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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]