Effect of low-passage number on dengue consensus genomes and intra-host variant frequencies
Abstract
Intra-host single nucleotide variants (iSNVs) have been increasingly used in genomic epidemiology to increase phylogenetic resolution and reconstruct fine-scale outbreak dynamics. These analyses are preferably done on sequence data from direct clinical samples, but in many cases due to low viral loads, there might not be enough genetic material for deep sequencing and iSNV determination. Isolation of the virus from clinical samples with low-passage number increases viral load, but few studies have investigated how dengue virus (DENV) culture isolation from a clinical sample impacts the consensus sequence and the intra-host virus population frequencies. In this study, we investigate consensus and iSNV frequency differences between DENV sequenced directly from clinical samples and their corresponding low-passage isolates. Twenty five DENV1 and DENV2 positive sera and their corresponding viral isolates (T. splendens inoculation and C6/36 passage) were obtained from a prospective cohort study in the Philippines. These were sequenced on MiSeq with minimum nucleotide depth of coverage of 500×, and iSNVs were detected using LoFreq. For both DENV1 and DENV2, we found a maximum of one consensus nucleotide difference between clinical sample and isolate. Interestingly, we found that iSNVs with frequencies ≥5 % were often preserved between the samples, and that the number of iSNV positions, and sample diversity, at this frequency cutoff did not differ significantly between the sample pairs (clinical sample and isolate) in either DENV1 or DENV2 data. Our results show that low-passage DENV isolate consensus genomes are largely representative of their direct sample parental viruses, and that low-passage isolates often mirror high frequency within-host variants from direct samples.
Document Details
- Document Type
- Pub Defense Publication
- Publication Date
- Feb 10, 2021
- Source ID
- 10.1099/jgv.0.001553
Entities
People
- Alan L. Rothman
- Anon Srikiatkhachorn
- Christian K. Fung
- Damon Ellison
- In-Kyu Yoon
- Irina Maljkovic Berry
- Jun Hang
- Louis R Macareo
- Maria Theresa Alera
- Richard G Jarman
- Simon Pollett
- Stefan Fernandez
- Tao Li
Organizations
- Armed Forces Health Surveillance Center
- Armed Forces Research Institute of Medical Sciences
- Coalition for Epidemic Preparedness Innovations
- National Institutes of Health
- University of Rhode Island
- Walter Reed Army Institute of Research