EP-4735633-A1 - PANCORONAVIRUS BIOMARKER PANEL

Abstract

The present disclosure provides pancoronavirus biomarker panels that can be used to detect a wide variety of characterized coronavirus strains and, in some embodiments, emerging or novel coronavirus strains. In certain embodiments, this detection can be carried out in a single, highly-multiplexed nucleic acid amplification assay.

Inventors

• MEUZELAAR, LINDA STRÖMQVIST
• WANG, NING

Assignees

• Cepheid

Dates

Publication Date

20260506

Application Date

20240626

Claims (1)

1. Docket No. CPHDP021WO/51-018610WO CLAIMS What is claimed is: 1. A set of primers and/or probes for detecting the presence of pancoronavirus in a sample, the set comprising: at least one primer pair and/or probe specific for the RdRP gene, the ORF1a gene, or a combination thereof, of α-coronavirus; and at least one primer pair and/or probe specific for the RdRP gene, the ORF1a gene, or a combination thereof, of all three of β-coronavirus, γ-coronavirus, and δ- coronavirus. 2. A set of primers and probes for detecting the presence of pancoronavirus in a sample, the set comprising: at least one primer pair and probe specific for the RdRP gene, the ORF1a gene, or a combination thereof, of α-coronavirus; and at least one primer pair and probe specific for the RdRP gene, the ORF1a gene, or a combination thereof, of β-coronavirus, γ-coronavirus, and δ-coronavirus. 3. A set of primers and/or probes for detecting the presence of pancoronavirus in a sample, the set comprising: at least one primer pair specific for the RdRP gene, the ORF1a gene, or a combination thereof, of α-coronavirus, γ-coronavirus, β-coronavirus and δ-coronavirus; at least one probe specific for the RdRP gene, the ORF1a gene, or a combination thereof, of α-coronavirus and γ-coronavirus; and at least one probe specific for the RdRP gene, the ORF1a gene, or a combination thereof, of β-coronavirus and δ-coronavirus. 4. The set of any one of claims 1-3, wherein the set additionally comprises: at least one primer pair and/or probe specific for the ORF1ab gene of β-coronavirus C. 5. The set of any one of claims 1-4, wherein the set additionally comprises: Docket No. CPHDP021WO/51-018610WO at least one primer pair and/or probe specific for the E gene, N gene, RDRP gene, or a combination thereof, of SARS-CoV-2, preferably all three of the E gene, N gene, and RDRP gene of SARS-CoV-2. 6. The set of any one of claims 1-5, wherein the set additionally comprises: at least one primer pair and/or probe specific for the N gene of β- coronavirus C. 7. The set of any one of claims 1-6, wherein the set additionally comprises: at least one primer pair and/or probe specific for the ORF1a gene, S2 gene, or a combination thereof, of SARS-CoV-1. 8. The set of any one of claims 1-7, wherein the set additionally comprises: at least one primer pair and/or probe specific for the ORF1a gene of β-coronavirus A. 9. The set of any one of claims 1-8, wherein the set additionally comprises: at least one primer pair and/or probe specific for the S gene of α- coronavirus. 10. A set of primers and/or probes for detecting the presence of pancoronavirus in a sample, the set comprising: at least one primer pair and/or probe specific for the N gene of β- coronavirus C; at least one primer pair and/or probe specific for the ORF1ab gene of β-coronavirus C; at least one primer pair and/or probe specific for the ORF1a gene, S gene, or a combination thereof, of SARS-CoV-1; at least one primer pair and/or probe specific for the E gene, N gene, RDRP gene, or a combination thereof, of SARS-CoV-2; at least one primer pair and/or probe specific for the ORF1a gene of β-coronavirus A; and Docket No. CPHDP021WO/51-018610WO at least one primer pair and/or probe specific for the S gene of α- coronavirus. 11. The set of claim 10, wherein the set additionally comprises: at least one primer pair specific for the RdRP gene, the ORF1a gene, or a combination thereof, of α-coronavirus, γ-coronavirus, β-coronavirus and δ-coronavirus; at least one probe specific for the RdRP gene, the ORF1a gene, or a combination thereof, of α-coronavirus and γ-coronavirus; and at least one probe specific for the RdRP gene, the ORF1a gene, or a combination thereof, of β-coronavirus and δ-coronavirus. 12. The set of any one of claims 1-11, wherein, when present: the at least one primer pair and/or probe specific for the N gene of β- coronavirus C comprises an oligonucleotide sequence present in MERS-CoV but not conserved across Merbecovirus; the at least one primer pair and/or probe specific for the ORF1ab gene of β-coronavirus C comprises an oligonucleotide sequence conserved across Merbecovirus; the at least one primer pair and/or probe specific for the E gene of SARS-CoV-2 comprises an oligonucleotide sequence conserved across Sarbecovirus; the at least one primer pair and/or probe specific for the ORF1a gene of β-coronavirus A comprises an oligonucleotide sequence present in CoV-OC43 and CoV- HKU1; and/or the at least one primer pair and/or probe specific for the S gene of α- coronavirus A comprises an oligonucleotide sequence present in CoV-229E and CoV- NL63. 13. The set of claim 12, wherein: the at least one primer pair and/or probe specific for the ORF1a gene of β-coronavirus A is not conserved across β-coronavirus A; and the at least one primer pair and/or probe specific for the S gene of α- coronavirus A is not conserved across α-coronavirus A. 14. The set of claim 12, wherein the set comprises the at least one primer pair and/or probe specific for the ORF1a gene of β-coronavirus A, which comprises: Docket No. CPHDP021WO/51-018610WO at least one primer pair and/or probe specific for the ORF1a gene of CoV-OC43; and/or at least one primer pair and/or probe specific for the ORF1a gene of CoV-HKU1. 15. The set of claim 14, wherein the at least one primer pair specific for the ORF1a gene of CoV-OC43 and the at least one primer pair specific for the ORF1a gene of CoV-HKU1 have greater than 85% homology. 16. The set of claim 12 or claim 14, wherein the set comprises at least one primer pair and/or probe specific for the S gene of α-coronavirus, which comprises: at least one primer pair and/or probe specific for the S gene of CoV- 229E; and/or at least one primer pair and/or probe specific for the S gene of CoV- NL63. 17. The set of claim 16, wherein the at least one primer pair specific for the S gene of CoV-229E and the at least one primer pair specific for the S gene of CoV- NL63 have greater than 85% homology. 18. The set of any one of claims 1-9, wherein: the at least one primer pair and/or probe specific for the RdRP gene, the ORF1a gene, or a combination thereof, of α-coronavirus comprises an oligonucleotide sequence conserved across α-coronavirus; and the at least one primer pair and/or probe specific for the RdRP gene, the ORF1a gene, or a combination thereof, of β-coronavirus, γ-coronavirus, and δ- coronavirus comprises an oligonucleotide sequence present in β-coronavirus A, β- coronavirus D, γ-coronavirus, and δ-coronavirus but not conserved in Merbecovirus (β- coronavirus C) and/or not in Sarbecovirus (β-coronavirus B). 19. The set of any one of claims 1-9, wherein: the at least one primer pair specific for the RdRP gene, the ORF1a gene, or a combination thereof, of α-coronavirus, γ-coronavirus, β-coronavirus and δ- coronavirus comprises an oligonucleotide sequence conserved across all α-coronavirus, γ- coronavirus, β-coronavirus and δ-coronavirus; Docket No. CPHDP021WO/51-018610WO the at least one probe specific for the RdRP gene, the ORF1a gene, or a combination thereof, of α-coronavirus and γ-coronavirus comprises at least one oligonucleotide sequence present in α-coronavirus, and at least one oligonucleotide sequence present in γ-coronavirus; and the at least one probe specific for the RdRP gene, the ORF1a gene, or a combination thereof, of β-coronavirus and δ-coronavirus comprises at least one oligonucleotide sequence present in β-coronavirus, and at least one oligonucleotide sequence present in δ-coronavirus, wherein the at least one oligonucleotide sequence present in β- coronavirus is not conserved in Merbecovirus (β-coronavirus C) and/or in Sarbecovirus (β- coronavirus B). 20. The set of claim 10, wherein: the at least one primer pair and/or probe specific for the N gene of β- coronavirus C comprises at least one primer pair and/or probe specific for the N gene of MERS-CoV, wherein the N gene is not conserved across Merbecovirus; the at least one primer pair and/or probe specific for the ORF1ab gene of β-coronavirus C comprises at least one primer pair and/or probe specific for the ORF1ab gene of MERS-CoV, wherein the ORF1ab gene is conserved across Merbecovirus; the at least one primer pair and/or probe specific for the ORF1a gene, S gene, or a combination thereof, of SARS-CoV-1 comprises: at least one primer pair and/or probe specific for the ORF1a gene of SARS-CoV-1, wherein the ORF1a gene is not conserved across Sarbecovirus; or at least one primer pair and/or probe specific for the S gene of SARS-CoV-1, wherein the S gene is not conserved across Sarbecovirus; the at least one primer pair and/or probe specific for the E gene, N gene, RDRP gene, or a combination thereof, of SARS-CoV-2 comprises: at least one primer pair and/or probe specific for the E gene of SARS-CoV-2, wherein the E gene is conserved across Sarbecovirus; and at least one primer pair and/or probe specific for the N gene of SARS-CoV-2, wherein the N gene is not conserved across Sarbecovirus; and/or Docket No. CPHDP021WO/51-018610WO at least one primer pair and/or probe specific for the RDRP gene of SARS-CoV-2, wherein the RDRP gene is not conserved across Sarbecovirus; the at least one primer pair and/or probe specific for the ORF1a gene of β-coronavirus A comprises: at least one primer pair and/or probe specific for the ORF1a gene of CoV-OC43, wherein the ORF1a gene is not conserved across β-coronavirus A; and at least one primer pair and/or probe specific for the ORF1a gene of CoV-HKU1, wherein the ORF1a gene is not conserved across β-coronavirus A; and the at least one primer pair and/or probe specific for the S gene of α- coronavirus comprises: at least one primer pair and/or probe specific for the S gene of CoV-229E, wherein the S gene is not conserved across α-coronavirus; and at least one primer pair and/or probe specific for the S gene of CoV-NL63, wherein the S gene is not conserved across α-coronavirus. 21. The set of any one of claims 1-9, wherein: the at least one primer pair and/or probe specific for the RdRP gene, the ORF1a gene, or a combination thereof, of α-coronavirus comprises at least one primer pair and/or probe specific for a RdRP gene or an ORF1ab gene that is conserved across α- coronavirus; the at least one primer pair and/or probe specific for the RdRP gene, the ORF1a gene, or a combination thereof, of β-coronavirus, γ-coronavirus, and δ- coronavirus comprises at least one primer pair and/or probe specific for a RdRP gene or an ORF1ab gene that is conserved across β-coronavirus A, β-coronavirus D, γ-coronavirus, and δ-coronavirus, but not conserved in Merbecovirus (β-coronavirus C) and/or not in Sarbecovirus (β-coronavirus B); and the set additionally comprises: at least one primer pair and/or probe specific for the N gene of MERS-CoV, wherein the N gene is not conserved across Merbecovirus; at least one primer pair and/or probe specific for the ORF1ab gene of MERS-CoV, wherein the ORF1ab gene is conserved across Merbecovirus; at least one primer pair and/or probe specific for the ORF1a gene of SARS-CoV-1, wherein the ORF1a gene is not conserved across Docket No. CPHDP021WO/51-018610WO Sarbecovirus; and/or at least one primer pair and/or probe specific for the S gene of SARS-CoV-1, wherein the S gene is not conserved across Sarbecovirus; at least one primer pair and/or probe specific for the N gene of SARS-CoV-2, wherein the N gene is not conserved across Sarbecovirus; and/or at least one primer pair and/or probe specific for the RDRP gene of SARS-CoV-2, wherein the RDRP gene is not conserved across Sarbecovirus; at least one primer pair and/or probe specific for the E gene of SARS-CoV-2, wherein the E gene is conserved across Sarbecovirus; at least one primer pair and/or probe specific for the ORF1a gene of CoV-OC43, wherein the ORF1a gene is not conserved across β-coronavirus A; at least one primer pair and/or probe specific for the ORF1a gene of CoV-HKU1, wherein the ORF1a gene is not conserved across β-coronavirus A; at least one primer pair and/or probe specific for the S gene of CoV-229E, wherein the S gene is not conserved across α-coronavirus; and at least one primer pair and/or probe specific for the S gene of CoV-NL63, wherein the S gene is not conserved across α-coronavirus. 22. The set of claim 1, wherein: at least one primer pair and/or probe specific for the RdRP gene, the ORF1a gene, or a combination thereof, of α-coronavirus, β-coronavirus, γ-coronavirus, and δ-coronavirus, wherein the at least one primer pair and/or probe is conserved across α- coronavirus, β-coronavirus A, β-coronavirus D, γ-coronavirus, and δ-coronavirus, but not conserved in Merbecovirus (β-coronavirus C) and in Sarbecovirus (β-coronavirus B); at least one primer pair and/or probe specific for the N gene of MERS-CoV, wherein the N gene is not conserved across Merbecovirus; at least one primer pair and/or probe specific for the ORF1ab gene of MERS-CoV, wherein the ORF1ab gene is conserved across Merbecovirus; at least one primer pair and/or probe specific for the ORF1a gene of SARS-CoV-1, wherein the ORF1a gene is not conserved across Sarbecovirus; and/or at least one primer pair and/or probe specific for the S gene of SARS-CoV-1, wherein the S gene is not conserved across Sarbecovirus; Docket No. CPHDP021WO/51-018610WO at least one primer pair and/or probe specific for the N gene of SARS-CoV-2, wherein the N gene is not conserved across Sarbecovirus; and/or at least one primer pair and/or probe specific for the RDRP gene of SARS-CoV-2, wherein the RDRP gene is not conserved across Sarbecovirus; at least one primer pair and/or probe specific for the E gene of SARS- CoV-2, wherein the E gene is conserved across Sarbecovirus. 23. The set of claim 3, wherein: the at least one primer pair specific for the RdRP gene, the ORF1a gene, or a combination thereof, of α-coronavirus, γ-coronavirus, β-coronavirus and δ- coronavirus comprise at least one nucleotide sequence having at least about 60% homology to an identical or complementary sequence of SEQ ID NO:61 and/or SEQ ID NO:74. 24. The set of claim 3, wherein: the at least one primer pair and/or probe specific for the RdRP gene, the ORF1a gene, or a combination thereof, of α-coronavirus, β-coronavirus, γ-coronavirus, and δ-coronavirus, comprise a degenerate nucleotide sequence. 25. The set of any one of claims 1-24, wherein: the at least one primer pair and/or probe specific for the ORF1ab gene of Merbecovirus, comprise a degenerate nucleotide sequence. 26. The set of any one of claims 20-22, wherein, when present, the primers and/or probe specific for the N gene of MERS- CoV comprise a sequence that is identical or complementary to at least 15 contiguous nucleotides of one or more of SEQ ID NO: 1, 21, 22, and 23; the primers and/or probe specific for the ORF1ab gene of β- coronavirus C (Merbecovirus) comprise a sequence that is identical or complementary to at least 15 contiguous nucleotides of one or more of SEQ ID NO: 4, 5, 24, 25, 26, 27, 28, 29, and 30; the primers and/or probe specific for the ORF1a gene of SARS-CoV-1 comprise a sequence that is identical or complementary to at least 15 contiguous nucleotides of one or more of SEQ ID NO: 9, 31, 32, and 33; the primers and/or probe specific for the S gene of SARS- CoV-1 comprise a sequence that is identical or complementary to at least 15 contiguous nucleotides of one or more of SEQ ID NO: 6, 7, 34, 35, and 36; Docket No. CPHDP021WO/51-018610WO the primers and/or probe specific for the N gene of SARS- CoV-2 comprise a sequence that is identical or complementary to at least 15 contiguous nucleotides of one or more of SEQ ID NO: 10, 37, 38, and 39; the primers and/or probe specific for the RDRP gene of SARS-CoV-2 comprise a sequence that is identical or complementary to at least 15 contiguous nucleotides of one or more of SEQ ID NO: 11, 40, 41, and 42; the primers and/or probe specific for the E gene of SARS- CoV-2 comprise a sequence that is identical or complementary to at least 15 contiguous nucleotides of one or more of SEQ ID NO: 12, 13, 43, 44, 45, and 46; the primers and/or probe specific for the ORF1a gene of CoV- OC43 comprise a sequence that is identical or complementary to at least 15 contiguous nucleotides of one or more of SEQ ID NO: 16, 47, 48, 49, and 50; the primers and/or probe specific for the ORF1a gene of CoV- HKU1 comprise a sequence that is identical or complementary to at least 15 contiguous nucleotides of one or more of SEQ ID NO: 17, 51, 52, 53, and 54; the primers and/or probe specific for the S gene of CoV-229E comprise a sequence that is identical or complementary to at least 15 contiguous nucleotides of one or more of SEQ ID NO: 14, 58, 59, and 60; the primers and/or probe specific for the S gene of CoV-NL63 comprise a sequence that is identical or complementary to at least 15 contiguous nucleotides of one or more of SEQ ID NO: 15, 555, 56, and 57; the primers and/or probe specific for the RdRP gene conserved across α-coronavirus comprise a sequence that is identical or complementary to at least 15 contiguous nucleotides of one or more of SEQ ID NO: 18, 19, 20, 61, 62, 63, 64, 65, 74, 75, 76, 80, 81, 82, 83, and 89; the primers and/or probe specific for the RdRP gene conserved in β-coronavirus, γ-coronavirus, and δ-coronavirus comprise a sequence that is identical or complementary to at least 15 contiguous nucleotides of one or more of SEQ ID NO: 18, 19, 20, and 90-104 ; the primers and/or probe specific for the RdRP gene, the ORF1a gene, or a combination thereof, of α-coronavirus, γ-coronavirus, β-coronavirus and δ- coronavirus comprise a sequence that is identical or complementary to at least 15 contiguous nucleotides of one or more of SEQ ID NO: 18, 19, 20, and 61-77; Docket No. CPHDP021WO/51-018610WO the primers and/or probe specific for the RdRP gene, the ORF1a gene, or a combination thereof, of α-coronavirus and γ-coronavirus comprise a sequence that is identical or complementary to at least 15 contiguous nucleotides of one or more of SEQ ID NO: 18, 19, 20, 80, 81, 82, 83, 84, and 85; and the primers and/or probe specific for the RdRP gene, the ORF1a gene, or a combination thereof, of β-coronavirus and δ-coronavirus comprise a sequence that is identical or complementary to at least 15 contiguous nucleotides of one or more of SEQ ID NO: 18, 19, 20, 78, 79, 86, 87, and 88. 27. The set of any one of claims 1-26, wherein at least one of the primers and/or probes comprises a detectable label. 28. The set of any one of claims 1-27, further comprises a primer pair specific for an exogenous control and/or an endogenous control, wherein the exogenous control is a sample processing control, and wherein the endogenous control is a sample adequacy control. 29. The set of any one of claims 1-28, wherein the set is contained within one or more cartridge(s). 30. The set of claim 29, wherein the set is contained in one cartridge. 31. The set of claim 30, wherein the cartridge comprises: a cartridge body having a plurality of chambers defined therein, wherein the plurality of chambers is in fluidic communication through a fluidic path of the cartridge; a reaction vessel comprising one or more reaction chambers and configured for amplification of the nucleic acid, wherein each reaction chamber is configured for detection of a plurality of amplification products, wherein the reaction vessel is attached to the cartridge body and fluidically coupled to the fluidic path of the cartridge; and a filter disposed in the fluidic path between the plurality of chambers and the reaction vessel. 32. The set of claim 30 or claim 31, wherein the at least one of the plurality of chambers comprises the set of primers and/or probes, or subset thereof, and at Docket No. CPHDP021WO/51-018610WO least one different chamber of the plurality of chambers comprises one or more lysis reagents for releasing nucleic acid from a sample. 33. A cartridge for detecting coronaviruses in a biological sample, the cartridge comprising: a cartridge body comprising a plurality of chambers therein, wherein the plurality of chambers includes: a sample chamber having at least a fluid outlet in fluid communication with another chamber of the plurality; and a lysis chamber in fluidic communication with the sample chamber, the lysis chamber comprising one or more lysis reagents for releasing nucleic acid, optionally wherein the sample chamber and lysis chamber are the same; a reaction vessel fluidically coupled to the plurality of chambers of the cartridge body and configured for i) amplification of nucleic acid and ii) detection of a plurality of amplification products; a filter disposed in a fluidic path between the lysis chamber and the reaction vessel; and a set of primers and/or probes according to any one of claims 1-29, the set disposed in one or more chambers of the plurality of chambers and/or in the reaction vessel for detection of nucleic acid sequences characteristic of β-coronavirus C, β- coronavirus A, α-coronavirus, SARS-CoV-1, and SARS-CoV-2. 34. A cartridge for detecting coronaviruses in a biological sample, the cartridge comprising: a first body having a plurality of chambers; a second body fluidically coupled to the first body; a valve assembly configured to rotate and having at least one port fluidically coupled to the second body; a reaction vessel fluidically coupled to the first body or the second body and configured for i) amplification of nucleic acid and ii) detection of a plurality of amplification products; and a set of primers and/or probes according to any one of claims 1-29, the set disposed in one or more chambers of the plurality of chambers and/or in the reaction Docket No. CPHDP021WO/51-018610WO vessel for detection of nucleic acid sequences characteristic of β-coronavirus C, β- coronavirus A, α-coronavirus, SARS-CoV-1, and SARS-CoV-2. 35. A method for detecting coronaviruses in a biological sample, the method comprising: a) contacting nucleic acid from the sample with a set of primers and optional probes according to any one of claims 1-28; b) subjecting the nucleic acid, primer pairs, and optional probes to amplification conditions; c) detecting the presence of amplification product(s), optionally via real-time PCR, melt curve analysis, or a combination thereof, and d) detecting the presence of a coronavirus in the sample based on detection of the amplification products. 36. The method of claim 35, wherein the method comprises administering a treatment regimen to a subject based on detecting the presence of a coronavirus in the sample. 37. The method of claim 35 or claim 36, wherein detecting the presence of amplification product(s) comprises: performing melt assay of the amplification products; and conducting melt curve analysis to detect the presence of one or more amplification products in the reaction vessel. 38. The method of claim 35 or claim 36, wherein detecting the presence of amplification product(s) comprises both real-time PCR and melt curve analysis. 39. The method of any one of claims 35-38, wherein detecting the presence of a coronavirus comprises differentially identifying MERS-CoV, β-coronavirus C (Merbecovirus), SARS-CoV-1, SARS-CoV-2, β-coronavirus B (Sarbecovirus), CoV-OC43 or CoV-HKU1, CoV-229E or CoV-NL63, α-coronavirus or γ-coronavirus, and β- coronavirus or δ-coronavirus. 40. The method of any one of claims 35-38, wherein detecting the presence of a coronavirus comprises differentially identifying MERS-CoV, β-coronavirus C (Merbecovirus), SARS-CoV-1, SARS-CoV-2, β-coronavirus B (Sarbecovirus), CoV-OC43, Docket No. CPHDP021WO/51-018610WO CoV-HKU1, CoV-229E, CoV-NL63, α-coronavirus, β-coronavirus, γ-coronavirus, and δ- coronavirus. 41. A system for detecting pathogens in a biological sample, the system comprising: a module having a receiving bay for receiving the cartridge of claim 33 or claim 34, wherein the module includes one or more mechansims within the receiving bay for manipulating a fluid sample within the cartridge, and an instrument that interfaces with the reaction vessel; and a memory having programmable instructions recorded thereon, that are specially configured to operate the module according to a pancoronavirus assay protocol to determine nucleic acid sequence characteristics of α-coronavirus, β-coronavirus, γ- coronavirus, or δ-coronavirus.

Description

Docket No. CPHDP021WO/51-018610WO PANCORONAVIRUS BIOMARKER PANEL CROSS-REFERENCE TO RELATED APPLICATIONS [0001] This application claims the benefit of U.S. provisional application no.63/523,603, filed June 27, 2023, which is hereby incorporated by reference in its entirety. STATEMENT AS TO RIGHTS TO INVENTIONS MADE UNDER FEDERALLY SPONSORED RESEARCH AND DEVELOPMENT [0002] Not applicable. FIELD [0003] The present invention relates to generally to the area of pancoronavirus detection. BACKGROUND [0004] The coronavirus disease-2019 (COVID-19) pandemic has changed the world, leading to millions of deaths and disability in some survivors. Despite advances in diagnosis and vaccination, the emergence of severe acute respiratory syndrome coronavirus 2 (SARS- CoV-2) variants continues to threaten human populations. The World Health Organization and the CDC have identified SARS-CoV-2 variants of concern (VOCs), which lead to increased disease severity, increased transmission, and immune/vaccine evasion. Variants of interest also have been identified that present theoretical risks because they possess mutations similar to the mutations in the VOC. Specific frequently occurring mutations also have been identified that can affect therapeutic antibody treatments for patients infected with such variants. [0005] Initially, the most common technique to identify, classify, and track variants of SARS-CoV-2 was deep sequencing. Although sequencing is accurate and can identify each mutation present in a sample, it is costly, slow, and requires specialized instruments and interpretation when compared with other genotyping techniques, such as polymerase chain reaction (PCR). Docket No. CPHDP021WO/51-018610WO [0006] PCR and other nucleic acid amplification methods can provide higher sensitivity and faster time to results than sequencing. However, current nucleic acid amplification methods have limitations because the amplification reaction and signal detection require a controlled environment and precise measurement with expensive instruments. Thus, the methods are often cost-prohibitive for use in point-of-care situations. Additionally, some methods are not optimized for detection of multiplexed target nucleic acids in single patient samples. Detection of multiplexed targets may be accomplished by signal multiplexing in single-pot reactions (fluorescent spectral multiplexing, arrays of electrochemical detectors), physical separation of multiple reactions into unique reaction vessels, or a combination thereof. Physical separation of multiple reactions into unique reaction vessels can lead to erroneous results due to differences in sampling or in assay conditions during reactions, which can confound efforts to make differential diagnoses. Multiplexing can overcome some of these difficulties, but presents its own technical challenges, particularly with attempts to assay for more than a few pathogens in a single reaction mixture. Since the early 2000s DNA-detection technologies have bifurcated into either massively multiplexed but slow systems (next-generation sequencing (NGS) and microarrays), or rapid assays with limited capacity for multiplexing (quantitative PCR (qPCR) and isothermal amplification). [0007] Furthermore, in the case of a CLIA-waived test, no more than three simple steps must be required by the user to simultaneously query a panel of target nucleic acids using a single patient sample. Physical separation of samples into discrete chambers quickly becomes infeasible for CLIA-waived tests, unless a complicated device or disposable automatically handles processing. Spectral multiplexing with fluorescence can reduce the number of unique reactions required to detect a panel of target nucleic acids, but spectral multiplexing LAMP reactions has required dramatic sacrifices in assay speed or signal strength, dampening prospects for successful application to point-of-care testing. [0008] The methods, compositions, and devices presented herein achieve rapid, sensitive, qualitative and optionally quantitative detection of many target nucleic acids (DNA and RNA) from a single sample, in some embodiments, using a closed and affordable instrument. Docket No. CPHDP021WO/51-018610WO SUMMARY [0009] Various embodiments contemplated herein may include, but need not be limited to, one or more of the following: [0010] Embodiment 1: A set of primers and/or probes for detecting the presence of pancoronavirus in a sample, the set comprising: at least one primer pair and/or probe specific for the RdRP gene, the ORF1a gene, or a combination thereof, of α-coronavirus [Pan-Cov-1]; and at least one primer pair and/or probe specific for the RdRP gene, the ORF1a gene, or a combination thereof, of all three of β-coronavirus, γ-coronavirus, and δ- coronavirus [Pan-Cov-2]. [0011] Embodiment 2: A set of primers and probes for detecting the presence of pancoronavirus in a sample, the set comprising: at least one primer pair and probe specific for t