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Table 1 Viruses included in target enrichment panel

From: Enrichment post-library preparation enhances the sensitivity of high-throughput sequencing-based detection and characterization of viruses from complex samples

Virus

Genome size (kb)

Genome type

NCBI accession(s) of reference used in probe design

Notes

Nipah virus

18,246

Negative sense ssRNA

NC_002728.1

New addition to probe panel

Bat Paramyxovirus

18,530

Negative sense ssRNA

NC_025256.1

New addition to probe panel

Cedar virus

18,162

Negative sense ssRNA

JQ001776.1

New addition to probe panel

Hendra virus

18,234

Negative sense ssRNA

NC_001906.3

New addition to probe panel

Tioman virus

15,522

Negative sense ssRNA

NC_004074.1

New addition to probe panel

Menangle virus

15,516

Negative sense ssRNA

NC_007620.1

New addition to probe panel

Middle East Respiratory Syndrome Coronavirus

30,094

Positive sense ssRNA

KJ614529.1

New addition to probe panel

Severe Acute Respiratory Syndrome virus

29,751

Positive sense ssRNA

NC_004718.3

New addition to probe panel

Lujo virus

10,352

Negative sense ssRNA

NC_012776.1, NC_012777.1

New addition to probe panel

Lassa fever virus

10,681

Negative sense ssRNA

NC_004296.1, NC_004297.1

New addition to probe panel

Machupo virus

10,635

Negative sense ssRNA

NC_005078.1, NC_005079.1

New addition to probe panel

Junin virus

10,525

Negative sense ssRNA

NC_005080.1, NC_005081.1

New addition to probe panel

Guanarito virus

10,424

Negative sense ssRNA

NC_005077.1, NC_005082.1

New addition to probe panel

Chapare virus

10,464

Negative sense ssRNA

NC_010562.1, NC_010563.1

New addition to probe panel

Sabia virus

10,499

Negative sense ssRNA

NC_006313.1, NC_006317.1

New addition to probe panel

Hantaan virus

11,845

Negative sense ssRNA

NC_005218.1, NC_005219.1, NC_005222.1

New addition to probe panel

Puumala virus

12,062

Negative sense ssRNA

NC_005223.1, NC_005224.1, NC_005225.1

New addition to probe panel

Sin nombre virus

12,317

Negative sense ssRNA

NC_005215.1, NC_005216.1, NC_005217.1

New addition to probe panel

Andes virus

12,104

Negative sense ssRNA

NC_003466.1, NC_003467.1, NC_003468.1

New addition to probe panel

Rift Valley fever virus

11,979

Negative sense ssRNA

NC_014395.1, NC_014396.1, NC_014397.1

New addition to probe panel

Crimean Congo hemorrhagic fever virus

19,146

Negative sense ssRNA

NC_005300.2, NC_005301.3, NC_005302.1

New addition to probe panel

Omsk hemorrhagic fever virus

10,787

Positive sense ssRNA

NC_005062.1

New addition to probe panel

Kyasanur forest disease virus

10,774

Positive sense ssRNA

JF416958.1

New addition to probe panel

Alkhurma hemorrhagic fever virus

10,685

Positive sense ssRNA

NC_004355.1

New addition to probe panel

Eastern equine encephalitis virus

11,703

Positive sense ssRNA

KJ469643.1

New addition to probe panel

Dengue type 1 virus

10,721

Positive sense ssRNA

AF309641.1

New addition to probe panel

Dengue type 2 virus

10,723

Positive sense ssRNA

EF051521.1

New addition to probe panel

Dengue type 3 virus

10,707

Positive sense ssRNA

AY662691

New addition to probe panel

Dengue type 4 virus

10,653

Positive sense ssRNA

AY618989

New addition to probe panel

Chikungunya virus

11,826

Positive sense ssRNA

NC_004162

New addition to probe panel

Bat coronavirus CDPHE15

28,035

Positive sense ssRNA

NC_022103.1

New addition to probe panel

Bat coronavirus 1A

28,326

Positive sense ssRNA

NC_010437.1

New addition to probe panel

Bat coronavirus 1B

28,476

Positive sense ssRNA

NC_010436.1

New addition to probe panel

Bat coronavirus HKU2

27,165

Positive sense ssRNA

NC_009988.1

New addition to probe panel

Bat SARS coronavirus HKU3–4

29,704

Positive sense ssRNA

GQ153539.1

New addition to probe panel

Bat coronavirus HKU4

30,286

Positive sense ssRNA

NC_009019

New addition to probe panel

Bat coronavirus HKU5–1

30,482

Positive sense ssRNA

NC_009020

New addition to probe panel

Bat coronavirus HKU8

28,773

Positive sense ssRNA

NC_010438.1

New addition to probe panel

Bat coronavirus HKU9–1

29,114

Positive sense ssRNA

NC_009021.1

New addition to probe panel

Bat coronavirus HKU10

28,494

Positive sense ssRNA

NC_018871.1

New addition to probe panel

Zika virus

10,794

Positive sense ssRNA

NC_012532

New addition to probe panel

Respiratory Syncytial virus B (S2)

15,190

Negative sense ssRNA

NC_001803.1

Previously used in [13, 20]

Respiratory Syncytial virus A

15,225

Negative sense ssRNA

AY353550

Previously used in [13, 20]

Influenza virus A (H9N2)

13,500

Negative sense ssRNA

NC_004905.2, NC_004906.1, NC_004907.1, NC_004908.1, NC_004909.1, NC_004910.1, NC_004911.1, NC_004912.1

Previously used in [13, 20]

Influenza virus A (H2N2)

13,460

Negative sense ssRNA

NC_007374.1, NC_007375.1, NC_007376.1, NC_007377.1, NC_007378.1, NC_007380.1, NC_007381.1, NC_007382.1

Previously used in [13, 20]

Influenza virus A (H3N2)

13,630

Negative sense ssRNA

NC_007366.1, NC_007367.1, NC_007368.1, NC_007369.1, NC_007370.1, NC_007371.1, NC_007372.1, NC_007373.1

Previously used in [13, 20]

Influenza virus A (H1N1)

13,590

Negative sense ssRNA

NC_002016.1, NC_002017.1, NC_002018.1, NC_002019.1, NC_002020.1, NC_002021.1, NC_002022.1, NC_002023.1,

Previously used in [13, 20]

Influenza virus A (H5N1)

13,590

Negative sense ssRNA

NC_007357.1, NC_007358.1, NC_007359.1, NC_007360.1, NC_007361.1, NC_007362.1, NC_007363.1, NC_007364.1

Previously used in [13, 20]

Influenza virus A (H7N9)

13,590

Negative sense ssRNA

KC885955, KC885956, KC885957, KC885958, KC885959, KC885960, KC885961, KC885962

Previously used in [13, 20]

Influenza virus B

14,450

Negative sense ssRNA

NC_002204.1, NC_002205.1, NC_002206.1, NC_002207.1, NC_002208.1, NC_002209.1, NC_002210.1, NC_002211.1

Previously used in [13, 20]

Parainfluenza virus 1

15,600

Negative sense ssRNA

NC_003461.1

Previously used in [13, 20]

Parainfluenza virus 2

15,650

Negative sense ssRNA

NC_003443.1

Previously used in [13, 20]

Parainfluenza virus 3

15,460

Negative sense ssRNA

NC_001796.2

Previously used in [13, 20]

Parainfluenza virus 4

17,050

Negative sense ssRNA

NC_021928.1

Previously used in [13, 20]

Human metapneumovirus

13,340

Negative sense ssRNA

NC_004148.2

Previously used in [13, 20]

Adenovirus C

35,937

dsDNA

NC_001405.1

Previously used in [13, 20]

Adenovirus B

35,343

dsDNA

NC_011203.1

Previously used in [13, 20]

Adenovirus E

35,994

dsDNA

NC_003266.2

Previously used in [13, 20]

Human Coronavirus HKU1

29,930

Positive sense ssRNA

NC_006577.2

Previously used in [13, 20]

Human Coronavirus NL63

27,550

Positive sense ssRNA

NC_005831.2

Previously used in [13, 20]

Human Coronavirus 229E

27,320

Positive sense ssRNA

NC_002645.1

Previously used in [13, 20]

Human Coronavirus OC43

30,738

Positive sense ssRNA

AY391777.1

Previously used in [13, 20]

Rhinovirus A

7150

Positive sense ssRNA

NC_001617.1

Previously used in [13, 20]

Rhinovirus C

7100

Positive sense ssRNA

NC_001490.1

Previously used in [13, 20]

Rhinovirus B14

7210

Positive sense ssRNA

NC_001490.1

Previously used in [13, 20]

Human Bocavirus 1

5299

ssDNA

NC_007455.1

Previously used in [13, 20]

Human Bocavirus 2

5196

ssDNA

NC_012042.1

Previously used in [13, 20]

Human Bocavirus 3

5242

ssDNA

NC_012564.1

Previously used in [13, 20]

Human Bocavirus 4

5104

ssDNA

NC_012729.2

Previously used in [13, 20]

KI polyomavirus

5040

dsDNA

NC_009238.1

Previously used in [13, 20]

WU polyomavirus

5229

dsDNA

NC_009539.1

Previously used in [13, 20]

Human parechovirus type 1

7296

Positive sense ssRNA

FM242866.1

Previously used in [13, 20]

Human parechovirus type 6

7347

Positive sense ssRNA

AB252582.1

Previously used in [13, 20]

Human Enterovirus C104

7408

Positive sense ssRNA

AB686524.1

Previously used in [13, 20]

Human Enterovirus C109

7354

Positive sense ssRNA

GQ865517.1

Previously used in [13, 20]

Lloviu cuevavirus

18,927

Negative sense ssRNA

NC_016144

Previously used in [9,10,11]

Bundibugyo ebolavirus

18,940

Negative sense ssRNA

NC_014373

Previously used in [9,10,11]

Zaire ebolavirus

18,959

Negative sense ssRNA

NC_002549

Previously used in [9,10,11]

Reston ebolavirus

18,891

Negative sense ssRNA

NC_004161

Previously used in [9,10,11]

Sudan ebolavirus

18,875

Negative sense ssRNA

NC_006432

Previously used in [9,10,11]

Tai Forest ebolavirus

18,935

Negative sense ssRNA

NC_014372

Previously used in [9,10,11]

Marburg virus (isolate Marburg virus)

19,111

Negative sense ssRNA

NC_001608

Previously used in [9,10,11]

Marburg virus (isolate Ravn virus)

19,114

Negative sense ssRNA

NC_024781

Previously used in [9,10,11]

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BMC Genomics

ISSN: 1471-2164

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