Author: Alex Greninger

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Preprints

Neutralizing antibodies correlate with protection from SARS-CoV-2 in humans during a fishery vessel outbreak with high attack rate

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  • Site-wide: 281
  • In infectious diseases: 103
• Year to date:
  • Site-wide: 1,451
• Since beginning of last month:
  • Site-wide: 4,815

DIRECT RT-qPCR DETECTION OF SARS-CoV-2 RNA FROM PATIENT NASOPHARYNGEAL SWABS WITHOUT AN RNA EXTRACTION STEP

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  • Site-wide: 368
  • In microbiology: 41
• Year to date:
  • Site-wide: 2,101
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  • Site-wide: 6,100

A human coronavirus evolves antigenically to escape antibody immunity

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  • Site-wide: 583
  • In microbiology: 67
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  • Site-wide: 347
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  • Site-wide: 7,592

Point-of-care testing for COVID-19 using SHERLOCK diagnostics

• Downloaded 9,729 times
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  • Site-wide: 979
  • In infectious diseases: 306
• Year to date:
  • Site-wide: 1,703
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  • Site-wide: 9,983

Cryptic transmission of SARS-CoV-2 in Washington State

• Downloaded 9,523 times
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  • Site-wide: 1,006
  • In epidemiology: 132
• Year to date:
  • Site-wide: 8,262
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  • Site-wide: 32,731

Variants of concern are overrepresented among post-vaccination breakthrough infections of SARS-CoV-2 in Washington State

• Downloaded 7,135 times
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  • Site-wide: 1,448
  • In infectious diseases: 400
• Year to date:
  • Site-wide: 274
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  • Site-wide: 19,669

Rapid metagenomic identification of viral pathogens in clinical samples by real-time nanopore sequencing analysis

• Downloaded 3,261 times
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  • Site-wide: 4,297
  • In genomics: 446
• Year to date:
  • Site-wide: 74,738
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  • Site-wide: 72,645

A SARS-CoV-2 Nucleocapsid Variant that Affects Antigen Test Performance

• Downloaded 2,151 times
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  • Site-wide: 7,855
  • In infectious diseases: 1,184
• Year to date:
  • Site-wide: 1,115
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  • Site-wide: 16,509

In vivo antiviral host response to SARS-CoV-2 by viral load, sex, and age

• Downloaded 1,988 times
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  • Site-wide: 8,834
  • In microbiology: 527
• Year to date:
  • Site-wide: 14,906
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  • Site-wide: 30,792

Reliability of self-sampling for accurate assessment of respiratory virus viral and immunologic kinetics

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  • Site-wide: 10,019
  • In infectious diseases: 1,360
• Year to date:
  • Site-wide: 26,243
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  • Site-wide: 29,703

Anti-SARS-CoV-2 antibody levels are concordant across multiple platforms but are not fully predictive of sterilizing immunity

• Downloaded 1,802 times
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  • Site-wide: 10,215
  • In infectious diseases: 1,378
• Year to date:
  • Site-wide: 1,413
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  • Site-wide: 773

Comparison of Commercially Available and Laboratory Developed Assays for in vitro Detection of SARS-CoV-2 in Clinical Laboratories

• Downloaded 1,773 times
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  • Site-wide: 10,469
  • In pathology: 56
• Year to date:
  • Site-wide: 49,989
• Since beginning of last month:
  • Site-wide: 28,240

Validation and Implementation of CLIA-Compliant Whole Genome Sequencing (WGS) in Public Health Laboratory

• Downloaded 1,380 times
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  • Site-wide: 15,141
  • In microbiology: 891
• Year to date:
  • Site-wide: 54,037
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  • Site-wide: None

Anti-SARS-CoV-2 IgG antibodies are associated with reduced viral load

• Downloaded 1,206 times
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  • Site-wide: 18,516
  • In infectious diseases: 1,832
• Year to date:
  • Site-wide: 32,308
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  • Site-wide: 33,190

Discovery of a persistent Zika virus lineage in Bahia, Brazil

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  • Site-wide: 18,619
  • In epidemiology: 1,188
• Year to date:
  • Site-wide: 110,940
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  • Site-wide: 82,366

SARS-CoV-2 ORF6 disrupts nucleocytoplasmic transport through interactions with Rae1 and Nup98

• Downloaded 1,183 times
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  • Site-wide: 19,046
  • In microbiology: 1,108
• Year to date:
  • Site-wide: 10,105
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  • Site-wide: 3,050

Retrospective Clinical Evaluation of Four Lateral Flow Assays for the Detection of SARS-CoV-2 Antibodies

• Downloaded 1,172 times
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  • Site-wide: 19,344
  • In infectious diseases: 1,868
• Year to date:
  • Site-wide: 16,884
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  • Site-wide: 14,661

In silico detection of SARS-CoV-2 specific B-cell epitopes and validation in ELISA for serological diagnosis of COVID-19

• Downloaded 910 times
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  • Site-wide: 27,924
  • In bioinformatics: 3,179
• Year to date:
  • Site-wide: 61,979
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  • Site-wide: None

Clinical metagenomic identification of Balamuthia mandrillaris encephalitis and assembly of the draft genome: the critical need for reference strain sequencing

• Downloaded 850 times
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  • Site-wide: 30,744
  • In genomics: 2,710
• Year to date:
  • Site-wide: 92,156
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  • Site-wide: 62,976

Recent Outbreaks of Shigellosis in California Caused by Two Distinct Populations of Shigella sonnei With Increased Virulence or Fluoroquinolone Resistance

• Downloaded 649 times
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  • Site-wide: 44,439
  • In microbiology: 2,743
• Year to date:
  • Site-wide: 105,533
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  • Site-wide: None

SARS-CoV-2 B.1.1.7 and B.1.351 variants of concern induce lethal disease in K18-hACE2 transgenic mice despite convalescent plasma therapy

• Downloaded 632 times
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  • Site-wide: 45,999
  • In microbiology: 2,841
• Year to date:
  • Site-wide: 6,044
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  • Site-wide: 929

Standard Issue: Copy number heterogeneity of JC virus standards discovered through next-generation sequencing

• Downloaded 623 times
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  • Site-wide: 46,741
  • In microbiology: 2,915
• Year to date:
  • Site-wide: 130,920
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  • Site-wide: None

VAPiD: a lightweight cross platform viral annotation pipeline and identification tool to facilitate virus genome submissions to NCBI GenBank

• Downloaded 608 times
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  • Site-wide: 48,176
  • In bioinformatics: 5,008
• Year to date:
  • Site-wide: 95,469
• Since beginning of last month:
  • Site-wide: 8,022

Myeloablation-associated deletion of ORF4 in a human coronavirus 229E infection

• Downloaded 523 times
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  • Site-wide: 58,047
  • In genomics: 4,295
• Year to date:
  • Site-wide: 101,994
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  • Site-wide: None

Genomic and proteomic analysis of Human herpesvirus 6 reveals distinct clustering of acute versus inherited forms and reannotation of reference strain

• Downloaded 515 times
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  • Site-wide: 59,039
  • In microbiology: 3,822
• Year to date:
  • Site-wide: 136,360
• Since beginning of last month:
  • Site-wide: 38,728

A novel qacA allele results in an elevated chlorhexidine gluconate minimum inhibitory concentration in cutaneous Staphylococcus epidermidis isolates

• Downloaded 508 times
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  • Site-wide: 59,986
  • In microbiology: 3,882
• Year to date:
  • Site-wide: 100,154
• Since beginning of last month:
  • Site-wide: 5,960

Pre-Procedural Surveillance Testing for SARS-CoV-2 in an Asymptomatic Population Shows Low Rates of Positivity

• Downloaded 483 times
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  • Site-wide: 63,342
  • In infectious diseases: 3,388
• Year to date:
  • Site-wide: 122,570
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  • Site-wide: None

The impact of interspecies recombination on human herpes simplex virus evolution and host immune recognition

• Downloaded 468 times
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  • Site-wide: 65,719
  • In genomics: 4,664
• Year to date:
  • Site-wide: 103,602
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  • Site-wide: 43,240

Limited marginal utility of deep sequencing for HIV drug resistance testing in the age of integrase inhibitors

• Downloaded 410 times
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  • Site-wide: 75,138
  • In epidemiology: 3,231
• Year to date:
  • Site-wide: 97,228
• Since beginning of last month:
  • Site-wide: 80,445

Rapid metagenomic next-generation sequencing during an investigation of hospital-acquired human parainfluenza virus 3 infections

• Downloaded 395 times
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  • Site-wide: 77,869
  • In microbiology: 5,344
• Year to date:
  • Site-wide: 134,469
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  • Site-wide: None

Ultrasensitive capture of human herpes simplex virus genomes directly from clinical samples reveals extraordinarily limited evolution in cell culture

• Downloaded 387 times
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  • Site-wide: 79,434
  • In genomics: 5,248
• Year to date:
  • Site-wide: 124,022
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  • Site-wide: None

Cooperating H3N2 influenza virus variants are not detectable in primary clinical samples

• Downloaded 374 times
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  • Site-wide: 81,751
  • In microbiology: 5,653
• Year to date:
  • Site-wide: 150,055
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  • Site-wide: None

Specific allelic discrimination of N501Y and other SARS-CoV-2 mutations by ddPCR detects B.1.1.7 lineage in Washington State

• Downloaded 366 times
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  • Site-wide: 83,391
  • In infectious diseases: 3,859
• Year to date:
  • Site-wide: 13,352
• Since beginning of last month:
  • Site-wide: 49,698

Divergent In vitro MIC Characteristics and underlying isogenic mutations in host-specialized Pseudomonas aeruginosa

• Downloaded 348 times
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  • Site-wide: 87,077
  • In microbiology: 6,086
• Year to date:
  • Site-wide: 92,967
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  • Site-wide: 59,151

Copy number heterogeneity, large origin tandem repeats, and interspecies recombination in HHV-6A and HHV-6B reference strains

• Downloaded 323 times
• Download rankings, all-time:
  • Site-wide: 92,427
  • In genomics: 5,779
• Year to date:
  • Site-wide: 134,324
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  • Site-wide: None

Inactivation of genes in oxidative respiration and iron acquisition pathways in pediatric clinical isolates of small-colony variant Enterobactericeae

• Downloaded 303 times
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  • Site-wide: 97,012
  • In microbiology: 6,947
• Year to date:
  • Site-wide: 96,244
• Since beginning of last month:
  • Site-wide: 86,116

LAVA: a streamlined visualization tool for longitudinal analysis of viral alleles

• Downloaded 285 times
• Download rankings, all-time:
  • Site-wide: 101,038
  • In bioinformatics: 8,720
• Year to date:
  • Site-wide: 112,272
• Since beginning of last month:
  • Site-wide: 93,113

Sensitive detection of highly fragmented cytomegalovirus nucleic acid in human cfDNA

• Downloaded 254 times
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  • Site-wide: 108,463
  • In microbiology: 7,888
• Year to date:
  • Site-wide: 134,714
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  • Site-wide: 22,126

Estimation of Full-Length TprK Diversity in Treponema pallidum subspecies pallidum

• Downloaded 247 times
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  • Site-wide: 110,363
  • In microbiology: 8,051
• Year to date:
  • Site-wide: 142,497
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  • Site-wide: None

Prospective real-time metagenomic sequencing during norovirus outbreak reveals discrete transmission clusters

• Downloaded 238 times
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  • Site-wide: 112,431
  • In genomics: 6,449
• Year to date:
  • Site-wide: 150,591
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  • Site-wide: 81,924

Inherited chromosomally integrated HHV-6 demonstrates tissue-specific RNA expression in vivo that correlates with increased antibody immune response.

• Downloaded 235 times
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  • Site-wide: 113,191
  • In genomics: 6,469
• Year to date:
  • Site-wide: 149,500
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  • Site-wide: 88,633

Phylogenetic estimates of SARS-CoV-2 introductions into Washington State

• Downloaded 232 times
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  • Site-wide: 113,966
  • In epidemiology: 4,754
• Year to date:
  • Site-wide: 25,020
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  • Site-wide: 36,230

Host-pathogen dynamics in longitudinal clinical specimens from patients with COVID-19

• Downloaded 198 times
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  • Site-wide: 122,505
  • In infectious diseases: 4,917
• Year to date:
  • Site-wide: 30,609
• Since beginning of last month:
  • Site-wide: 105,937

Comparative Genomics and Full-Length TprK Profiling of Treponema pallidum subsp. pallidum Reinfection

• Downloaded 190 times
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  • Site-wide: 124,454
  • In microbiology: 9,337
• Year to date:
  • Site-wide: 150,781
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  • Site-wide: 42,466

Phenotypic and Genotypic Antiviral Resistance Testing of HSV-1 Causing Recurrent Cutaneous Lesions in a Patient with DOCK8 Deficiency

• Downloaded 174 times
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  • Site-wide: 128,232
  • In genomics: 6,934
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  • Site-wide: 138,100
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  • Site-wide: None

Herpes Simplex Virus Mistyping due to HSV-1 x HSV-2 Interspecies Recombination in Viral Gene Encoding Glycoprotein B

• Downloaded 156 times
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  • Site-wide: 132,234
  • In genomics: 7,058
• Year to date:
  • Site-wide: 131,088
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  • Site-wide: None

A bifluorescent-based assay for the identification of neutralizing antibodies against SARS-CoV-2 variants of concern in vitro and in vivo

• Downloaded 135 times
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  • Site-wide: 136,944
  • In microbiology: 10,444
• Year to date:
  • Site-wide: 47,431
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  • Site-wide: 28,778

Estimating the false positive rate of highly automated SARS-CoV-2 nucleic acid amplification testing

• Downloaded 131 times
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  • Site-wide: 137,687
  • In infectious diseases: 5,394
• Year to date:
  • Site-wide: 48,746
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  • Site-wide: 51,941

Trajectory of viral load in a prospective population-based cohort with incident SARS-CoV-2 G614 infection

• Downloaded 86 times
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  • Site-wide: 146,091
  • In infectious diseases: 5,700
• Year to date:
  • Site-wide: 71,853
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  • Site-wide: 500

Rapid adaptation to human protein kinase R by a unique genomic rearrangement in rhesus cytomegalovirus.

• Downloaded 78 times
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  • Site-wide: 147,276
  • In microbiology: 11,419
• Year to date:
  • Site-wide: 142,383
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  • Site-wide: None

In vivo generation of BK and JC polyomavirus defective viral genomes in human urine samples associated with higher viral loads

• Downloaded 73 times
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  • Site-wide: 147,880
  • In microbiology: 11,477
• Year to date:
  • Site-wide: 82,247
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  • Site-wide: None

Longitudinal accumulation of in vivo and in vitro-grown Treponema pallidum subsp. pallidum TprK variants in the presence and absence of immune pressure

• Downloaded 29 times
• Download rankings, all-time:
  • Site-wide: 151,353
  • In microbiology: 11,850
• Year to date:
  • Site-wide: 135,468
• Since beginning of last month:
  • Site-wide: 54,631

Genome sequencing of 196 Treponema pallidum strains from six continents reveals additional variability in vaccine candidate genes and dominance of Nichols clade strains in Madagascar

• Downloaded 1 times
• Download rankings, all-time:
  • Site-wide: 154,497
  • In genomics: 7,684
• Year to date:
  • Site-wide: 154,383
• Since beginning of last month:
  • Site-wide: 44,579