Diagnosis of cytomegalovirus infection from clinical whole genome sequencing

Abstract

Rapid whole genome sequencing (rWGS) of peripheral blood has been used to detect microbial DnA in acute infections. cytomegalovirus (cMV) is a herpesvirus capable of causing severe disease in neonates and immunocompromised patients. We identified CMV in patients undergoing diagnostic rWGS by matching reads that did not align to the human reference genome to a database of microbial genomes. rWGS was conducted on peripheral blood obtained from ill pediatric patients (age 1 day to 18 years). Reads not aligning to the human genome were analyzed using an in-house pipeline to identify DNA consistent with CMV infection. Of 669 patients who received rWGS from July 2016 through July 2019, we identified 28 patients (4.2%) with reads that aligned to the CMV reference genome. Six of these patients had clinical findings consistent with symptomatic CMV infection. positive results were highly correlated (R 2 > 0.99, p < 0.001) to a CMV-qPCR assay conducted on DNA isolated from whole blood samples. in acutely ill children receiving rWGS for diagnosis of genetic disease, we propose analysis of patient genetic data to identify cMV, which could impact treatment of up to 4% of children in the intensive care unit. Rapid whole genome sequencing (rWGS) of peripheral blood can rapidly diagnose genetic diseases and impact clinical care within 24 h 1,2. A recent study showed a diagnosis rate of 43% in critically ill patients with a resultant change in management in 33% of patients 1. rWGS allows clinicians to make actionable diagnoses in critically ill patients who may have an underpinning genetic or metabolic disease and is increasingly becoming a part of standard care. The concept of applying rWGS to detect infectious pathogens has also been utilized 3-6. While plasma polymerase chain reaction (PCR) is often used for detection of infectious organisms, we theorized that an advantage of sequencing whole blood is that organisms that reside intracellularly within white blood cells are included in rWGS reads. Cytomegalovirus (CMV) is human herpesvirus 5 (HHV-5) and capable of causing disease in critically ill patients 7. It can be found both intracellularly and extracellularly in humans. CMV can cause hepatitis, marrow suppression (including thrombocytopenia), encephalitis, retinitis, and pneumonitis. In neonates, CMV may also manifest as growth restriction, microcephaly, neurologic defects (including sensorineural hearing loss), and intellectual disability. Prevalence of congenital CMV ranges from 0.2 to 2.0% of pregnancies. Although most infected infants will have only latent infection without any sequelae, up to 12%representing approximately 9,600 children per year in the United States-will experience neurological sequelae related to congenital CMV infection 8. Recent studies have demonstrated improved outcomes in neonates with congenitally acquired CMV infection if antiviral treatment is started within the first 30 days of life 9. Identifying CMV infection in critically ill children who are undergoing rWGS has the potential to significan...

Rapid genomic sequencing for genetic disease diagnosis and therapy in intensive care units: a review

“…One study aligned RGS reads to reference pathogen genomes as well as the reference human genome, enabling metagenomic diagnosis of infectious diseases 38 . As has been observed in case reports, pathogens were identified in 6 (3%) of 202 infants, each of whom had symptoms of sepsis, and guided antibiotic treatment 13 , 38 , 47 . Since sepsis is suspected in many NICU infants at time of admission, the addition of this simple additional bioinformatic step is likely to become generally adopted.…”

“…Fourth the sequence fragments (reads) are mapped to a reference human genome and ~5 million variants are identified and genotyped (30 min). For metagenomic pathogen detection, reads are also mapped to a collection of pathogen genomes 13 , 47 , 48 . Fifth, each variant is annotated with results of a batch of over twenty automated software tools and variants (or variant diplotypes) are rank ordered in terms of predicted pathogenicity (20 min) 12 , 14 .…”

An Overview of Cytomegalovirus Infection in Pregnancy

“…The symptoms can be absent or mild, and they include a fever, commonly of unknown origin; rashes; pharyngitis; and lymphadenopathy. Paraclinical findings may show leukocytosis, anemia, thrombocytopenia, increased liver enzymes, and occasionally abnormal immune antibodies [ 12 ]. CMV infection can also cause pneumonia, encephalitis, neuropathy, hepatitis, posterior poll eye damage, digestive and urinary tract disease, and other conditions [ 1 , 2 ].…”

Ultra‐rapid whole genome sequencing: A paradigm shift in the pre‐transplant evaluation of neonatal acute liver failure

“…The diagnostic sensitivity of urWGS is superior to standard genetic testing and if employed early in the evaluation process can reduce the cost of care. [5] urWGS has even demonstrated the ability to detect cytomegalovirus (CMV) infection, [6] and thus there is future potential for urWGS to detect other viral etiologies of NALF.…”