Myeloablation-associated deletion of ORF4 in a human coronavirus 229E infection

Greninger, Alexander L.; Pepper, Gregory; Shean, Ryan C.; Cent, Anne; Palileo, Isabel; Kuypers, Jane; Schiffer, Joshua T.; Jerome, Keith R.

doi:10.1038/s41525-017-0033-4

Cited by 7 publications

(4 citation statements)

References 27 publications

(23 reference statements)

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“…Reverse transcription-PCR (RT-PCR) was performed using 35 cycles of the default parameters (melting temperature [ T m ], 55°C) in the One-Step RT-PCR kit (Qiagen) with PCR primers HPIV3-7477F (F stands for forward) (5′-TACAGATAGGGATAATAACTGTAAA-3′) and HPIV3-8635R (R stands for reverse) (5′-GCTTTGCTCCTAAGTTTTTTATATT-3′). Amplicons were purified using 1.0× Ampure beads, and dual-indexed TruSeq libraries were prepared using the Kapa HyperPrep kit with eight cycles of PCR amplification ( 52 ).…”

Section: Methodsmentioning

confidence: 99%

Viral Entry Properties Required for Fitness in Humans Are Lost through Rapid Genomic Change during Viral Isolation

Iketani

Shean

Ferren

et al. 2018

mBio

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IMPORTANCEHuman parainfluenza virus 3 is an important cause of morbidity and mortality among infants, the immunocompromised, and the elderly. Using deep genomic sequencing of HPIV-3-positive clinical material and its subsequent viral isolate, we discover a number of known and novel coding mutations in the main HPIV-3 attachment protein HN during brief exposure to immortalized cells. These mutations significantly alter function of the fusion complex, increasing fusion promotion by HN as well as generally decreasing neuraminidase activity and increasing HN-receptor engagement. These results show that viruses may evolve rapidly in culture even during primary isolation of the virus and before the first passage and reveal features of fitness for humans that are obscured by rapid adaptation to laboratory conditions.

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Section: Methodsmentioning

confidence: 99%

Viral Entry Properties Required for Fitness in Humans Are Lost through Rapid Genomic Change during Viral Isolation

Iketani

Shean

Ferren

et al. 2018

mBio

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“…De novo assembly methods that allow for the rapid reconstruction of near complete genomes have also dramatically improved over the past decade and can handle widely disparate coverage for each contig (Grabherr et al, 2011;Bankevich et al, 2012). All of these properties often make metagenomics the first method of choice when trying to recover sequence from even a known RNA virus (Greninger et al, 2017a;Ogimi et al, 2017).…”

Section: Diversitymentioning

confidence: 99%

A decade of RNA virus metagenomics is (not) enough

2018

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It is hard to overemphasize the role that metagenomics has had on our recent understanding of RNA virus diversity. Metagenomics in the 21st century has brought with it an explosion in the number of RNA virus species, genera, and families far exceeding that following the discovery of the microscope in the 18th century for eukaryotic life or culture media in the 19th century for bacteriology or the 20th century for virology. When the definition of success in organism discovery is measured by sequence diversity and evolutionary distance, RNA viruses win. This review explores the history of RNA virus metagenomics, reasons for the successes so far in RNA virus metagenomics, and methodological concerns. In addition, the review briefly covers clinical metagenomics and environmental metagenomics and highlights some of the critical accomplishments that have defined the fast pace of RNA virus discoveries in recent years. Slightly more than a decade in, the field is exhausted from its discoveries but knows that there is yet even more out there to be found.

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“…2014 ). Explicit patient consent to share such data may also be obtained, although blanket consent forms often include provisions that patient data will be anonymized before release ( Greninger et al. 2017d ).…”

Section: Discussionmentioning

confidence: 99%

Private collection: high correlation of sample collection and patient admission date in clinical microbiological testing complicates sharing of phylodynamic metadata

Shean

Greninger

2018

Virus Evolution

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Infectious pathogens are known for their rapid evolutionary rates with new mutations arising over days to weeks. The ability to rapidly recover whole genome sequences and analyze the spread and evolution of pathogens using genetic information and pathogen collection dates has lead to interest in real-time tracking of infectious transmission and outbreaks. However, the level of temporal resolution afforded by these analyses may conflict with definitions of what constitutes protected health information (PHI) and privacy requirements for de-identification for publication and public sharing of research data and metadata. In the United States, dates and locations associated with patient care that provide greater resolution than year or the first three digits of the zip code are generally considered patient identifiers. Admission and discharge dates are specifically named as identifiers in Department of Health and Human Services guidance. To understand the degree to which one can impute admission dates from specimen collection dates, we examined sample collection dates and patient admission dates associated with more than 270,000 unique microbiological results from the University of Washington Laboratory Medicine Department between 2010 and 2017. Across all positive microbiological tests, the sample collection date exactly matched the patient admission date in 68.8% of tests. Collection dates and admission dates were identical from emergency department and outpatient testing 86.7% and 96.5% of the time, respectively, with >99% of tests collected within 1 day from the patient admission date. Samples from female patients were significantly more likely to be collected closer to admission date that those from male patients. We show that PHI-associated dates such as admission date can confidently be imputed from deposited collection date. We suggest that publicly depositing microbiological collection dates at greater resolution than the year may not meet routine Safe Harbor-based requirements for patient de-identification. We recommend the use of Expert Determination to determine PHI for a given study and/or direct patient consent if clinical laboratories or phylodynamic practitioners desire to make these data available.

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Myeloablation-associated deletion of ORF4 in a human coronavirus 229E infection

Cited by 7 publications

References 27 publications

Viral Entry Properties Required for Fitness in Humans Are Lost through Rapid Genomic Change during Viral Isolation

Viral Entry Properties Required for Fitness in Humans Are Lost through Rapid Genomic Change during Viral Isolation

A decade of RNA virus metagenomics is (not) enough

Private collection: high correlation of sample collection and patient admission date in clinical microbiological testing complicates sharing of phylodynamic metadata

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