Journal: NPJ Genomic Medicine

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

doi: 10.1038/s41525-017-0033-4

Figure Lengend Snippet: Detection of a 548-nucleotide deletion in a HCoV 229E strain associated with myeloablation. a Depiction of the case history surrounding myeloablation and coronavirus infection. A woman in her 40s with AML was found to be infected with a HCoV 229E just before her HCT. Due to the patient’s advanced disease, the decision was made to continue with the transplant. Four successive HCoV-positive nasal swab specimens were available from the patient; two from before treatment with myeloablative cyclophosphamide and total body irradiation and two from after. All days are reported relative to HCT. b Coverage plots of mNGS reads mapped to the reference genome for HCoV 229E (NC_002645) of three samples from the patient revealed the generation of a 548-nucleotide deletion in the ORF4a/4b gene. In addition to deleting 83% of the coding region from ORF4a/4b, the deletion resulted in a frame shift that resulted in a premature stop codon 10 amino acids before the reference genome stop codon. Primer binding sites are denoted in blue for confirmatory junction RT-PCR. c Confirmatory junction RT-PCR of the four available HCoV-positive nasal swabs revealed the absence of the deletion before myeloablation and the presence of the deletion in specimens taken after myeloablation. NTC , no template control

Article Snippet: No CPE was visualized for any of the patient’s four clinical samples and HCoV 229E RNA levels in the culture supernatant were undetectable by qRT-PCR after inoculation, while viral growth was apparent in the positive control HCoV 229E ATCC type strain (Figure ).

Techniques: Infection, Irradiation, Binding Assay, Reverse Transcription Polymerase Chain Reaction, Control

Journal: NPJ Genomic Medicine

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

doi: 10.1038/s41525-017-0033-4

Figure Lengend Snippet: Specimens sequenced in this study

Article Snippet: No CPE was visualized for any of the patient’s four clinical samples and HCoV 229E RNA levels in the culture supernatant were undetectable by qRT-PCR after inoculation, while viral growth was apparent in the positive control HCoV 229E ATCC type strain (Figure ).

Techniques: