
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Practical Guidance for Clinical Microbiology Laboratories: Viruses Causing Acute Respiratory Tract Infections. Clin Microbiol Rev 2018; 32:32/1/e00042-18. [PMID: 30541871 DOI: 10.1128/cmr.00042-18] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Respiratory viral infections are associated with a wide range of acute syndromes and infectious disease processes in children and adults worldwide. Many viruses are implicated in these infections, and these viruses are spread largely via respiratory means between humans but also occasionally from animals to humans. This article is an American Society for Microbiology (ASM)-sponsored Practical Guidance for Clinical Microbiology (PGCM) document identifying best practices for diagnosis and characterization of viruses that cause acute respiratory infections and replaces the most recent prior version of the ASM-sponsored Cumitech 21 document, Laboratory Diagnosis of Viral Respiratory Disease, published in 1986. The scope of the original document was quite broad, with an emphasis on clinical diagnosis of a wide variety of infectious agents and laboratory focus on antigen detection and viral culture. The new PGCM document is designed to be used by laboratorians in a wide variety of diagnostic and public health microbiology/virology laboratory settings worldwide. The article provides guidance to a rapidly changing field of diagnostics and outlines the epidemiology and clinical impact of acute respiratory viral infections, including preferred methods of specimen collection and current methods for diagnosis and characterization of viral pathogens causing acute respiratory tract infections. Compared to the case in 1986, molecular techniques are now the preferred diagnostic approaches for the detection of acute respiratory viruses, and they allow for automation, high-throughput workflows, and near-patient testing. These changes require quality assurance programs to prevent laboratory contamination as well as strong preanalytical screening approaches to utilize laboratory resources appropriately. Appropriate guidance from laboratorians to stakeholders will allow for appropriate specimen collection, as well as correct test ordering that will quickly identify highly transmissible emerging pathogens.
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Pathogen Clearance and New Respiratory Tract Infections Among Febrile Children in Zanzibar Investigated With Multitargeting Real-Time Polymerase Chain Reaction on Paired Nasopharyngeal Swab Samples. Pediatr Infect Dis J 2018; 37:643-648. [PMID: 29889810 DOI: 10.1097/inf.0000000000001876] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
BACKGROUND New molecular methods have revealed frequent and often polymicrobial respiratory infections in children in low-income settings. It is not known whether presence of multiple pathogens is due to prolonged infections or to frequent exposure. The aim of this study was to analyze short-term pathogen clearance from nasopharynx and the rate of new respiratory tract infections in febrile preschool children. METHODS Children (n = 207) with uncomplicated acute febrile illness 2-59 months of age presenting to a health center in Zanzibar, Tanzania, April-July 2011, were included. Paired nasopharyngeal swab samples, collected at enrolment and after 14 days, were analyzed by multiple real-time polymerase chain reaction for Adenovirus, bocavirus, Bordetella pertussis, Chlamydophila pneumoniae, Coronaviruses, Enterovirus, influenza A and B virus, metapneumovirus, measles virus, Mycoplasma pneumoniae, parainfluenza virus, Parechovirus, respiratory syncytial virus and Rhinovirus. An age-matched and geographically matched healthy control group (n = 166) underwent nasopharyngeal sampling on 1 occasion. RESULTS At baseline, 157/207 (76%) patients had at least 1 pathogen detected, in total 199 infections. At follow-up (day 14), 162/199 (81%) of these infections were not detected, including >95% of the previously detected infections with Enterovirus, influenza A virus, influenza B virus, metapneumovirus or parainfluenza virus. Still 115 (56%) children were positive for at least 1 pathogen at follow-up, of which 95/115 (83%) were not found at baseline. Detection of influenza B on day 14 was significantly associated with fever during follow-up. CONCLUSION The results suggest that children with acute febrile illness in Zanzibar rapidly clear respiratory tract infections but frequently acquire new infections within 14 days.
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Measurements of Intrahost Viral Diversity Are Extremely Sensitive to Systematic Errors in Variant Calling. J Virol 2016; 90:6884-95. [PMID: 27194763 DOI: 10.1128/jvi.00667-16] [Citation(s) in RCA: 91] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2016] [Accepted: 05/11/2016] [Indexed: 12/22/2022] Open
Abstract
UNLABELLED With next-generation sequencing technologies, it is now feasible to efficiently sequence patient-derived virus populations at a depth of coverage sufficient to detect rare variants. However, each sequencing platform has characteristic error profiles, and sample collection, target amplification, and library preparation are additional processes whereby errors are introduced and propagated. Many studies account for these errors by using ad hoc quality thresholds and/or previously published statistical algorithms. Despite common usage, the majority of these approaches have not been validated under conditions that characterize many studies of intrahost diversity. Here, we use defined populations of influenza virus to mimic the diversity and titer typically found in patient-derived samples. We identified single-nucleotide variants using two commonly employed variant callers, DeepSNV and LoFreq. We found that the accuracy of these variant callers was lower than expected and exquisitely sensitive to the input titer. Small reductions in specificity had a significant impact on the number of minority variants identified and subsequent measures of diversity. We were able to increase the specificity of DeepSNV to >99.95% by applying an empirically validated set of quality thresholds. When applied to a set of influenza virus samples from a household-based cohort study, these changes resulted in a 10-fold reduction in measurements of viral diversity. We have made our sequence data and analysis code available so that others may improve on our work and use our data set to benchmark their own bioinformatics pipelines. Our work demonstrates that inadequate quality control and validation can lead to significant overestimation of intrahost diversity. IMPORTANCE Advances in sequencing technology have made it feasible to sequence patient-derived viral samples at a level sufficient for detection of rare mutations. These high-throughput, cost-effective methods are revolutionizing the study of within-host viral diversity. However, the techniques are error prone, and the methods commonly used to control for these errors have not been validated under the conditions that characterize patient-derived samples. Here, we show that these conditions affect measurements of viral diversity. We found that the accuracy of previously benchmarked analysis pipelines was greatly reduced under patient-derived conditions. By carefully validating our sequencing analysis using known control samples, we were able to identify biases in our method and to improve our accuracy to acceptable levels. Application of our modified pipeline to a set of influenza virus samples from a cohort study provided a realistic picture of intrahost diversity and suggested the need for rigorous quality control in such studies.
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