Efren Sandoval
A5105660314- SARS-CoV-2 and COVID-19 Research
- Animal Virus Infections Studies
- SARS-CoV-2 detection and testing
- COVID-19 Clinical Research Studies
- Viral gastroenteritis research and epidemiology
- Genomic variations and chromosomal abnormalities
- Plant Virus Research Studies
- Genomics and Rare Diseases
- Genomics and Phylogenetic Studies
- COVID-19 diagnosis using AI
- Genetic Associations and Epidemiology
- Pluripotent Stem Cells Research
- Respiratory Support and Mechanisms
- Intensive Care Unit Cognitive Disorders
- Long-Term Effects of COVID-19
- PARP inhibition in cancer therapy
- Biosensors and Analytical Detection
- Vaccine Coverage and Hesitancy
- Hemophilia Treatment and Research
- Family and Patient Care in Intensive Care Units
- Maternal and Neonatal Healthcare
- Respiratory viral infections research
- Genetics and Neurodevelopmental Disorders
- Advanced Thermodynamics and Statistical Mechanics
- Liver Disease Diagnosis and Treatment
Helix (United States)
2020-2025
Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo
2020
Human Longevity (United States)
2016-2017
We report on the sequencing of 10,545 human genomes at 30×-40× coverage with an emphasis quality metrics and novel variant sequence discovery. find that 84% individual genome can be sequenced confidently. This high-confidence region includes 91.5% exon 95.2% known pathogenic positions. present distribution over 150 million single-nucleotide variants in coding noncoding genome. Each newly contributes average 8,579 variants. In addition, each carries 0.7 Mb is not found main build hg38...
Summary As of January 2021, the highly transmissible B.1.1.7 variant SARS-CoV-2, which was first identified in United Kingdom (U.K.), has gained a strong foothold across world. Because sudden and rapid rise B.1.1.7, we investigated prevalence growth dynamics this States (U.S.), tracking it back to its early emergence onward local transmission. We found that RT-qPCR testing anomaly S gene target failure (SGTF), observed U.K., reliable proxy for detection. sequenced 212 SARS-CoV-2 genomes...
The use of saliva collection for SARS-CoV-2 diagnostics in the ambulatory setting provides several advantages when compared to nasopharyngeal swabs (NPS), including ease self-collection and reduced personal protective equipment (PPE). In addition could be advantageous advising if a convalescent patient is able return work after period self-quarantine. We investigated utility community at Renown Health prospective Diagnostic Cohort 88 patients Convalescent 24 patients. Cohort, we find that...
Host genetics is a key determinant of COVID-19 outcomes. Previously, the Genetics Initiative genome-wide association study used common variants to identify multiple loci associated with However, largest impact on outcomes are expected be rare in population. Hence, studying may provide additional insights into disease susceptibility and pathogenesis, thereby informing therapeutics development. Here, we combined whole-exome whole-genome sequencing from 21 cohorts across 12 countries performed...
This study reports on the displacement of Alpha (B.1.1.7) by Delta (B.1.617.2 and its substrains AY.1, AY.2, AY.3) in United States. By analyzing RT-qPCR testing results viral sequencing samples collected across States, we show that percentage SARS-CoV-2 positive cases caused dropped from 67% May 2021 to less than 3.0% just 10 weeks. We also variant has outcompeted Iota (B.1.526) interest Gamma (P.1) concern. An analysis mean quantification cycles (Cq) values tests over time reveal...
Abstract Between November 2021 and February 2022, SARS-CoV-2 Delta Omicron variants co-circulated in the United States, allowing for co-infections possible recombination events. We sequenced 29,719 positive samples during this period analyzed presence fraction of reads supporting mutations specific to either or variant. identified 18 co-infections, one which displayed evidence a low Delta-Omicron recombinant viral population. also two independent cases infection by virus, where 100% RNA came...
The rapid emergence of SARS-CoV-2 variants raised public health questions concerning the capability diagnostic tests to detect new strains, efficacy vaccines, and how map geographical distribution understand transmission patterns loads on healthcare resources. Next-generation sequencing (NGS) is primary method for detecting tracing variants, but it expensive, can take weeks before sequence data are available in repositories. This article describes a customizable reverse transcription PCR...
As part of a multi-state viral genomic surveillance program, we conducted case-only analysis to evaluate the effectiveness XBB.1.5-adapated mRNA vaccines in preventing severe illness among individuals with medically attended SARS-CoV-2 infection. We compared prior receipt an XBB.1.5-adapted vaccine between SARS-CoV-2-infected adults inpatient or emergency department (ED) visits (as proxy for illness) vs those outpatient mild illness). Among 6,551 patients September 2023 and January 2024,...
ABSTRACT Within a multi-state viral genomic surveillance program, we conducted case-control analysis comparing prior receipt of XBB.1.5-adapted mRNA vaccination between SARS-CoV-2-infected adults with inpatient/ED visits (proxy for severe illness) vs outpatient visits. Among 6,551 patients from September 2023-January 2024, 6.1% 12.0% had received XBB.1.5 (aOR=0.41; 95%CI:0.32-0.53). This protective association was weaker among JN.1 (aOR=0.62; 95%CI:0.40-0.96) XBB-lineage (aOR=0.28;...
Abstract We report on the sequencing of 10,545 human genomes at 30-40x coverage with an emphasis quality metrics and novel variant sequence discovery. find that 84% individual genome can be sequenced confidently. This high confidence region includes 91.5% exon 95.2% known pathogenic positions. present thedistribution over 150 million single nucleotide variants in coding non-coding genome. Each newly contributes average 8,579 variants. In addition, each carries 0.7 Mb is not found main build...
Abstract Within a multistate viral genomic surveillance program, we evaluated whether proportions of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections attributed to the JN.1 variant and XBB-lineage variants (including HV.1 EG.5) differed between inpatient outpatient care settings during periods cocirculation. Both were less likely than EG.5 account for among inpatients versus outpatients (adjusted odds ratio [aOR], 0.60 [95% confidence interval (CI), .43–.84; P = .003]...
Within a multistate clinical cohort, SARS-CoV-2 antiviral prescribing patterns were evaluated from April 2022-June 2023 among nonhospitalized patients with risk factors for severe COVID-19. Among 3247 adults, only 31.9% prescribed an agent (87.6% nirmatrelvir/ritonavir, 11.9% molnupiravir, 0.5% remdesivir), highlighting the need to identify and address treatment barriers.
ABSTRACT Within a multi-state viral genomic surveillance program, proportions of SARS-CoV-2 infections attributed to the JN.1 and HV.1 variants, compared EG.5, were each lower among inpatients versus outpatients (aOR=0.33 [95% CI: 0.20-0.55] aOR=0.62 0.44-0.86], respectively). variants may be associated with risk severe illness.
Abstract The rapid emergence of new SARS-CoV-2 variants raises a number public health questions including the capability diagnostic tests to detect strains, efficacy vaccines, and how map geographical distribution better understand patterns transmission possible load on healthcare resources. Next-Generation Sequencing (NGS) is primary method for detecting tracing variants, but it expensive, can take weeks before sequence data available in repositories. Here, we describe Polymerase Chain...
Between November 2021 and February 2022, SARS-CoV-2 Delta Omicron variants co-circulated in the United States, allowing for co-infections possible recombination events. We sequenced 29,719 positive samples during this period analyzed presence fraction of reads supporting mutations specific to either or variant. identified 18 co-infections, one which displayed evidence a low Delta-Omicron recombinant viral population. also two independent cases infection by virus, where 100% RNA came from...
The sequencing of 74,348 SARS-CoV-2 positive samples collected across the United States showed that Delta variant was responsible for majority infections by July 1, 2021, and accounted >99.9% tests in September 2021. displaced Alpha, which dominant at time. also directly outcompeted Gamma concern as well Iota Mu variants interest. An analysis mean quantification cycles (Cq) values revealed lead to a higher viral load on average compared Alpha infections, but this increase only ~1.7x...
Abstract Host genetics is a key determinant of COVID-19 outcomes. Previously, the Genetics Initiative genome-wide association study used common variants to identify multiple loci associated with However, largest impact on outcomes are expected be rare in population. Hence, studying may provide additional insights into disease susceptibility and pathogenesis, thereby informing therapeutics development. Here, we combined whole-exome whole-genome sequencing from 21 cohorts across 12 countries...