Challenges in Harnessing Shared Within-Host Severe Acute Respiratory Syndrome Coronavirus 2 Variation for Transmission Inference.
Open forum infectious diseases
2023; 10 (2): ofad001
The limited variation observed among severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) consensus sequences makes it difficult to reconstruct transmission linkages in outbreak settings. Previous studies have recovered variation within individual SARS-CoV-2 infections but have not yet measured the informativeness of within-host variation for transmission inference.We performed tiled amplicon sequencing on 307 SARS-CoV-2 samples, including 130 samples from 32 individuals in 14 households and 47 longitudinally sampled individuals, from 4 prospective studies with household membership data, a proxy for transmission linkage.Consensus sequences from households had limited diversity (mean pairwise distance, 3.06 single-nucleotide polymorphisms [SNPs]; range, 0-40). Most (83.1%, 255 of 307) samples harbored at least 1 intrahost single-nucleotide variant ([iSNV] median, 117; interquartile range [IQR], 17-208), above a minor allele frequency threshold of 0.2%. Pairs in the same household shared significantly more iSNVs (mean, 1.20 iSNVs; 95% confidence interval [CI], 1.02-1.39) than did pairs in different households infected with the same viral clade (mean, 0.31 iSNVs; 95% CI, .28-.34), a signal that decreases with increasingly stringent minor allele frequency thresholds. The number of shared iSNVs was significantly associated with an increased odds of household membership (adjusted odds ratio, 1.35; 95% CI, 1.23-1.49). However, the poor concordance of iSNVs detected across sequencing replicates (24.8% and 35.0% above a 0.2% and 1% threshold) confirms technical concerns that current sequencing and bioinformatic workflows do not consistently recover low-frequency within-host variants.Shared within-host variation may augment the information in consensus sequences for predicting transmission linkages. Improving sensitivity and specificity of within-host variant identification will improve the informativeness of within-host variation.
View details for DOI 10.1093/ofid/ofad001
View details for PubMedID 36751652
View details for PubMedCentralID PMC9898879
Feasibility of Specimen Self-collection in Young Children Undergoing SARS-CoV-2 Surveillance for In-Person Learning
JAMA Network Open
View details for DOI 10.1001/jamanetworkopen.2021.48988
COVID-19 Diagnostic Testing For All - Using Non-Dilutive Saliva Sample Collection, Stabilization and Ambient Transport Devices.
medRxiv : the preprint server for health sciences
COVID-19 testing is not accessible for millions during this pandemic despite our best efforts. Without greatly expanded testing of asymptomatic individuals, contact tracing and subsequent isolation of spreaders remains as a means for control. In an effort to increase RT-PCR assay testing for the presence of the novel beta-coronavirus SARS-CoV-2 as well as improve sample collection safety, GenTegra LLC has introduced two products for saliva collection and viral RNA stabilization: GTR-STM™ (GenTegra Saliva Transport Medium) and GTR-STMdk™ (GenTegra Saliva Transport Medium Direct to PCR). Both products contain a proprietary formulation based on GenTegra's novel "Active Chemical Protection™" (ACP) technology that gives non-dilutive, error-free saliva sample collection using RNA stabilization chemicals already dried in the collection tube. GTR-STM can be used for safer saliva-based sample collection at home (or at a test site). Following saliva collection, the sample-containing GTR-STM can be kept at ambient temperature during shipment to an authorized CLIA lab for analysis. SARS-CoV-2 viral RNA in GTR-STM is stable for over a month at ambient temperature, easily surviving the longest transit times from home to lab. GTR-STM enhances patient comfort, convenience, compliance and reduces infectious virus exposure to essential medical and lab professionals. Alternatively, the GTR-STMdk direct-into-PCR product can be used to improve lab throughput and reduce reagent costs for saliva sample collection and testing at any lab site with access to refrigeration. GTR-STMdk reduces lab process time by 25% and reagent costs by 30% compared to other approaches. Since GTR-STMdk retains SARS-CoV-2 viral RNA stability for three days at ambient temperature, it is optimized for lab test site rather than at home saliva collection. SARS-COV-2 viral RNA levels as low as 0.4 genome equivalents/uL are detected in saliva samples using GTR-STMdk. The increased sensitivity of SARS-CoV-2 detection can expand COVID-19 testing to include asymptomatic individuals using pooled saliva.GTR-STM and Direct-into-PCR GTR-STMdk offer substantive improvements in SARS-CoV-2 viral RNA stability, safety, and RT-PCR process efficiency for COVID-19 testing by using a non-dilutive saliva sample collection system for individuals at home or onsite respectively.
View details for DOI 10.1101/2021.01.20.20243782
View details for PubMedID 33532800
View details for PubMedCentralID PMC7852251