Prolonged Shedding of Human Coronavirus in Hematopoietic Cell Transplant Recipients: Risk Factors and Viral Genome Evolution

Ogimi, Chikara; Greninger, Alexander L.; Waghmare, Alpana; Kuypers, Jane; Shean, Ryan C.; Xie, Hu; Leisenring, Wendy; Stevens-Ayers, Terry; Jerome, Keith R.; Englund, Janet A.; Boeckh, Michael

doi:10.1093/infdis/jix264

Cited by 70 publications

(77 citation statements)

References 33 publications

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“…In immunocompetent individuals they usually infect the upper respiratory tract, where they are mainly associated with 15-30% of upper respiratory tract infections (URI): rhinitis, laryngitis/pharyngitis as well as otitis. Being highly opportunistic pathogens [14], HCoV can reach the lower respiratory tract and be associated with more severe illnesses, such as bronchitis, bronchiolitis, pneumonia, exacerbations of asthma and respiratory distress syndrome [17,31,[208][209][210][211][212][213][214].…”

Section: Human Coronaviruses: Eclosions Of Recognized Respiratory Patmentioning

confidence: 99%

Human Coronaviruses and Other Respiratory Viruses: Underestimated Opportunistic Pathogens of the Central Nervous System?

Desforges

Coupanec

Dubeau

et al. 2019

Viruses

940

997

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Respiratory viruses infect the human upper respiratory tract, mostly causing mild diseases. However, in vulnerable populations, such as newborns, infants, the elderly and immune-compromised individuals, these opportunistic pathogens can also affect the lower respiratory tract, causing a more severe disease (e.g., pneumonia). Respiratory viruses can also exacerbate asthma and lead to various types of respiratory distress syndromes. Furthermore, as they can adapt fast and cross the species barrier, some of these pathogens, like influenza A and SARS-CoV, have occasionally caused epidemics or pandemics, and were associated with more serious clinical diseases and even mortality. For a few decades now, data reported in the scientific literature has also demonstrated that several respiratory viruses have neuroinvasive capacities, since they can spread from the respiratory tract to the central nervous system (CNS). Viruses infecting human CNS cells could then cause different types of encephalopathy, including encephalitis, and long-term neurological diseases. Like other well-recognized neuroinvasive human viruses, respiratory viruses may damage the CNS as a result of misdirected host immune responses that could be associated with autoimmunity in susceptible individuals (virus-induced neuro-immunopathology) and/or viral replication, which directly causes damage to CNS cells (virus-induced neuropathology). The etiological agent of several neurological disorders remains unidentified. Opportunistic human respiratory pathogens could be associated with the triggering or the exacerbation of these disorders whose etiology remains poorly understood. Herein, we present a global portrait of some of the most prevalent or emerging human respiratory viruses that have been associated with possible pathogenic processes in CNS infection, with a special emphasis on human coronaviruses.

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Section: Human Coronaviruses: Eclosions Of Recognized Respiratory Patmentioning

confidence: 99%

Human Coronaviruses and Other Respiratory Viruses: Underestimated Opportunistic Pathogens of the Central Nervous System?

Desforges

Coupanec

Dubeau

et al. 2019

Viruses

940

997

View full text Add to dashboard Cite

show abstract

“…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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“…The symptoms associated with CoV infection were first described over four decades ago [1], and can range from relatively mild upper-to more severe lower-respiratory tract infections with increased severity in certain patient populations [1,2]. It has been reported that immunocompromised patients, particularly hematopoietic cell transplant recipients, are at increased risk of lower respiratory tract infections, prolonged viral shedding and mortality, often comparable to what is seen with influenza virus [3,4]. Similar to other non-influenza respiratory viruses, CoVs are still relatively understudied despite being a common cause of hospital-and community-acquired respiratory infection [5,6].…”

Section: Introductionmentioning

confidence: 99%

Severity of coronavirus respiratory tract infections in adults admitted to acute care in Toronto, Ontario

Kozak

Prost

Yip

et al. 2020

Journal of Clinical Virology

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Background: The World Health Organization has highlighted the need for improved surveillance and understanding of the health burden imposed by non-influenza RNA respiratory viruses. Human coronaviruses (CoVs) are a major cause of respiratory and gastrointestinal tract infections with associated morbidity and mortality. Objectives: The objective of our study was to characterize the epidemiology of CoVs in our tertiary care centre, and identify clinical correlates of disease severity. Study design: A cross-sectional study was performed of 226 patients admitted with confirmed CoV respiratory tract infection between 2010 and 2016. Variables consistent with a severe disease burden were evaluated including symptoms, length of stay, intensive care unit (ICU) admission and mortality. Results: CoVs represented 11.3% of all positive respiratory virus samples and OC43 was the most commonly identified CoV. The majority of infections were community-associated while 21.6% were considered nosocomial. The average length of stay was 11.8 days with 17.3% of patients requiring ICU admission and an all-cause mortality of 7%. In a multivariate model, female gender and smoking were associated with increased likelihood of admission to ICU or death. Conclusion: This study highlights the significant burden of CoVs and justifies the need for surveillance in the acute care setting.

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Prolonged Shedding of Human Coronavirus in Hematopoietic Cell Transplant Recipients: Risk Factors and Viral Genome Evolution

Abstract: High viral load, high-dose steroids, and myeloablative conditioning were associated with prolonged shedding of HCoV in HCT recipients. Genome changes were consistent with the expected molecular clock of HCoV.

Cited by 70 publications

References 33 publications

Human Coronaviruses and Other Respiratory Viruses: Underestimated Opportunistic Pathogens of the Central Nervous System?

Human Coronaviruses and Other Respiratory Viruses: Underestimated Opportunistic Pathogens of the Central Nervous System?

A decade of RNA virus metagenomics is (not) enough

Severity of coronavirus respiratory tract infections in adults admitted to acute care in Toronto, Ontario

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