Human coronavirus (HCoV) among other respiratory diseases, is associated with increased mortality in hematopoietic cell transplant (HCT) recipients. These diseases are associated with prolonged viral shedding allowing viral spread and higher rates of lower respiratory tract disease in these immunocompromised populations. Therefore, it is important to create effective preventions diagnostics, and therapeutics against these viruses. In order to do this, the field needs more information on host virus interactions including viral load, shedding and genome evolution within a host. Better understanding of these factors could lead to better vaccine design and thus, protection for HCT recipients where mortality is increased with HCoV infection. A collaborative effort including researchers from Fred Hutch (Vaccine and Infectious Disease Division) used modern virological assays to identify HCT recipients positive for HCoV and studied the viral and host factors at play during infection in a work recently published in The Journal of Infectious Diseases.
By collecting nasal samples from HCT recipients the group identified 44 HCT recipients with respiratory HCoV by viral strain specific PCR. The group could differentiate four strains of HCoV in the samples including OC43 (35%), NL63 (32%), 229E (13%), and HKU1 (19%). However, of the 31 samples they were unable to type 13 samples (30%) to the exact strain. Along with strain identification the group examined at viral shedding. To identify the duration of shedding in a recipient, nasal samples were collected and tested by PCR. Duration of viral shedding was measured from the first positive sample to the first negative sample. Overall the median length of viral shedding was 14 days and the duration did not differ between viral strains. There were 17 long term shedders identified in the group having a duration of 21 days or more.
Univariable and bivariable logistic regression analyses were performed to elucidate host viral factors associated with prolonged shedding. Analyses indicated that initial high viral load was associated with the prolonged shedding. Prolonged shedding was also associated with both high-dose steroid use prior to HCoV diagnosis and myeloablative conditioning regimen. In addition to viral shedding, whole genome sequencing was completed on samples from 5 HCT recipients where samples were available from day 19 to 132 following the first positive sample. This was done to look for intrahost genomic variability. No consensus variants were found less than 30 days after shedding. Single-nucleotide variants did accumulate at a rate of one variant per 3-4 weeks, however this is consistent with HCoV molecular clock estimates.
Overall, this study is the first to evaluate risk factors from prolonged HCoV shedding in HCT recipients as well as evaluating samples over time for intrahost genomic evolution by sequencing. The authors found an association with initial high viral load, steroid use, and myeloabalative conditioning regimen with prolonged shedding. By following the viral genome over time in multiple recipients, the group found an expected rate of genome changes suggesting there was no accelerated viral evolution taking place in immunocompromised population with prolonged shedding. This slow evolution is promising for therapeutic development and antiviral resistance.
Funding was provided by the National Institutes of Health and Fred Hutch.
Ogimi C, Greninger AL, Waghmare AA, Kuypers JM, Shean RC,Xie H, Leisenring WM, Stevens-Ayers TL, Jerome KR, Englund JA, Boeckh M. 2017. Prolonged Shedding of Human Coronavirus in Hematopoietic Cell Transplant Recipients: Risk Factors and Viral Genome Evolution. Journal of Infectious Diseases, 216(2), 203-209.