Methods, oligonucleotides, and kits for detection and treatment of coronavirus

An oligonucleotide having a 5′ terminus and a 3′ terminus, wherein the nucleotide sequence of the oligonucleotide consists of 40 or less continuous nucleotides from a nucleotide sequence selected from the group consisting of:

• SEQ ID NO:1, SEQ ID NO:2. SEQ ID NO:3, SEQ ID NO:4, and SEQ ID NO:5, 40 or less continuous nucleotides from a sequence complementary to a nucleotide sequence selected from the group consisting of:
• SEQ ID NO:
• 1, SEQ ID NO:2, SEQ ID NO:3, SEQ ID NO:
• 4, and SEQ ID NO:5, or is a variant thereof.

A method of detecting the presences of a coronavirus polynucleotides in a biological sample in vitro, comprising:

• (a) mixing the biological sample in vitro with a primer pair that is capable of amplifying a coronavirus amplicon product comprising a region of a nucleotide sequence selected from the group consisting of:
• SEQ ID NO:1, SEQ ID NO:2, SEQ ID NO:3, SEQ ID NO:4, and SEQ ID NO:5, if the coronavirus polynucleotide is present in the biological sample, wherein the sequence of at least one primer of the primer pair comprises 40 or less continuous nucleotides from a nucleotide sequence selected from the group consisting of:
• SEQ ID NO:1, SEQ ID NO:2, SEQ ID NO:3, SEQ ID NO:4, and SEQ ID NO:5, or is a variant thereof;
• (b) amplifying the coronavirus amplicon product:
• (c) contacting the coronavirus amplicon product with a probe having a nucleotide sequence capable of hybridizing to the coronavirus amplicon product, the probe being modified with an internal spacer or detectable label:
• and
• (d) detecting whether coronavirus polynucleotides are present in the biological sample by detecting the detectable label when the probe hybridizes to the coronavirus amplicon.

A method of detecting a coronavirus in a sample, comprising:

• extracting nucleic acids from the sample:
• amplifying a 3′ untranslated region (UTR) of the coronavirus genome to produce an amplification product:
• and
• detecting in the amplification product the presence or absence of one or more single nucleotide polymorphisms (SNPs), wherein the one or more SNPs correspond to a nucleotide position of the coronavirus genome selected from the group consisting of position 29567, position 29581, position 29582, position 29597, position 29631, position 29635, position 29637, position 29649, position 29651, position 29688, position 29732, position 29735, position 29758, and position 29769.