Author: Jesse D Bloom

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Preprints

Emergence and spread of a SARS-CoV-2 variant through Europe in the summer of 2020

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  • Site-wide: 82
  • In epidemiology: 17
• Year to date:
  • Site-wide: 219
• Since beginning of last month:
  • Site-wide: 533

Recovery of deleted deep sequencing data sheds more light on the early Wuhan SARS-CoV-2 epidemic

• Downloaded 65,776 times
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  • Site-wide: 111
  • In evolutionary biology: 3
• Year to date:
  • Site-wide: 31
• Since beginning of last month:
  • Site-wide: 253

Comprehensive mapping of mutations to the SARS-CoV-2 receptor-binding domain that affect recognition by polyclonal human serum antibodies

• Downloaded 56,948 times
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  • Site-wide: 132
  • In microbiology: 10
• Year to date:
  • Site-wide: 38
• Since beginning of last month:
  • Site-wide: 1,273

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

• Downloaded 27,209 times
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  • Site-wide: 319
  • In infectious diseases: 118
• Year to date:
  • Site-wide: 1,501
• Since beginning of last month:
  • Site-wide: 2,561

A human coronavirus evolves antigenically to escape antibody immunity

• Downloaded 15,006 times
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  • Site-wide: 635
  • In microbiology: 72
• Year to date:
  • Site-wide: 481
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  • Site-wide: 8,904

Deep mutational scanning of SARS-CoV-2 receptor binding domain reveals constraints on folding and ACE2 binding

• Downloaded 11,920 times
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  • Site-wide: 864
  • In microbiology: 89
• Year to date:
  • Site-wide: 1,848
• Since beginning of last month:
  • Site-wide: 27,289

Protocol and reagents for pseudotyping lentiviral particles with SARS-CoV-2 Spike protein for neutralization assays

• Downloaded 8,672 times
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  • Site-wide: 1,301
  • In microbiology: 122
• Year to date:
  • Site-wide: 2,690
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  • Site-wide: 33,609

Prospective mapping of viral mutations that escape antibodies used to treat COVID-19

• Downloaded 6,397 times
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  • Site-wide: 1,910
  • In microbiology: 156
• Year to date:
  • Site-wide: 1,113
• Since beginning of last month:
  • Site-wide: 15,844

Complete mapping of mutations to the SARS-CoV-2 spike receptor-binding domain that escape antibody recognition

• Downloaded 4,450 times
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  • Site-wide: 3,156
  • In microbiology: 225
• Year to date:
  • Site-wide: 3,254
• Since beginning of last month:
  • Site-wide: 33,563

Seroprevalence of SARS-CoV-2 among children visiting a hospital during the initial Seattle outbreak

• Downloaded 3,113 times
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  • Site-wide: 5,208
  • In infectious diseases: 996
• Year to date:
  • Site-wide: 23,278
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  • Site-wide: 48,018

Genetic and structural basis for recognition of SARS-CoV-2 spike protein by a two-antibody cocktail

• Downloaded 2,921 times
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  • Site-wide: 5,738
  • In immunology: 213
• Year to date:
  • Site-wide: 1,215
• Since beginning of last month:
  • Site-wide: 1,981

Mutational escape from the polyclonal antibody response to SARS-CoV-2 infection is largely shaped by a single class of antibodies

• Downloaded 2,776 times
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  • Site-wide: 6,156
  • In microbiology: 388
• Year to date:
  • Site-wide: 1,300
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  • Site-wide: 10,741

The SARS-CoV-2 mRNA-1273 vaccine elicits more RBD-focused neutralization, but with broader antibody binding within the RBD

• Downloaded 2,772 times
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  • Site-wide: 6,168
  • In microbiology: 389
• Year to date:
  • Site-wide: 1,302
• Since beginning of last month:
  • Site-wide: 1,630

Dynamics of neutralizing antibody titers in the months after SARS-CoV-2 infection

• Downloaded 2,569 times
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  • Site-wide: 6,911
  • In infectious diseases: 1,180
• Year to date:
  • Site-wide: 4,749
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  • Site-wide: 10,139

Antibodies to the SARS-CoV-2 receptor-binding domain that maximize breadth and resistance to viral escape

• Downloaded 2,467 times
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  • Site-wide: 7,334
  • In microbiology: 437
• Year to date:
  • Site-wide: 1,511
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  • Site-wide: 8,428

Single-cell virus sequencing of influenza infections that trigger innate immunity

• Downloaded 2,435 times
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  • Site-wide: 7,468
  • In microbiology: 446
• Year to date:
  • Site-wide: 118,315
• Since beginning of last month:
  • Site-wide: 158,421

Structural basis for broad sarbecovirus neutralization by a human monoclonal antibody

• Downloaded 2,033 times
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  • Site-wide: 9,735
  • In immunology: 342
• Year to date:
  • Site-wide: 1,931
• Since beginning of last month:
  • Site-wide: 8,980

Complete map of SARS-CoV-2 RBD mutations that escape the monoclonal antibody LY-CoV555 and its cocktail with LY-CoV016

• Downloaded 1,607 times
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  • Site-wide: 13,836
  • In microbiology: 803
• Year to date:
  • Site-wide: 2,698
• Since beginning of last month:
  • Site-wide: 34,834

An experimentally determined evolutionary model dramatically improves phylogenetic fit

• Downloaded 1,553 times
• Download rankings, all-time:
  • Site-wide: 14,606
  • In evolutionary biology: 457
• Year to date:
  • Site-wide: 138,806
• Since beginning of last month:
  • Site-wide: 147,089

ACE2 binding is an ancestral and evolvable trait of sarbecoviruses

• Downloaded 1,505 times
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  • Site-wide: 15,393
  • In evolutionary biology: 491
• Year to date:
  • Site-wide: 2,985
• Since beginning of last month:
  • Site-wide: 3,140

Identification of positive selection in genes is greatly improved by using experimentally informed site-specific models

• Downloaded 1,449 times
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  • Site-wide: 16,309
  • In evolutionary biology: 525
• Year to date:
  • Site-wide: 133,739
• Since beginning of last month:
  • Site-wide: 146,329

Extreme heterogeneity of influenza virus infection in single cells

• Downloaded 1,443 times
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  • Site-wide: 16,408
  • In genomics: 1,580
• Year to date:
  • Site-wide: 109,123
• Since beginning of last month:
  • Site-wide: 51,724

Multivalent designed proteins protect against SARS-CoV-2 variants of concern

• Downloaded 1,416 times
• Download rankings, all-time:
  • Site-wide: 16,902
  • In synthetic biology: 199
• Year to date:
  • Site-wide: 3,250
• Since beginning of last month:
  • Site-wide: 4,541

Expanding the Atlas of Functional Missense Variation for Human Genes

• Downloaded 1,345 times
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  • Site-wide: 18,264
  • In molecular biology: 491
• Year to date:
  • Site-wide: 74,159
• Since beginning of last month:
  • Site-wide: 39,077

The inherent mutational tolerance and antigenic evolvability of influenza hemagglutinin

• Downloaded 1,178 times
• Download rankings, all-time:
  • Site-wide: 22,316
  • In microbiology: 1,296
• Year to date:
  • Site-wide: 120,459
• Since beginning of last month:
  • Site-wide: 68,866

Reconciling disparate estimates of viral genetic diversity during human influenza infections

• Downloaded 1,153 times
• Download rankings, all-time:
  • Site-wide: 23,041
  • In evolutionary biology: 867
• Year to date:
  • Site-wide: 120,679
• Since beginning of last month:
  • Site-wide: 92,885

An experimentally informed evolutionary model improves phylogenetic fit to divergent lactamase homologs

• Downloaded 1,086 times
• Download rankings, all-time:
  • Site-wide: 25,290
  • In evolutionary biology: 996
• Year to date:
  • Site-wide: 157,707
• Since beginning of last month:
  • Site-wide: 150,068

Attenuated influenza virions expressing the SARS-CoV-2 receptor-binding domain induce neutralizing antibodies in mice

• Downloaded 1,050 times
• Download rankings, all-time:
  • Site-wide: 26,610
  • In microbiology: 1,554
• Year to date:
  • Site-wide: 37,352
• Since beginning of last month:
  • Site-wide: 33,654

Comprehensive profiling of translation initiation in influenza virus infected cells

• Downloaded 1,021 times
• Download rankings, all-time:
  • Site-wide: 27,746
  • In microbiology: 1,613
• Year to date:
  • Site-wide: 100,049
• Since beginning of last month:
  • Site-wide: 144,452

Stabilization of the SARS-CoV-2 Spike receptor-binding domain using deep mutational scanning and structure-based design

• Downloaded 945 times
• Download rankings, all-time:
  • Site-wide: 31,049
  • In microbiology: 1,825
• Year to date:
  • Site-wide: 5,907
• Since beginning of last month:
  • Site-wide: 2,811

Software for the analysis and visualization of deep mutational scanning data

• Downloaded 938 times
• Download rankings, all-time:
  • Site-wide: 31,406
  • In bioinformatics: 3,445
• Year to date:
  • Site-wide: 151,699
• Since beginning of last month:
  • Site-wide: 145,745

Linking influenza virus evolution within and between human hosts

• Downloaded 845 times
• Download rankings, all-time:
  • Site-wide: 36,557
  • In evolutionary biology: 1,597
• Year to date:
  • Site-wide: 102,772
• Since beginning of last month:
  • Site-wide: 53,387

Experimental estimation of the effects of all amino-acid mutations to HIV Env

• Downloaded 824 times
• Download rankings, all-time:
  • Site-wide: 37,962
  • In microbiology: 2,269
• Year to date:
  • Site-wide: 159,699
• Since beginning of last month:
  • Site-wide: 146,645

Mapping person-to-person variation in viral mutations that escape polyclonal serum targeting influenza hemagglutinin

• Downloaded 811 times
• Download rankings, all-time:
  • Site-wide: 38,809
  • In microbiology: 2,319
• Year to date:
  • Site-wide: 109,185
• Since beginning of last month:
  • Site-wide: 72,548

Deep mutational scanning of hemagglutinin helps predict evolutionary fates of human H3N2 influenza variants

• Downloaded 802 times
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  • Site-wide: 39,461
  • In evolutionary biology: 1,758
• Year to date:
  • Site-wide: 137,075
• Since beginning of last month:
  • Site-wide: 145,624

An antigenic atlas of HIV-1 escape from broadly neutralizing antibodies

• Downloaded 794 times
• Download rankings, all-time:
  • Site-wide: 39,957
  • In immunology: 1,289
• Year to date:
  • Site-wide: 147,957
• Since beginning of last month:
  • Site-wide: 150,334

Phage-DMS: a comprehensive method for fine mapping of antibody epitopes

• Downloaded 782 times
• Download rankings, all-time:
  • Site-wide: 40,897
  • In immunology: 1,317
• Year to date:
  • Site-wide: 81,526
• Since beginning of last month:
  • Site-wide: 47,978

Site-specific amino-acid preferences are mostly conserved in two closely related protein homologs

• Downloaded 767 times
• Download rankings, all-time:
  • Site-wide: 42,042
  • In evolutionary biology: 1,904
• Year to date:
  • Site-wide: 152,732
• Since beginning of last month:
  • Site-wide: 155,297

A SARS-CoV-2 variant elicits an antibody response with a shifted immunodominance hierarchy

• Downloaded 767 times
• Download rankings, all-time:
  • Site-wide: 42,121
  • In microbiology: 2,518
• Year to date:
  • Site-wide: 8,208
• Since beginning of last month:
  • Site-wide: 625

Complete mapping of viral escape from neutralizing antibodies

• Downloaded 755 times
• Download rankings, all-time:
  • Site-wide: 42,995
  • In microbiology: 2,579
• Year to date:
  • Site-wide: 150,770
• Since beginning of last month:
  • Site-wide: 143,879

A public broadly neutralizing antibody class targets a membrane-proximal anchor epitope of influenza virus hemagglutinin

• Downloaded 724 times
• Download rankings, all-time:
  • Site-wide: 45,647
  • In immunology: 1,447
• Year to date:
  • Site-wide: 8,996
• Since beginning of last month:
  • Site-wide: 7,342

Quantifying the effects of single mutations on viral escape from broad and narrow antibodies to an H1 influenza hemagglutinin

• Downloaded 724 times
• Download rankings, all-time:
  • Site-wide: 45,679
  • In microbiology: 2,742
• Year to date:
  • Site-wide: 125,731
• Since beginning of last month:
  • Site-wide: 144,052

Comprehensive mapping of avian influenza polymerase adaptation to the human host

• Downloaded 712 times
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  • Site-wide: 46,722
  • In microbiology: 2,823
• Year to date:
  • Site-wide: 130,834
• Since beginning of last month:
  • Site-wide: 59,434

Structure, receptor recognition and antigenicity of the human coronavirus CCoV-HuPn-2018 spike glycoprotein

• Downloaded 684 times
• Download rankings, all-time:
  • Site-wide: 49,389
  • In microbiology: 2,993
• Year to date:
  • Site-wide: 9,830
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  • Site-wide: 742

Comprehensive mapping of HIV-1 escape from a broadly neutralizing antibody

• Downloaded 681 times
• Download rankings, all-time:
  • Site-wide: 49,692
  • In microbiology: 3,020
• Year to date:
  • Site-wide: 150,970
• Since beginning of last month:
  • Site-wide: 162,061

Deep mutational scanning identifies sites in influenza nucleoprotein that affect viral inhibition by MxA

• Downloaded 654 times
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  • Site-wide: 52,508
  • In microbiology: 3,228
• Year to date:
  • Site-wide: 149,166
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  • Site-wide: 147,081

Deep mutational scanning comprehensively maps how Zika envelope protein mutations affect viral growth and antibody escape

• Downloaded 619 times
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  • Site-wide: 56,512
  • In microbiology: 3,510
• Year to date:
  • Site-wide: 124,490
• Since beginning of last month:
  • Site-wide: 158,789

Mapping mutational effects along the evolutionary landscape of HIV envelope

• Downloaded 595 times
• Download rankings, all-time:
  • Site-wide: 59,427
  • In microbiology: 3,710
• Year to date:
  • Site-wide: 137,714
• Since beginning of last month:
  • Site-wide: 59,488

Accurate measurement of the effects of all amino-acid mutations to influenza hemagglutinin

• Downloaded 580 times
• Download rankings, all-time:
  • Site-wide: 61,387
  • In microbiology: 3,843
• Year to date:
  • Site-wide: 155,654
• Since beginning of last month:
  • Site-wide: 157,547

Influenza H3 and H1 hemagglutinins have different genetic barriers for resistance to broadly neutralizing stem antibodies

• Downloaded 575 times
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  • Site-wide: 62,045
  • In microbiology: 3,891
• Year to date:
  • Site-wide: 70,629
• Since beginning of last month:
  • Site-wide: 118,414

Modeling site-specific amino-acid preferences deepens phylogenetic estimates of viral divergence

• Downloaded 540 times
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  • Site-wide: 66,951
  • In evolutionary biology: 3,310
• Year to date:
  • Site-wide: 156,038
• Since beginning of last month:
  • Site-wide: 147,654

When two are better than one: Modeling the mechanisms of antibody mixtures

• Downloaded 536 times
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  • Site-wide: 67,626
  • In biophysics: 2,362
• Year to date:
  • Site-wide: 109,475
• Since beginning of last month:
  • Site-wide: 135,824

Complete functional mapping of infection- and vaccine-elicited antibodies against the fusion peptide of HIV

• Downloaded 495 times
• Download rankings, all-time:
  • Site-wide: 74,136
  • In immunology: 2,248
• Year to date:
  • Site-wide: 162,801
• Since beginning of last month:
  • Site-wide: 153,423

Identification of antibodies targeting the H3N2 hemagglutinin receptor binding site following vaccination of humans

• Downloaded 485 times
• Download rankings, all-time:
  • Site-wide: 75,746
  • In microbiology: 5,012
• Year to date:
  • Site-wide: 148,437
• Since beginning of last month:
  • Site-wide: 143,431

phydms: Software for phylogenetic analyses informed by deep mutational scanning

• Downloaded 481 times
• Download rankings, all-time:
  • Site-wide: 76,546
  • In evolutionary biology: 3,839
• Year to date:
  • Site-wide: 153,493
• Since beginning of last month:
  • Site-wide: 136,623

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

• Downloaded 430 times
• Download rankings, all-time:
  • Site-wide: 86,230
  • In microbiology: 5,772
• Year to date:
  • Site-wide: 138,823
• Since beginning of last month:
  • Site-wide: 62,273

Estimating the frequency of multiplets in single-cell RNA sequencing from cell-mixing experiments

• Downloaded 419 times
• Download rankings, all-time:
  • Site-wide: 88,359
  • In genomics: 5,618
• Year to date:
  • Site-wide: 159,413
• Since beginning of last month:
  • Site-wide: 160,928

Humoral immunogenicity of the seasonal influenza vaccine before and after CAR-T-cell therapy

• Downloaded 417 times
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  • Site-wide: 88,864
  • In infectious diseases: 4,414
• Year to date:
  • Site-wide: 21,333
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  • Site-wide: 21,858

alignparse: A Python package for parsing complex features from high-throughput long-read sequencing

• Downloaded 398 times
• Download rankings, all-time:
  • Site-wide: 92,940
  • In bioinformatics: 8,137
• Year to date:
  • Site-wide: 160,774
• Since beginning of last month:
  • Site-wide: 152,540

dms-view: Interactive visualization tool for deep mutational scanning data

• Downloaded 386 times
• Download rankings, all-time:
  • Site-wide: 95,616
  • In bioinformatics: 8,324
• Year to date:
  • Site-wide: 127,480
• Since beginning of last month:
  • Site-wide: 143,259

Antibody-mediated broad sarbecovirus neutralization through ACE2 molecular mimicry

• Downloaded 368 times
• Download rankings, all-time:
  • Site-wide: 99,846
  • In immunology: 2,997
• Year to date:
  • Site-wide: 25,765
• Since beginning of last month:
  • Site-wide: 1,956

Sera from individuals with narrowly focused influenza virus antibodies rapidly select viral escape mutations in ovo

• Downloaded 334 times
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  • Site-wide: 108,001
  • In microbiology: 7,573
• Year to date:
  • Site-wide: 156,957
• Since beginning of last month:
  • Site-wide: 158,894

High-resolution mapping of the neutralizing and binding specificities of polyclonal rabbit serum elicited by HIV Env trimer immunization

• Downloaded 297 times
• Download rankings, all-time:
  • Site-wide: 117,409
  • In microbiology: 8,380
• Year to date:
  • Site-wide: 102,757
• Since beginning of last month:
  • Site-wide: 108,698

Massively parallel profiling of HIV-1 resistance to the fusion inhibitor enfuvirtide

• Downloaded 278 times
• Download rankings, all-time:
  • Site-wide: 122,405
  • In microbiology: 8,832
• Year to date:
  • Site-wide: 147,621
• Since beginning of last month:
  • Site-wide: 155,114

Antibody neutralization of an influenza virus that uses neuraminidase for receptor binding

• Downloaded 230 times
• Download rankings, all-time:
  • Site-wide: 135,100
  • In microbiology: 9,963
• Year to date:
  • Site-wide: 130,454
• Since beginning of last month:
  • Site-wide: 130,778

Functional development of a V3-specific broadly neutralizing antibody isolated from a case of HIV superinfection

• Downloaded 207 times
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  • Site-wide: 140,810
  • In microbiology: 10,455
• Year to date:
  • Site-wide: 56,199
• Since beginning of last month:
  • Site-wide: 24,915

Identification of HIV-1 Envelope Mutations that Enhance Entry Using Macaque CD4 and CCR5

• Downloaded 206 times
• Download rankings, all-time:
  • Site-wide: 141,019
  • In microbiology: 10,472
• Year to date:
  • Site-wide: 157,416
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  • Site-wide: 157,358

APOBEC3C tandem domain proteins create super restriction factors against HIV-1

• Downloaded 168 times
• Download rankings, all-time:
  • Site-wide: 149,620
  • In microbiology: 11,281
• Year to date:
  • Site-wide: 164,113
• Since beginning of last month:
  • Site-wide: 152,155