Biology subjects

Wadford, D. A.

Publications and source records attributed to Wadford, D. A..

4 recordsLinked to original sources

bioRxiv2025

Genomic and epidemiologic characteristics of SARS-CoV-2 persistent infections in California, January 2021 - July 2023

Novel SARS-CoV-2 variants demonstrating considerable intra-host evolution emerged throughout the pandemic. The persistent infections thought to give rise to these variants, however, have been difficult to identify at scale. This study sought to detect and characterize persistent infection cases in California using routine epidemiologic and genomic surveillance data. We identified 69 persistent infection cases with collection dates between January 2021 and July 2023 ranging from 21 to 400 days in duration, with an average of 44 days. Significant differences were identified in age distribution, sex, hospitalizations, and deaths between persistent infection cases and all sequenced California SARS-CoV-2 cases. Underlying health conditions were identified for the majority of cases with available medical records. The mutations found in these cases were suggestive of positive selection in the Spike receptor binding domain and convergent evolution toward immune evasion and residues observed in previous persistent infections. We describe a 400-day B.1.429 infection that demonstrates substantial intra-host evolution, and a BA.5.11 persistent infection revealing apparent competition between two intra-host viral subpopulations. By establishing a framework for detecting persistent infections, this study lays the groundwork for other public health organizations to monitor and investigate highly divergent SARS-CoV-2 viruses. Author SummaryGenomic surveillance has been used to monitor the evolution and spread of SARS-CoV-2 variants throughout the pandemic. When a new variant emerges, it is often due to the accumulation of mutations during a persistent infection, i.e. in an individual who was unable to clear the virus after an infection. Using genomic and epidemiologic surveillance data, we identify 69 of these persistent infections in California and provide demographic and clinical characteristics of these infections compared to the broader population of SARS-CoV-2 infections. The identification of risk factors for persistent infections provides important insight into the epidemiology of SARS-CoV-2, while the identification of shared mutations between these infections enhances our understanding of SARS-CoV-2 evolution that may result in new variants. Ultimately, our work may help public health labs to better monitor persistent infections in the future, prior to the potential emergence and spread of novel variants into the community.

genomics↗

bioRxiv2023

SARS-CoV-2 lineage assignments using phylogenetic placement/UShER are superior to pangoLEARN machine learning method

With the rapid spread and evolution of SARS-CoV-2, the ability to monitor its transmission and distinguish among viral lineages is critical for pandemic response efforts. The most commonly used software for the lineage assignment of newly isolated SARS-CoV-2 genomes is pangolin, which offers two methods of assignment, pangoLEARN and pUShER. PangoLEARN rapidly assigns lineages using a machine learning algorithm, while pUShER performs a phylogenetic placement to identify the lineage corresponding to a newly sequenced genome. In a preliminary study, we observed that pangoLEARN (decision tree model), while substantially faster than pUShER, offered less consistency across different versions of pangolin v3. Here, we expand upon this analysis to include v3 and v4 of pangolin, which moved the default algorithm for lineage assignment from pangoLEARN in v3 to pUShER in v4, and perform a thorough analysis confirming that pUShER is not only more stable across versions but also more accurate. Our findings suggest that future lineage assignment algorithms for various pathogens should consider the value of phylogenetic placement.

bioinformatics↗

bioRxiv2020

Identification of a polymorphism in the N gene of SARS-CoV-2 that adversely impacts detection by a widely-used RT-PCR assay

We identify a mutation in the N gene of SARS-CoV-2 that adversely affects annealing of a commonly used RT-PCR primer; epidemiologic evidence suggests the virus retains pathogenicity and competence for spread. This reinforces the importance of using multiple targets, preferably in at least 2 genes, for robust SARS-CoV-2 detection. Article Summary LineA SARS-CoV-2 variant that occurs worldwide and has spread in California significantly affects diagnostic sensitivity of an N gene assay, highlighting the need to employ multiple viral targets for detection.

molecular biology↗

bioRxiv2019

Serological and metagenomic interrogation of cerebrospinal fluid implicates enteroviruses in pediatric acute flaccid myelitis

BackgroundSince 2014, the United States has experienced a biennial spike in pediatric acute flaccid myelitis (AFM). Epidemiologic evidence suggests non-polio enteroviruses (EVs) are a potential etiology, yet EV RNA is rarely detected in cerebrospinal fluid (CSF) and only inconsistently identified from the respiratory tract, serum, or stool.\n\nMethodsWe interrogated CSF from children with AFM (n=42) and pediatric controls with other neurologic diseases (OND) (n=58). Samples were incubated with T7 bacteriophage expressing 481,966 sixty-two amino acid peptides with a fourteen amino acid overlap tiled across all known vertebrate virus and arbovirus genomes, an adaption of the VirScan method. Antibody-bound phage were deep sequenced to quantify enriched peptides with normalized counts expressed as reads per hundred thousand (rpK). EV antibody findings were confirmed with ELISA using whole viral protein 1 (VP1) from contemporary enterovirus (EV) A71 and D68 strains. Separately, metagenomic next-generation sequencing (mNGS) of CSF RNA, both unbiased and with targeted enrichment for EVs, was performed.\n\nResultsThe most significantly enriched viral family by VirScan of CSF in AFM versus OND controls was Picornaviridae (mean rpK 11,266 versus mean rpK 950, p-adjusted < 0.001, Wilcoxon signed-rank test with Bonferroni adjustment). Enriched Picornaviridae peptides belonged almost entirely to the genus Enterovirus. The mean EV VP1 ELISA signal in AFM (mean OD 0.51) was significantly higher than OND controls (mean OD 0.08, p-value < 0.001, Mann-Whitney test). mNGS did not detect additional enterovirus RNA in CSF.\n\nConclusionDespite the rare detection of EV RNA in the CNS of patients with AFM, a pan-viral serologic assay identified high levels of CSF EV antibodies in AFM CSF compared to CSF from OND controls. These results provide further evidence for a causal role of non-polio enteroviruses in AFM.

microbiology↗