Author: Alexander L. 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: 228
  • In infectious diseases: 88
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  • Site-wide: 708
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  • Site-wide: 629

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

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  • Site-wide: 297
  • In microbiology: 33
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  • Site-wide: 694
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  • Site-wide: 1,409

A human coronavirus evolves antigenically to escape antibody immunity

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  • Site-wide: 729
  • In microbiology: 73
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  • Site-wide: 71
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  • Site-wide: 14

Cryptic transmission of SARS-CoV-2 in Washington State

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  • Site-wide: 775
  • In epidemiology: 106
• Year to date:
  • Site-wide: 3,610
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  • Site-wide: 4,567

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

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  • Site-wide: 919
  • In infectious diseases: 252
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  • Site-wide: None
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  • Site-wide: 4,116

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

• Downloaded 3,171 times
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  • Site-wide: 3,322
  • In genomics: 392
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  • Site-wide: None
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  • Site-wide: 73,696

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

• Downloaded 1,706 times
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  • Site-wide: 8,171
  • In microbiology: 448
• Year to date:
  • Site-wide: 2,540
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  • Site-wide: 1,725

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

• Downloaded 1,652 times
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  • Site-wide: 8,613
  • In pathology: 43
• Year to date:
  • Site-wide: 34,406
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  • Site-wide: 21,070

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

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  • Site-wide: 9,309
  • In infectious diseases: 1,033
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  • Site-wide: None
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  • Site-wide: 47,712

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

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  • Site-wide: 12,813
  • In microbiology: 714
• Year to date:
  • Site-wide: 39,115
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  • Site-wide: 33,267

Discovery of a persistent Zika virus lineage in Bahia, Brazil

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  • Site-wide: 14,664
  • In epidemiology: 894
• Year to date:
  • Site-wide: 69,340
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  • Site-wide: 59,041

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

• Downloaded 1,021 times
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  • Site-wide: 17,718
  • In infectious diseases: 1,394
• Year to date:
  • Site-wide: 56,312
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  • Site-wide: 20,067

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

• Downloaded 898 times
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  • Site-wide: 21,388
  • In infectious diseases: 1,499
• Year to date:
  • Site-wide: 4,611
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  • Site-wide: 3,823

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

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  • Site-wide: 24,477
  • In bioinformatics: 2,985
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  • Site-wide: 24,134
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  • Site-wide: 16,805

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

• Downloaded 789 times
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  • Site-wide: 25,697
  • In genomics: 2,464
• Year to date:
  • Site-wide: 77,196
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  • Site-wide: 56,543

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

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  • Site-wide: 30,088
  • In microbiology: 1,778
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  • Site-wide: None
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  • Site-wide: 28,210

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

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  • Site-wide: 36,768
  • In microbiology: 2,226
• Year to date:
  • Site-wide: 35,018
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  • Site-wide: 54,665

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

• Downloaded 592 times
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  • Site-wide: 37,787
  • In microbiology: 2,295
• Year to date:
  • Site-wide: 71,773
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  • Site-wide: 70,521

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

• Downloaded 546 times
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  • Site-wide: 41,788
  • In bioinformatics: 4,570
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  • Site-wide: None
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  • Site-wide: 79,177

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

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  • Site-wide: 49,005
  • In microbiology: 3,121
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  • Site-wide: None
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  • Site-wide: 102,763

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

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  • Site-wide: 49,704
  • In genomics: 3,937
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  • Site-wide: 74,010
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  • Site-wide: 38,943

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

• Downloaded 451 times
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  • Site-wide: 52,141
  • In microbiology: 3,386
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  • Site-wide: None
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  • Site-wide: 47,174

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

• Downloaded 447 times
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  • Site-wide: 52,701
  • In infectious diseases: 2,331
• Year to date:
  • Site-wide: 74,291
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  • Site-wide: 101,730

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

• Downloaded 423 times
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  • Site-wide: 55,803
  • In genomics: 4,245
• Year to date:
  • Site-wide: 32,076
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  • Site-wide: 67,498

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

• Downloaded 369 times
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  • Site-wide: 63,815
  • In microbiology: 4,316
• Year to date:
  • Site-wide: 52,894
• Since beginning of last month:
  • Site-wide: 76,163

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

• Downloaded 361 times
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  • Site-wide: 65,031
  • In microbiology: 4,418
• Year to date:
  • Site-wide: 52,600
• Since beginning of last month:
  • Site-wide: 84,310

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

• Downloaded 355 times
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  • Site-wide: 66,059
  • In epidemiology: 2,717
• Year to date:
  • Site-wide: 61,453
• Since beginning of last month:
  • Site-wide: 85,999

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

• Downloaded 352 times
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  • Site-wide: 66,585
  • In genomics: 4,736
• Year to date:
  • Site-wide: 79,769
• Since beginning of last month:
  • Site-wide: 91,529

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

• Downloaded 292 times
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  • Site-wide: 77,320
  • In microbiology: 5,430
• Year to date:
  • Site-wide: 43,535
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  • Site-wide: 85,507

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

• Downloaded 283 times
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  • Site-wide: 79,140
  • In genomics: 5,215
• Year to date:
  • Site-wide: None
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  • Site-wide: 93,662

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

• Downloaded 251 times
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  • Site-wide: 85,784
  • In microbiology: 6,159
• Year to date:
  • Site-wide: 35,864
• Since beginning of last month:
  • Site-wide: 43,471

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

• Downloaded 242 times
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  • Site-wide: 87,534
  • In bioinformatics: 7,857
• Year to date:
  • Site-wide: 65,425
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  • Site-wide: 76,565

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

• Downloaded 230 times
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  • Site-wide: 90,004
  • In microbiology: 6,546
• Year to date:
  • Site-wide: 31,220
• Since beginning of last month:
  • Site-wide: 59,623

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

• Downloaded 223 times
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  • Site-wide: 91,501
  • In genomics: 5,657
• Year to date:
  • Site-wide: 81,712
• Since beginning of last month:
  • Site-wide: 111,593

Sensitive detection of highly fragmented cytomegalovirus nucleic acid in human cfDNA

• Downloaded 220 times
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  • Site-wide: 92,112
  • In microbiology: 6,748
• Year to date:
  • Site-wide: None
• Since beginning of last month:
  • Site-wide: 112,654

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

• Downloaded 218 times
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  • Site-wide: 92,688
  • In genomics: 5,682
• Year to date:
  • Site-wide: 84,910
• Since beginning of last month:
  • Site-wide: 106,954

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

• Downloaded 172 times
• Download rankings, all-time:
  • Site-wide: 102,119
  • In microbiology: 7,675
• Year to date:
  • Site-wide: None
• Since beginning of last month:
  • Site-wide: 113,140

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

• Downloaded 148 times
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  • Site-wide: 106,763
  • In genomics: 6,126
• Year to date:
  • Site-wide: 75,483
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  • Site-wide: 62,677

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

• Downloaded 122 times
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  • Site-wide: 111,287
  • In genomics: 6,275
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  • Site-wide: None
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  • Site-wide: 116,537

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

• Downloaded 49 times
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  • Site-wide: 121,844
  • In microbiology: 9,540
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  • Site-wide: None
• Since beginning of last month:
  • Site-wide: 57,318

Liver immune abnormalities persist after cure of Hepatitis C Virus by anti-viral therapy

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  • Site-wide: 122,557
  • In infectious diseases: 3,863
• Year to date:
  • Site-wide: 44,634
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  • Site-wide: 21,302