Multi-allelic molecular detection of SARS-associated coronavirus

Abstract

The subject invention relates to a multiple-allelic RT-real-time polymerase chain reaction (PCR) assay for coronaviruses including the SARS virus. Multiple target sequences within the SARS-CoV, S, E, M and N genes are identified. The use of the four different targets enhances the likelihood that the fundamental genetic drift of the virus will not lead to a false negative result. Multiplex assays format for the assay are envisioned. Thus, the present invention allows for early diagnosis of a SARS infection. The assay would be useful in the context of monitoring treatment regimens, screening potential anti SARS agents, and similar applications requiring qualitative and quantitative determinations.

Description

[0001] This Patent Application is a Non-Provisional Patent Application based on Provisional Patent Application Ser. No. 60 / 496,995 (Attorney Docket 42392-191812) filed Aug. 22, 2003, and Provisional Application Ser. No. 60 / 576,314 (Attorney Docket 42392-203685) filed on Jun. 3, 2004, the contents of which are incorporated herein by reference in their entiretyBACKGROUND OF THE INVENTION [0002] 1. Field of Invention [0003] This invention is directed to methods for the detection and / or quantitation of the SARS virus, reagents and test kits containing the same for use in the method. [0004] 2. Background of the Invention [0005] Severe acute respiratory syndrome (SARS) is one of the most recent emerging infectious diseases. The cause of SARS has been identified as a new coronavirus—a virus within the family Coronaviridae—designated as the “SARS coronavirus” (SARS-CoV) [1, 2] by the World Health Organization, following assessment of causation according to Koch's postulates, including monke...

AI Technical Summary

Benefits of technology

[0014] Multiple target sequences within the SARS-CoV S, E, M and N genes (Urbani and Tor2 strains) were identified. The S, M, and E genes encode structural proteins that are present on the outside of the virus, whereas the N gene encodes a structural protein that is required for viral RNA packaging inside the virion. The principle underlying the selection of four target sequences that uniquely identify SARS-CoV (rather than only one target sequence) is that the use of four different targets enhances the likelihood that the fundamental genetic drift of the virus will not lead to a false negative result—that is, one has better chance of hitting a moving target with a shotgun than with a rifle. Thus, by detecting four different target alleles in the same assay tube, and by using a single-fluorophore detection system, the design of the assay significantly minimizes the likelihood of missing the presence of the SARS-CoV in a clinical sample due to the continuous viral evolution of the viral sequence. Moreover, by simultaneously detecting four different target sequences in the same assay tube, the intrinsic sensitivity of the assay is enhanced.

[0016] The criteria for selecting SARS-CoV gene-specific PCR primers were based on: a) the identification of genomic regions in SARS-CoV that, as a result of an examination of the sequence alignments, showed the highest genetic distance between SARS-CoV and other coronavirus strains; b) selection of primer sequences for amplification of the SARS-CoV targets that form primer-target hybrids whose theoretical melting temperature maximizes the ability of the primer to bind to the target even if nucleotide substitutions are present (mismatch tolerance), and yet enable all of the primers to hybridize to their targets at the same temperature in a multiplex assay (Tm approximately 60° C.); and c) selection of primer sequences that enable the amplicons containing each of the four target sequences to be approximately the same (relatively short) length (approximately 100 nucleotides long).

[0017] The criteria for selecting the molecular beacon probe sequences, and their arm sequences, were based on: a) the identification of approximately 30-nucleotide-long regions in SARS-CoV (within the amplicons to be generated) that, as a result of an examination of the sequence alignments, showed the highest genetic distance between SARS-CoV and other coronavirus strains (with special emphasis on probe target sequences that encompass gaps or deletions in the SARS-CoV sequence compared to the sequence of other coronaviruses); b) selection of probe sequences that form probe-target hybrids whose theoretical melting temperature maximizes the ability of the probe to bind to the target sequence even if nucleotide substitutions are present (mismatch tolerance), and yet enable all of the probes to hybridize to their targets at the same temperature in a multiplex assay (Tm approximately 63° C.); and c) selection of arm sequences that provide the same degree of stability for the stem hybrids of all of the molecular beacon probes (stem Tm of approximately 70° C.).

Problems solved by technology

The main problems with current molecular diagnostic assays are: a) failure to consider the intrinsically polymorphic nature of coronaviruses, including the current SARS-CoV strains originated from the Tor2 and Urbani isolates—the ability of the virus to mutate and recombine during the period of time it is within the infected individual, and during horizontal transmission; and b) failure to account for the possibility of continuous and / or multiple introduction of non non-genetically identical SARS-CoV strains into the human population.

Coronaviruses, including SARS-CoV, are quite sloppy when it comes to replicating their genetic material, producing one error for every 10,000 nucleotides that they copy, which is roughly the same error rate as occurs during the replication of the human immunodeficiency virus, HIV-1.

Moreover, if one of these jumps is imprecise, a whole chunk of genome can get skipped, resulting in the deletion of part of an important gene.

The consequences can be dramatic, particularly if the change affects the protein spikes that enable the virus to bind to the surface of the host's cells.

Although the new disease was not generally lethal, it has since spread worldwide, and it has complicated the diagnosis of the gut disease.

Images