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Author: Edward C Holmes

Rankings

  • All-time downloads: 120,879 (rank: 1,104 )
  • Categories:
    • bioinformatics: 2,034 (rank: 8,776 (tie) )
    • ecology: 2,194 (rank: 1,693 (tie) )
    • epidemiology: 14,795 (rank: 1,228 )
    • evolutionary biology: 6,246 (rank: 542 (tie) )
    • genetic and genomic medicine: 1,160 (rank: 3,859 (tie) )
    • immunology: 492 (rank: 24,533 (tie) )
    • infectious diseases: 9,746 (rank: 6,168 )
    • microbiology: 62,433 (rank: 231 )
    • molecular biology: 2,710 (rank: 2,009 )
    • pathology: 15,427 (rank: 48 )
    • public and global health: 2,019 (rank: 2,615 (tie) )
    • zoology: 1,623 (rank: 145 (tie) )

Downloads per author, site-wide

Preprints

Identification of 2019-nCoV related coronaviruses in Malayan pangolins in southern China

microbiology more details view paper
  • Downloaded 23,482 times
  • Download rankings, all-time:
    • Site-wide: 386
    • In microbiology: 43
  • Year to date:
    • Site-wide: 2,753
  • Since beginning of last month:
    • Site-wide: 12,141

Complete genome characterisation of a novel coronavirus associated with severe human respiratory disease in Wuhan, China

pathology more details view paper
  • Downloaded 15,029 times
  • Download rankings, all-time:
    • Site-wide: 635
    • In pathology: 5
  • Year to date:
    • Site-wide: 2,125
  • Since beginning of last month:
    • Site-wide: 5,230

Epidemiological and evolutionary considerations of SARS-CoV-2 vaccine dosing regimes

epidemiology more details view paper
  • Downloaded 10,458 times
  • Download rankings, all-time:
    • Site-wide: 1,042
    • In epidemiology: 139
  • Year to date:
    • Site-wide: 299
  • Since beginning of last month:
    • Site-wide: 24,171

A novel bat coronavirus reveals natural insertions at the S1/S2 cleavage site of the Spike protein and a possible recombinant origin of HCoV-19

microbiology more details view paper
  • Downloaded 9,991 times
  • Download rankings, all-time:
    • Site-wide: 1,093
    • In microbiology: 101
  • Year to date:
    • Site-wide: 1,141
  • Since beginning of last month:
    • Site-wide: 2,918

A dynamic nomenclature proposal for SARS-CoV-2 to assist genomic epidemiology

microbiology more details view paper
  • Downloaded 8,663 times
  • Download rankings, all-time:
    • Site-wide: 1,305
    • In microbiology: 123
  • Year to date:
    • Site-wide: 1,357
  • Since beginning of last month:
    • Site-wide: 7,689

Identification of novel bat coronaviruses sheds light on the evolutionary origins of SARS-CoV-2 and related viruses

microbiology more details view paper
  • Downloaded 6,204 times
  • Download rankings, all-time:
    • Site-wide: 2,000
    • In microbiology: 163
  • Year to date:
    • Site-wide: 503
  • Since beginning of last month:
    • Site-wide: 11,029

Genomic epidemiology reveals transmission patterns and dynamics of SARS-CoV-2 in Aotearoa New Zealand

infectious diseases more details view paper
  • Downloaded 4,089 times
  • Download rankings, all-time:
    • Site-wide: 3,531
    • In infectious diseases: 772
  • Year to date:
    • Site-wide: 17,208
  • Since beginning of last month:
    • Site-wide: 40,116

Virus genomes reveal the factors that spread and sustained the West African Ebola epidemic.

epidemiology more details view paper
  • Downloaded 2,554 times
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    • Site-wide: 6,984
    • In epidemiology: 593
  • Year to date:
    • Site-wide: 74,360
  • Since beginning of last month:
    • Site-wide: 93,841

REVEALING COVID-19 TRANSMISSION BY SARS-CoV-2 GENOME SEQUENCING AND AGENT BASED MODELLING

microbiology more details view paper
  • Downloaded 2,491 times
  • Download rankings, all-time:
    • Site-wide: 7,238
    • In microbiology: 430
  • Year to date:
    • Site-wide: 32,804
  • Since beginning of last month:
    • Site-wide: 98,651

Retrospective screening of routine respiratory samples revealed undetected community transmission and missed intervention opportunities for SARS-CoV-2 in the United Kingdom

infectious diseases more details view paper
  • Downloaded 2,136 times
  • Download rankings, all-time:
    • Site-wide: 9,061
    • In infectious diseases: 1,386
  • Year to date:
    • Site-wide: 17,192
  • Since beginning of last month:
    • Site-wide: 61,050

CCMetagen: comprehensive and accurate identification of eukaryotes and prokaryotes in metagenomic data

bioinformatics more details view paper
  • Downloaded 2,034 times
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    • Site-wide: 9,735
    • In bioinformatics: 1,087
  • Year to date:
    • Site-wide: 39,657
  • Since beginning of last month:
    • Site-wide: 36,319

Total virome characterizations of game animals in China reveals a spectrum of emerging viral pathogens

zoology more details view paper
  • Downloaded 1,623 times
  • Download rankings, all-time:
    • Site-wide: 13,634
    • In zoology: 23
  • Year to date:
    • Site-wide: 2,668
  • Since beginning of last month:
    • Site-wide: 239

High levels of antibiotic resistance gene expression among birds living in a wastewater treatment plant

ecology more details view paper
  • Downloaded 1,620 times
  • Download rankings, all-time:
    • Site-wide: 13,658
    • In ecology: 180
  • Year to date:
    • Site-wide: 66,278
  • Since beginning of last month:
    • Site-wide: 114,639

An emergent clade of SARS-CoV-2 linked to returned travellers from Iran

microbiology more details view paper
  • Downloaded 1,570 times
  • Download rankings, all-time:
    • Site-wide: 14,362
    • In microbiology: 827
  • Year to date:
    • Site-wide: 91,591
  • Since beginning of last month:
    • Site-wide: 142,828

Matryoshka RNA virus 1: a novel RNA virus associated with Plasmodium parasites in human malaria

evolutionary biology more details view paper
  • Downloaded 1,247 times
  • Download rankings, all-time:
    • Site-wide: 20,467
    • In evolutionary biology: 733
  • Year to date:
    • Site-wide: 77,228
  • Since beginning of last month:
    • Site-wide: 66,975

Genome-scale rates of evolutionary change in bacteria

evolutionary biology more details view paper
  • Downloaded 1,100 times
  • Download rankings, all-time:
    • Site-wide: 24,818
    • In evolutionary biology: 972
  • Year to date:
    • Site-wide: 134,694
  • Since beginning of last month:
    • Site-wide: 90,514

The ongoing COVID-19 epidemic in Minas Gerais, Brazil: insights from epidemiological data and SARS-CoV-2 whole genome sequencing.

public and global health more details view paper
  • Downloaded 1,078 times
  • Download rankings, all-time:
    • Site-wide: 25,595
    • In public and global health: 507
  • Year to date:
    • Site-wide: 64,602
  • Since beginning of last month:
    • Site-wide: 125,465

COVID-19 severity is associated with immunopathology and multi-organ damage

infectious diseases more details view paper
  • Downloaded 1,049 times
  • Download rankings, all-time:
    • Site-wide: 26,678
    • In infectious diseases: 2,405
  • Year to date:
    • Site-wide: 42,478
  • Since beginning of last month:
    • Site-wide: 56,854

Vaccine nationalism and the dynamics and control of SARS-CoV-2

epidemiology more details view paper
  • Downloaded 962 times
  • Download rankings, all-time:
    • Site-wide: 30,295
    • In epidemiology: 1,675
  • Year to date:
    • Site-wide: 5,777
  • Since beginning of last month:
    • Site-wide: 8,730

Off-season RSV epidemics in Australia after easing of COVID-19 restrictions

public and global health more details view paper
  • Downloaded 941 times
  • Download rankings, all-time:
    • Site-wide: 31,308
    • In public and global health: 586
  • Year to date:
    • Site-wide: 5,974
  • Since beginning of last month:
    • Site-wide: 4,014

Infectious disease phylodynamics with occurrence data

evolutionary biology more details view paper
  • Downloaded 911 times
  • Download rankings, all-time:
    • Site-wide: 32,826
    • In evolutionary biology: 1,394
  • Year to date:
    • Site-wide: 46,213
  • Since beginning of last month:
    • Site-wide: 57,241

Metatranscriptomics as a tool to identify fungal species and subspecies in mixed communities

molecular biology more details view paper
  • Downloaded 909 times
  • Download rankings, all-time:
    • Site-wide: 32,931
    • In molecular biology: 912
  • Year to date:
    • Site-wide: 102,366
  • Since beginning of last month:
    • Site-wide: 60,328

Characterisation of the faecal virome of captive and wild Tasmanian devils using virus-like particles metagenomics and meta-transcriptomics

molecular biology more details view paper
  • Downloaded 862 times
  • Download rankings, all-time:
    • Site-wide: 35,547
    • In molecular biology: 991
  • Year to date:
    • Site-wide: 100,242
  • Since beginning of last month:
    • Site-wide: 110,528

Eighteenth century Yersinia pestis genomes reveal the long-term persistence of an historical plague focus

microbiology more details view paper
  • Downloaded 853 times
  • Download rankings, all-time:
    • Site-wide: 36,064
    • In microbiology: 2,137
  • Year to date:
    • Site-wide: 115,868
  • Since beginning of last month:
    • Site-wide: 63,756

How accurately can we assess zoonotic risk?

microbiology more details view paper
  • Downloaded 825 times
  • Download rankings, all-time:
    • Site-wide: 37,966
    • In microbiology: 2,270
  • Year to date:
    • Site-wide: 43,121
  • Since beginning of last month:
    • Site-wide: 80,118

Virome composition in marine fish revealed by meta-transcriptomics

microbiology more details view paper
  • Downloaded 809 times
  • Download rankings, all-time:
    • Site-wide: 38,965
    • In microbiology: 2,336
  • Year to date:
    • Site-wide: 25,901
  • Since beginning of last month:
    • Site-wide: 19,439

Pathogenicity, tissue tropism and potential vertical transmission of SARSr-CoV-2 in Malayan pangolins

microbiology more details view paper
  • Downloaded 807 times
  • Download rankings, all-time:
    • Site-wide: 39,178
    • In microbiology: 2,348
  • Year to date:
    • Site-wide: 38,247
  • Since beginning of last month:
    • Site-wide: 54,119

Genomic epidemiology reveals how restriction measures shaped the SARS-CoV-2 epidemic in Brazil

genetic and genomic medicine more details view paper
  • Downloaded 760 times
  • Download rankings, all-time:
    • Site-wide: 42,652
    • In genetic and genomic medicine: 201
  • Year to date:
    • Site-wide: 8,383
  • Since beginning of last month:
    • Site-wide: 650

Influenza A viruses serially passaged in different MDCK cell lines exhibit limited sequence variation across their genomes, with the exception of the hemagglutinin gene

microbiology more details view paper
  • Downloaded 688 times
  • Download rankings, all-time:
    • Site-wide: 49,013
    • In microbiology: 2,970
  • Year to date:
    • Site-wide: 22,295
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    • Site-wide: 40,675

The power and limitations of genomics to track COVID-19 outbreaks: a case study from New Zealand

infectious diseases more details view paper
  • Downloaded 645 times
  • Download rankings, all-time:
    • Site-wide: 53,573
    • In infectious diseases: 3,436
  • Year to date:
    • Site-wide: 33,135
  • Since beginning of last month:
    • Site-wide: 67,997

Meta-transcriptomic comparison of the RNA viromes of the mosquito vectors Culex pipiens and Culex torrentium in northern Europe

evolutionary biology more details view paper
  • Downloaded 617 times
  • Download rankings, all-time:
    • Site-wide: 56,822
    • In evolutionary biology: 2,770
  • Year to date:
    • Site-wide: 100,268
  • Since beginning of last month:
    • Site-wide: 142,285

The Impact of Migratory Flyways on the Spread of Avian Influenza Virus in North America

evolutionary biology more details view paper
  • Downloaded 613 times
  • Download rankings, all-time:
    • Site-wide: 57,320
    • In evolutionary biology: 2,792
  • Year to date:
    • Site-wide: 154,746
  • Since beginning of last month:
    • Site-wide: 158,311

Virome heterogeneity and connectivity in waterfowl and shorebird communities

ecology more details view paper
  • Downloaded 574 times
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    • Site-wide: 62,222
    • In ecology: 1,518
  • Year to date:
    • Site-wide: 144,417
  • Since beginning of last month:
    • Site-wide: 148,707

The impact of early public health interventions on SARS-CoV-2 transmission and evolution

epidemiology more details view paper
  • Downloaded 535 times
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    • Site-wide: 67,780
    • In epidemiology: 3,045
  • Year to date:
    • Site-wide: 37,404
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    • Site-wide: 41,271

Limited intra-host diversity and background evolution accompany 40 years of canine parvovirus host adaptation and spread

evolutionary biology more details view paper
  • Downloaded 534 times
  • Download rankings, all-time:
    • Site-wide: 67,885
    • In evolutionary biology: 3,370
  • Year to date:
    • Site-wide: 131,462
  • Since beginning of last month:
    • Site-wide: 147,284

Novel hepatitis D-like agents in vertebrates and invertebrates

evolutionary biology more details view paper
  • Downloaded 520 times
  • Download rankings, all-time:
    • Site-wide: 70,112
    • In evolutionary biology: 3,489
  • Year to date:
    • Site-wide: 120,919
  • Since beginning of last month:
    • Site-wide: 104,608

Extensive Diversity of RNA Viruses in Australian Ticks

microbiology more details view paper
  • Downloaded 508 times
  • Download rankings, all-time:
    • Site-wide: 72,020
    • In microbiology: 4,700
  • Year to date:
    • Site-wide: 157,361
  • Since beginning of last month:
    • Site-wide: 158,518

A divergent hepatitis D-like agent in birds

molecular biology more details view paper
  • Downloaded 505 times
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    • Site-wide: 72,509
    • In molecular biology: 2,069
  • Year to date:
    • Site-wide: 152,968
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    • Site-wide: 148,234

Comparative analysis reveals adaptive evolution of bat IFITMs and a novel antiviral determinant

immunology more details view paper
  • Downloaded 492 times
  • Download rankings, all-time:
    • Site-wide: 74,569
    • In immunology: 2,277
  • Year to date:
    • Site-wide: 141,862
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    • Site-wide: 158,208

Total Infectomes Characterization of Respiratory Infections in pre-COVID-19 Wuhan, China

infectious diseases more details view paper
  • Downloaded 468 times
  • Download rankings, all-time:
    • Site-wide: 78,881
    • In infectious diseases: 4,122
  • Year to date:
    • Site-wide: 17,843
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    • Site-wide: 41,953

A household case evidences shorter shedding of SARS-CoV-2 in naturally infected cats compared to their human owners.

infectious diseases more details view paper
  • Downloaded 457 times
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    • Site-wide: 80,868
    • In infectious diseases: 4,195
  • Year to date:
    • Site-wide: 56,913
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    • Site-wide: 78,699

Emergence and spread of SARS-CoV-2 lineages B.1.1.7 and P.1 in Italy

infectious diseases more details view paper
  • Downloaded 443 times
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    • Site-wide: 83,758
    • In infectious diseases: 4,257
  • Year to date:
    • Site-wide: 19,435
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    • Site-wide: 82,594

Metagenomic identification of diverse animal hepaciviruses and pegiviruses

microbiology more details view paper
  • Downloaded 437 times
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    • Site-wide: 84,844
    • In microbiology: 5,680
  • Year to date:
    • Site-wide: 105,080
  • Since beginning of last month:
    • Site-wide: 113,485

Metagenomic identification of viral sequences in laboratory reagents

molecular biology more details view paper
  • Downloaded 434 times
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    • Site-wide: 85,553
    • In molecular biology: 2,532
  • Year to date:
    • Site-wide: 20,052
  • Since beginning of last month:
    • Site-wide: 17,914

Sustained virome diversity in Antarctic penguins and their ticks: geographical connectedness and no evidence for low pathogen pressure

microbiology more details view paper
  • Downloaded 424 times
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    • Site-wide: 87,471
    • In microbiology: 5,887
  • Year to date:
    • Site-wide: 117,575
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    • Site-wide: 126,519

Meta-transcriptomic analysis of virus diversity in urban wild birds with paretic disease

microbiology more details view paper
  • Downloaded 422 times
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    • Site-wide: 87,887
    • In microbiology: 5,913
  • Year to date:
    • Site-wide: 154,194
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    • Site-wide: 162,827

Divergent influenza-like viruses of amphibians and fish support an ancient evolutionary association

microbiology more details view paper
  • Downloaded 409 times
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    • Site-wide: 90,561
    • In microbiology: 6,141
  • Year to date:
    • Site-wide: 133,312
  • Since beginning of last month:
    • Site-wide: 149,324

Punctuated evolution of myxoma virus: rapid and disjunct evolution of a recent viral lineage in Australia

evolutionary biology more details view paper
  • Downloaded 404 times
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    • Site-wide: 91,735
    • In evolutionary biology: 4,590
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    • Site-wide: 149,938
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    • Site-wide: 137,364

Meta-transcriptomic detection of diverse and divergent RNA viruses in green and chlorarachniophyte algae

microbiology more details view paper
  • Downloaded 403 times
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    • Site-wide: 91,899
    • In microbiology: 6,247
  • Year to date:
    • Site-wide: 94,276
  • Since beginning of last month:
    • Site-wide: 97,025

Portable sequencing in the field and the classroom: a retrospective examination of the circulation of DENV1 and DENV2 in Brazil

genetic and genomic medicine more details view paper
  • Downloaded 400 times
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    • Site-wide: 92,414
    • In genetic and genomic medicine: 482
  • Year to date:
    • Site-wide: 82,754
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    • Site-wide: 91,976

Metagenomic discovery and co-infection of diverse wobbly possum disease viruses and novel hepaciviruses in Australian brushtail possums

pathology more details view paper
  • Downloaded 398 times
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    • Site-wide: 92,911
    • In pathology: 473
  • Year to date:
    • Site-wide: 148,524
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    • Site-wide: 125,787

Slippery when wet: cross-species transmission of divergent coronaviruses in bony and jawless fish and the evolutionary history of the Coronaviridae

microbiology more details view paper
  • Downloaded 391 times
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    • Site-wide: 94,502
    • In microbiology: 6,492
  • Year to date:
    • Site-wide: 23,579
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    • Site-wide: 36,970

Red fox viromes across an urban-rural gradient

microbiology more details view paper
  • Downloaded 385 times
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    • Site-wide: 95,897
    • In microbiology: 6,586
  • Year to date:
    • Site-wide: 73,920
  • Since beginning of last month:
    • Site-wide: 59,277

Metagenomic sequencing reveals a lack of virus exchange between native and invasive freshwater fish across the Murray-Darling Basin, Australia

microbiology more details view paper
  • Downloaded 382 times
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    • Site-wide: 96,529
    • In microbiology: 6,645
  • Year to date:
    • Site-wide: 24,449
  • Since beginning of last month:
    • Site-wide: 61,862

Influenza Viruses in Mice: Deep Sequencing Analysis of Serial Passage and Effects of Sialic Acid Structural Variation

microbiology more details view paper
  • Downloaded 373 times
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    • Site-wide: 98,779
    • In microbiology: 6,822
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    • Site-wide: 147,985
  • Since beginning of last month:
    • Site-wide: 142,128

Limited overlap in RNA virome composition among rabbits and their ectoparasites reveals barriers to virus transmission

microbiology more details view paper
  • Downloaded 372 times
  • Download rankings, all-time:
    • Site-wide: 98,965
    • In microbiology: 6,836
  • Year to date:
    • Site-wide: 117,215
  • Since beginning of last month:
    • Site-wide: 98,739

Epidemiological and Genomic analysis of a Sydney Hospital COVID-19 Outbreak

infectious diseases more details view paper
  • Downloaded 312 times
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    • Site-wide: 113,662
    • In infectious diseases: 5,076
  • Year to date:
    • Site-wide: 32,860
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    • Site-wide: 51,316

A Reptilian Endogenous Foamy Virus Sheds Light on the Early Evolution of Retroviruses

evolutionary biology more details view paper
  • Downloaded 300 times
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    • Site-wide: 116,682
    • In evolutionary biology: 5,749
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    • Site-wide: 157,922
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    • Site-wide: 133,734

Circumpolar diversification of the Ixodes uriae tick virome

microbiology more details view paper
  • Downloaded 288 times
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    • Site-wide: 120,038
    • In microbiology: 8,613
  • Year to date:
    • Site-wide: 147,557
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    • Site-wide: 157,639

Assessment of COVID-19 intervention strategies in the Nordic countries using genomic epidemiology

epidemiology more details view paper
  • Downloaded 286 times
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    • Site-wide: 120,378
    • In epidemiology: 5,104
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    • Site-wide: 36,958
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    • Site-wide: 51,046

Frequent intergenotypic recombination between the non-structural and structural genes is a major driver of epidemiological fitness in caliciviruses

microbiology more details view paper
  • Downloaded 276 times
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    • Site-wide: 123,237
    • In microbiology: 8,890
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    • Site-wide: 38,921
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    • Site-wide: 35,735

The discovery of three new hare lagoviruses reveals unexplored viral diversity in this genus

microbiology more details view paper
  • Downloaded 257 times
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    • Site-wide: 128,161
    • In microbiology: 9,326
  • Year to date:
    • Site-wide: 162,944
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    • Site-wide: 153,790

A novel rubi-like virus in the Pacific electric ray (Tetronarce californica) reveals the complex evolutionary history of the Matonaviridae

microbiology more details view paper
  • Downloaded 210 times
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    • Site-wide: 140,208
    • In microbiology: 10,407
  • Year to date:
    • Site-wide: 55,423
  • Since beginning of last month:
    • Site-wide: 116,861

A divergent Articulavirus in an Australian gecko identified using meta-transcriptomics and protein structure comparisons

microbiology more details view paper
  • Downloaded 187 times
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    • Site-wide: 145,837
    • In microbiology: 10,929
  • Year to date:
    • Site-wide: 157,064
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    • Site-wide: 152,675

Meta-transcriptomic identification of divergent Amnoonviridae in fish

microbiology more details view paper
  • Downloaded 180 times
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    • Site-wide: 147,422
    • In microbiology: 11,056
  • Year to date:
    • Site-wide: 119,756
  • Since beginning of last month:
    • Site-wide: 118,448

Retrospective meta-transcriptomic identification of severe dengue in a traveller returning from Africa to Sweden, 1990

infectious diseases more details view paper
  • Downloaded 147 times
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    • Site-wide: 153,893
    • In infectious diseases: 6,267
  • Year to date:
    • Site-wide: 135,181
  • Since beginning of last month:
    • Site-wide: 121,093

Meta-transcriptomic discovery of a divergent circovirus and a chaphamaparvovirus in captive reptiles with proliferative respiratory syndrome

microbiology more details view paper
  • Downloaded 146 times
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    • Site-wide: 154,017
    • In microbiology: 11,700
  • Year to date:
    • Site-wide: 157,713
  • Since beginning of last month:
    • Site-wide: 159,886

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