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Volume 19, Number 11—November 2013

Dispatch

Middle East Respiratory Syndrome Coronavirus in Bats, Saudi Arabia

Ziad A. Memish, Nischay Mishra, Kevin J. Olival, Shamsudeen F. Fagbo, Vishal Kapoor, Jonathan H. Epstein, Rafat AlHakeem, Abdulkareem Durosinloun, Mushabab Al Asmari, Ariful Islam, Amit Kapoor, Thomas Briese, Peter Daszak, Abdullah A. Al Rabeeah, and W. Ian LipkinComments to Author 
Author affiliations: Ministry of Health, Riyadh, Saudi Arabia (Z.A. Memish, S.F. Fagbo, R. AlHakeem, A. Durosinloun, A.A. Al Rabeeah); Columbia University, New York, New York, USA (N. Mishra, V. Kapoor, A. Kapoor, T. Briese, W.I. Lipkin); EcoHealth Alliance, New York (K.J. Olival, J.H. Epstein, P. Daszak); Ministry of Health, Bisha, Saudi Arabia (M. Al Asmari); EcoHealth Alliance, Dhaka, Bangladesh (A. Islam)

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Table 1

PCRs and primers used in CoV detection*

PCRs (reference) Primers, 5′→3′ Nested fragment size, region (primer locations on the reference) genome)† Type of CoV (no.)
Nested pan-CoV-I (6) PLQ-F1, CGTTGGIACWAAYBTVCCWYTICARBTRGG ≈400 nt, RdRp (18310–187450) α-CoV (8), β-CoV (1)
PLQ-R1, GGTCATKATAGCRTCAVMASWWGCNACATG
PLQ-F2, GGCWCCWCCHGGNGARCAATT
PLQ-R2, GGWAWCCCCAYTGYTGWAYRTC
Nested pan-CoV-II (7) WT-COV-F1, GGTTGGGAYTAYCCHAARTGTGA ≈430 nt, RdRp (15260–15700) α-CoV (5), β-CoV (2)
WT-COV-R1, CCATCATCASWYRAATCATCATA
WT-COV-F2, GAYTAYCCHAARTGTGAYAGAGC
WT-COV-F3, GAYTAYCCHAARTGTGAUMGWGC
Hemi-nested RdRp-sequence assay (9) EMC-SeqRdRP-Rev, GCATWGCNCWGTCACACTTAGG ≈230 nt, RdRp (15048–15290) α-CoV (2), β-CoV (1)
EMC-SeqRdRP-Fwd, TGCTATWAGTGCTAAGAATAGRGC
EMC-SeqRdRP-Rnest, CACTTAGGRTARTCCCAWCCCA
Hemi-nested N-sequence assay (9) EMC-SeqN-Fwd, CCTTCGGTACAGTGGAGCCA ≈280 nt,N seq (29,549–29,860)
EMC-SeqN-Rev, GATGGGGTTGCCAAACACAAAC
EMC-SeqN-Fnest, TGACCCAAAGAATCCCAACTAC
Nested CII-pan-CoV-III NM-CoV-2F1, ACWGTTCARGGICCWCCIGG ≈355 nt, helicase (17,060–17,410) β-CoV (2)
NM-CoV-2F2, GTTCARGGGCCWCCGGGNAC
NM-CoV-2R1, GGCAGCTGWGCWGGRTCICCNACRTA
NM-CoV-2R2, AGCTGWGCWGGRTCGCCIACRTANAC
Nested CII-MERS-RdRp NM-HCOV-F1, GTGCTAAGAATAGAGCTCGCACT
NM-HCOV-F2, AGAGCTCGCACTGTTGCAGGC ≈190 nt, RdRp (15068–15249) β-CoV (1, MERS CoV)
NM-HCOV-F2, AGAGCTCGCACTGTTGCAGGC
NM-HCOV-R1, ACCCATAAGATGCGGATTATCAAC
NM-HCOV-R2, TGCGGATTATCAACATCTTTGTAC
Hemi-nested CII-MERS N sequence NM-NSeq-F-1, ACTTCCTTCGGTACAGTGGAGC ≈170 nt, N seq (29545–29713)
NM-NSeq-R-1, GGCACTGTTCACTTGCAATC
NM-NSeq-R-2, GGAGGTTCAGACATTTGGTCT
upE and ORF1b real-time assays (8) upE-Fwd: GCAACGCGCGATTCAGTT Upstream of E gene and ORF 1b
upE-Prb: FAM-CTCTTCACATAATCGCCCCGAGCTCG-TAMRA
upE-Rev: GCCTCTACACGGGACCCATA
ORF1b-Fwd: TTCGATGTTGAGGGTGCTCAT
ORF1b-Prb: FAM-CCCGTAATGCATGTGGCACCAATGT-TAMRA
ORF1b-Rev: TCACACCAGTTGAAAATCCTAATTG

* CoV, coronavirus; MERS, Middle East respiratory syndrome; RdRp, RNA-dependent RNA polymerase; –, not applicable; ORF, open reading frame.
†Primer locations are based on human β-CoV 2c EMC/2012, complete genome (GenBank accession no. JX869059).

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