Table 1.
In-house-developed specific primers used for nested RT-PCR of SARS-CoV-2 virus.
| Stage Polarity | Primer Name | Nucleotide Position | Nucleotide Sequence (5′-3′) | |
|---|---|---|---|---|
| hCoV-Spike-D | PCR 1st Sense | 22,632S | 22,632–22,652 | GAATCAGCAACTGTGTTGCTG |
| PCR 1st Sense | 22,659S | 22,659–22,680 | CTGTCCTATATAATTCCGCATC | |
| PCR 1st Sense | 22,659S-Omi | 22,659–22,680 | CTGTCCTATATAATCTCGCACC | |
| PCR 1st Antisense | SP35AS | 23,612–23,631 | TGACTAGCTACACTACGTGC | |
| PCR 1st Antisense | SP36AS | 23,577–23,598 | TTAGTCTGAGTCTGATAACTAG | |
| PCR 2nd Sense | 22,687S | 22,687–22,708 | CACTTTTAAGTGTTATGGAGTG | |
| PCR 2nd Sense | 22,712S | 22,712–22,734 | CCTACTAAATTAAATGATCTCTG | |
| PCR 2nd Antisense | SP37AS | 23,556–23,575 | GCATATACCTGCACCAATGG | |
| PCR 2nd Antisense | SP38AS | 23,533–23,554 | TATGTCACACTCATATGAGTTG | |
| hCoV-full-a | PCR 1st Sense | 45S | 37–64 | CAACTTTCGATCTCTTGTAGATCTGTTC |
| PCR 1st Antisense | a-1-2 | 1926–1953 | TGTAAAACACGCACAGAATTTTGAGCAG | |
| PCR 2nd Sense | 85S | 77–102 | TTAAAATCTGTGTGGCTGTCACTCGG | |
| PCR 2nd Antisense | a-2-2 | 1890–1914 | CGGGAGAAAATTGATCGTACAACAC | |
| hCoV-full-b | PCR 1st Sense | b-1-1 | 1721–1743 | GCTTTTGTGGAAACTGTGAAAGG |
| PCR 1st Antisense | b-1-2 | 3878–3902 | GCTTAACTTCCTCTTTAGGAATCTC | |
| PCR 2nd Sense | b-2-1 | 1763–1785 | AAACAAATTGTTGAATCCTGTGG | |
| PCR 2nd Antisense | b-2-2 | 3838–3863 | CAACTTGCTTTTCACTCTTCATTTCC | |
| hCoV-full-c | PCR 1st Sense | c-1-1 | 3642–3666 | AAGACATTCAACTTCTTAAGAGTGC |
| PCR 1st Antisense | c-1-2 | 5830–5854 | AATAGGACCTTTGTATTCTGAGGAC | |
| PCR 2nd Sense | c-2-1 | 3683–3706 | CAGCACGAAGTTCTACTTGCACCA | |
| PCR 2nd Antisense | c-2-2 | 5750–5775 | TTATAGTGACCACACTGGTAATTACC | |
| hCoV-full-d | PCR 1st Sense | d-1-1 | 5572–5597 | GTACATGGGCACACTTTCTTATGAAC |
| PCR 1st Antisense | d-1-2 | 7764–7790 | CAGCTTTATCAAAGTAAAGATGGATGG | |
| PCR 2nd Sense | d-2-1 | 5610–5634 | GTGTTCAGATACCTTGTACGTGTGG | |
| PCR 2nd Antisense | d-2-2 | 7725–7751 | CTGTAACACTATCAACGATGTAAGAAG | |
| hCoV-full-e | PCR 1st Sense | e-1-1 | 7533–7560 | GTACAACTATTGTTAATGGTGTTAGAAG |
| PCR 1st Antisense | e-1-2 | 9729–9753 | CTCTTTAGGTAATTACTAAAGAACC | |
| PCR 2nd Sense | e-2-1 | 7570–7594 | TGTCTATGCTAATGGAGGTAAAGGC | |
| PCR 2nd Antisense | e-2-2 | 9692–9719 | GCTTTGTGGAAATACAAATGATATAAGC | |
| hCoV-full-f | PCR 1st Sense | f-1-1 | 9518–9543 | TTCCTTATGTCATTCACTGTACTCTG |
| PCR 1st Antisense | f-1-2 | 11,669–11,694 | ACACCAAGAGTCAGTCTAAAGTAGCG | |
| PCR 2nd Sense | f-2-1 | 9558–9584 | ACTCATTCTTACCTGGTGTTTATTCTG | |
| PCR 2nd Antisense | f-2-2 | 11,634–11,659 | ACAAAAGAGGCCAAAGTAACAAGTAC | |
| hCoV-full-g | PCR 1st Sense | g-1-1 | 11,459–11,483 | TCCATGTGGGCTCTTATAATCTCTG |
| PCR 1st Antisense | g-1-2 | 13,598–13,624 | CTTCGTCCTTTTCTTGGAAGCGACAAC | |
| PCR 2nd Sense | g-2-1 | 11,494–11,518 | CTACTCAGGTGTAGTTACAACTGTC | |
| PCR 2nd Antisense | g-2-2 | 13,554–13,579 | TAGCAAAACCAGCTACTTTATCATTG | |
| hCoV-full-h | PCR 1st Sense | h-1-1 | 13,384–13,407 | CGGTATGTGGAAAGGTTATGGCTG |
| PCR 1st Antisense | h-1-2 | 15,569–15,595 | ACTTATCGGCAATTTTGTTACCATCAG | |
| PCR 2nd Sense | h-2-1 | 13,418–13,441 | CAACTCCGCGAACCCATGCTTCAG | |
| PCR 2nd Antisense | h-2-2 | 15,538–15,563 | AAAAGTGCATTAACATTGGCCGTGAC | |
| hCoV-full-i | PCR 1st Sense | i-1-1 | 15,334–15,359 | ATTATGGCCTCACTTGTTCTTGCTCG |
| PCR 1st Antisense | i-1-2 | 17,506–17,533 | CTATAGTTTTCATAAGTCTACACACTCC | |
| PCR 2nd Sense | i-2-1 | 15,380–15,406 | GCTTGTCACACCGTTTCTATAGATTAG | |
| PCR 2nd Antisense | i-2-2 | 17,453–17,478 | CTTAGTTAGCAATGTGCGTGGTGCAG | |
| hCoV-full-j | PCR 1st Sense | j-1-1 | 17,278–17,304 | GTGAATTCAACATTAGAACAGTATGTC |
| PCR 1st Antisense | j-1-2 | 19,477–19,502 | GCATGATGTCTACAGACAGCACCACC | |
| PCR 2nd Sense | j-2-1 | 17,317–17,341 | AATGCATTGCCTGAGACGACAGCAG | |
| PCR 2nd Antisense | j-2-2 | 19,448–19,473 | ATTGCAACGTGTTATACACGTAGCAG | |
| hCoV-full-k | PCR 1st Sense | k-1-1 | 19,239–19,264 | ATTTGACACTAGAGTGCTATCTAACC |
| PCR 1st Antisense | k-1-2 | 21,423–21,449 | TCTTTTAAAGACATAACAGCAGTACCC | |
| PCR 2nd Sense | k-2-1 | 19,275–19,300 | TGGTTGTGATGGTGGCAGTTTGTATG | |
| PCR 2nd Antisense | k-2-2 | 21,386–21,412 | GGGGAAATTTACTCATGTCAAATAAAG | |
| hCoV-full-l | PCR 1st Sense | l-1-1 | 25,369–25,396 | ATTACATTACACATAAACGAACTTATGG |
| PCR 1st Antisense | l-1-2 | 27,416–27,442 | GCTCACAAGTAGCGAGTGTTATCAGTG | |
| PCR 2nd Sense | l-2-1 | 25,398–25,424 | TTTGTTTATGAGAATCTTCACAATTGG | |
| PCR 2nd Antisense | l-2-2 | 27,358–27,384 | ATCAATCTCCATTGGTTGCTCTTCATC | |
| hCoV-full-m | PCR 1st Sense | m-1-1 | 27,175–27,201 | CTTTGCTTGTACAGTAAGTGACAACAG |
| PCR 1st Antisense | m-1-2 | 28,771–28,797 | CTTCTGCGTAGAAGCCTTTTGGCAATG | |
| PCR 2nd Sense | m-2-1 | 27,211–27,236 | CTCGTTGACTTTCAGGTTACTATAGC | |
| PCR 2nd Antisense | m-2-2 | 28,737–28,763 | TTGAGGAAGTTGTAGCACGATTGCAGC | |
| hCoV-full-n | PCR 1st Sense | n-1-1 | 28,539–28,563 | AGAGCTACCAGACGAATTCGTGGTG |
| PCR 1st Antisense | n-1-2 | 29,854–29,882 | TTTTTTTTTTTGTCATTCTCCTAAGAAGC | |
| PCR 2nd Sense | n-2-1 | 28,595–28,621 | ATGGTATTTCTACTACCTAGGAACTGG | |
| PCR 2nd Antisense | n-2-2 | 29,826–29,852 | ATTAAAATCACATGGGGATAGCACTAC | |
| hCoV-full-S1 | PCR 1st Sense | 20,963S | 20,955–20,980 | TCTTAATGACTTTGTCTCTGATGCAG |
| PCR 1st Sense | 21,018S | 21,010–21,034 | GTACATACAGCTAATAAATGGGATC | |
| PCR 1st Antisense | 23,504AS | 23,496–23,518 | CCCTATTAAACAGCCTGCACGTG | |
| PCR 2nd Sense | 21,050S | 21,042–21,065 | TAGTGATATGTACGAC CCTAAGAC | |
| PCR 2nd Sense | 21,018S | 21,010–21,034 | GTACATACAGCTAATAAATGGGATC | |
| PCR 2nd Antisense | 23,461AS | 23,453–23,476 | TGTAGAATAAACACGCCAAGTAGG | |
| hCoV-full-S2 | PCR 1st Sense | 23,254S | 23,246–23,270 | TTYCAACAATTTGGCAGAGACATTG |
| PCR 1st Antisense | 25,666AS | 25,658–25,681 | CGAGCAAAAGGTGTGAGTAAACTG | |
| PCR 2nd Sense | 23,283S | 23,275–23,297 | CACTACTGATGCTGTCCGTGATC | |
| PCR 2nd Antisense | 25,619AS | 25,611–25,633 | AAACAAAGTGAACACCCTTGGAG |