Biology subjects

Elder, J.

Publications and source records attributed to Elder, J..

3 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↗

bioRxiv2018

Congenital glaucoma with anterior segment dysgenesis in individuals with biallelic CPAMD8 variants

PurposeCongenital glaucoma is a significant cause of irreversible blindness. In some instances glaucoma is associated with developmental abnormalities of the ocular anterior segment, which can impair drainage of aqueous humor, leading to an increase in intraocular pressure.\n\nMethodsGenome sequencing was performed on a parent-proband congenital glaucoma trio, with exome sequencing of 79 additional individuals with suspected primary congenital glaucoma.\n\nResultsWe describe a unique ocular anterior segment dysgenesis associated with congenital glaucoma in four individuals from three unrelated families. In each case, disease was associated with compound heterozygous variants in CPAMD8, a gene of unknown function recently associated with ocular anterior segment dysgenesis, myopia, and ectopia lentis. CPAMD8 expression was highest in neural crest-derived tissues of the adult anterior segment, suggesting that CPAMD8 variation may cause malformation of key drainage structures and the development of high intraocular pressure and glaucoma.\n\nConclusionsThis study reveals a unique genetic cause of childhood glaucoma, and expands the phenotypic spectrum of CPAMD8-associated ocular disease.

genetics↗

bioRxiv2016

Statistical and biological uncertainties associated with vaccine efficacy estimates and their implications for dengue vaccine impact projections

Given the limited effectiveness of strategies based solely on vector control to reduce dengue virus (DENV) transmission, it is expected that an effective vaccine could play a pivotal role in reducing the global disease burden of dengue. Of several dengue vaccines under development, Dengvaxia(R) from Sanofi Pasteur recently became the first to become licensed in select countries and to achieve WHO recommendation for use in certain settings, despite the fact that a number of uncertainties about its profile complicate projections of its public health impact. We used a stochastic, agent-based model for DENV transmission to perform simulations of the public health impact of dengue vaccines in light of two key uncertainties: (1) \"statistical uncertainty\" about the numerical value of the vaccines efficacy against disease, and (2) \"biological uncertainty\" about the extent to which its efficacy against disease derives from the amelioration of symptoms, blocking of DENV infection, or some combination thereof. Simulations of a generic dengue vaccine showed that the proportion of disease episodes averted following 20 years of routine vaccination of nine-year olds at 80% coverage was sensitive to both the numerical value of vaccine efficacy and to the extent to which efficacy derives from blocking of DENV infection. Simulations of a vaccine resembling Dengvaxia(R) took into account that vaccine trial results substantially reduced statistical uncertainty but did not address biological uncertainty, resulting in the proportion of disease episodes averted being more sensitive to biological uncertainty than to statistical uncertainty. Taken together, our results indicate limitations associated with the use of symptomatic disease as the primary endpoint of dengue vaccine trials and highlight the importance of considering multiple forms of uncertainty in projections of a vaccines public health impact.

epidemiology↗