Methods for genetic analysis of SARS virus

• US 20050136395A1
• Filed: 05/10/2004
• Published: 06/23/2005
• Est. Priority Date: 05/08/2003
• Status: Abandoned Application

• Current Assignee: Affymetrix, Inc. (Thermo Fisher Scientific Incorporated)
• Original Assignee: Affymetrix, Inc. (Thermo Fisher Scientific Incorporated)
• Inventors: Schell, Eric B., Mittmann, Michael P.
• Application Number:
  US10/843,527
• Publication Number:
  US 20050136395A1
• Time in Patent Office: Days
• US Class Current: 435/5
• CPC Class Codes: C12Q 1/6837 using probe arrays or probe chips C12Q1/6874 takes precedence
• CPC Class Codes: C12Q 1/701 Specific hybridization probes

Abstract

The invention provides arrays and probes for resequencing a SARS virus using an array of probes that are complementary to a SARS reference sequence and to each possible single nucleotide substitution of the reference sequence. Methods of identifying mutations in viral sequences and methods of characterizing viral isolates are also provided. The invention also provides high throughput methods to monitor epidemics and pandemics caused by pathogens such as viruses.

Claims

1. An array comprising a plurality of nucleic acid probes, wherein said plurality of nucleic acid probes comprises each of the sequences listed in SEQ ID Nos. 1-238,192 wherein each different sequence is attached to the surface of the array in a different localized area.

2. A method of identifying mutations in an isolate of SARS virus comprising:

hybridizing nucleic acid derived from the isolate to the array of claim 1;

and

analyzing the hybridization pattern to estimate at least 1000 bases of the sequence of the isolate.

3. A method of identifying genetic variation in a plurality of isolates of SARS virus comprising:

hybridizing nucleic acids derived from each of a plurality of isolates of the SARS virus to the array claim 1 to generate a hybridization pattern for each isolate;

analyzing the hybridization pattern for each isolate to determine a sequence of at least 1000 bases for each isolate; and

comparing the sequences to identify genetic variation.

4. An array of nucleic acid probes immobilized on a solid support, the array comprising:

(1) a first probe set comprising a plurality of probes, each probe comprising a segment of at least ten nucleotides exactly complementary to a subsequence of a SARS virus reference sequence, the segment including at least one interrogation position complementary to a corresponding nucleotide in the SARS virus reference sequence; and

(2) second, third and fourth probe sets, each probe set comprising a corresponding probe for each probe in the first probe set, the probes in the second, third and fourth probe sets being identical to the corresponding probe from the first probe set or a subsequence of at least ten nucleotides thereof that includes the interrogation position, except that the interrogation position is occupied by a different nucleotide in each of the four corresponding probes from the four probe sets.

5. The array of claim 4, wherein the probes in the first probe set have a single interrogation position, and the array further comprises a fifth probe set comprising:

a probe for each interrogation position in the first probe set, each probe in the fifth probe set being identical to a sequence comprising a corresponding probe from the first probe set or a subsequence of at least ten nucleotides thereof that includes the interrogation position, except that the interrogation position is deleted in the corresponding probe from the fifth probe set.

6. The array of claim 4, wherein the probes in the first probe set have a single interrogation position, and the array further comprises a fifth probe set comprising:

a probe for each interrogation position in the first probe set, each probe in the fifth probe set being identical to a sequence comprising the corresponding probe from the first probe set or a subsequence of at least ten nucleotides thereof that includes the interrogation position, except that an additional nucleotide is inserted adjacent to the single interrogation position in the corresponding probe from the first probe set.

7. The array of claim 4, wherein the first probe set has at least three interrogation positions respectively corresponding to each of three nucleotides in the reference sequence that are positions of known variation.

8. The array of claim 4, wherein the first probe set has at least 50 interrogation positions respectively corresponding to each of 50 nucleotides in the reference sequence that are positions of known variation.

9. The array of claim 4, wherein the array has between 10,000 and 1,000,000 probes.

10. The array of claim 4, wherein the array has between 1,000,000 and 2,600,000 probes.

11. The array of claim 4, wherein the array has between 2,600,000 probes and 20,000,000 probes.

12. The array of claim 4, wherein the segment in each probe of the first probe set that is exactly complementary to the subsequence of the reference sequence is 9 to 35 nucleotides.

13. The array of claim 4 wherein the array interrogates at least 1000 contiguous bases of a SARS virus for variation.

14. The array of claim 4 further comprising:

(1) a fifth probe set comprising a plurality of probes, each probe comprising a segment of at least ten nucleotides exactly complementary to a subsequence of a second reference sequence, the segment including at least one interrogation position complementary to a corresponding nucleotide in the second reference sequence; and

(2) sixth, seventh and eighth probe sets, wherein the sixth, seventh and eigth probe sets each comprise a corresponding probe for each probe in the fifth probe set, the probes in the sixth, seventh and eighth probe sets being identical to the corresponding probe from the fifth probe set, or a subsequence of at least ten nucleotides thereof that includes the interrogation position, except that the interrogation position is occupied by a different nucleotide in each of the four corresponding probes from the fifth, sixth, seventh and eighth probe sets.

15. The array of claim 14 wherein the second reference sequence is an influenza viral sequence.

16. A method of monitoring genetic variation of SARS virus in a population of individuals comprising:

acquiring viral isolates from a plurality of individuals suspected of being infected with the virus;

estimating the sequence of at least one virus in each viral isolate by hybridizing nucleic acid derived from the viral isolate to the array of claim 4;

and

comparing the estimated sequences to identify the presence or absence of variation between individual isolates.

17. The method of claim 16 wherein one or more steps of the method are performed in a high throughput assay.

18. A method of generating a database of viral sequences comprising:

isolating viral samples from a plurality of sources;

hybridizing nucleic acid derived from each of the viral samples to the array of claim 4 to generate a hybridization pattern for each viral sample;

determining the sequence of each viral sample from the hybridization pattern; and

combining the sequence of each viral sample from each source in the plurality of sources into a database of viral sequences.

19. A method of controlling an outbreak of SARS comprising:

estimating the sequence of isolates of SARS virus from a plurality of affected individuals using the array of claim 4;

comparing the sequences to a database of sequences of viral strains that are associated with high rates of transmission;

identifying one or more individuals carrying an isolate of the virus that is known to be associated with high rates of transmission; and

minimizing the contact between said one or more individuals and unaffected individuals.

20. A method of limiting the mortality or morbidity resulting from an outbreak of SARS comprising:

estimating the sequence of isolated of SARS virus from affected individuals using the array of claim 4;

comparing the sequences to a database of SARS virus sequences that are associated with high rates or mortality or morbidity;

identifying one or more individuals carrying a SARS virus that is associated with high rates of mortality or morbidity; and

minimizing the contact between said one or more individuals and unaffected individuals.

21. A method of monitoring an outbreak of a disease caused by a virus of interest comprising:

isolating a nucleic acid sample from each of a plurality of individuals suspected of being infected with the virus of interest;

amplifying viral nucleic acid from the virus of interest in each of the nucleic acid samples;

hybridizing the amplified nucleic acids to a resequencing array comprising probes to a reference sequence of the virus of interest;

estimating at least part of the sequence of the virus of interest in each of the samples; and

comparing the sequences to determine the variation between individual isolates.

22. The method of claim 21 wherein the virus of interest is a SARS virus.

23. The method of claim 21 wherein the virus of interest is an influenza virus.

24. The method of claim 21 wherein one or more steps of the method are performed in a high throughput assay.

25. An array of nucleic acid probes immobilized on a solid support, the array comprising at least two sets of probes,

(1) a first probe set comprising a plurality of probes wherein each probe comprises a segment of at least ten nucleotides that is perfectly complementary to a subsequence of a first reference sequence, the subsequence including at least one interrogation position complementary to a corresponding nucleotide in the first reference sequence,

(2) a second probe set comprising a plurality of probes wherein each probe comprises a subsequence of at least ten nucleotides that is perfectly complementary to a subsequence of a second reference sequence, the subsequence including at least one interrogation position complementary to a corresponding nucleotide in the second reference sequence, wherein the first reference sequence is a first isolate of a SARS virus and the second reference sequence is a second isolate of a SARS virus.

26. The array of claim 25, wherein the first reference sequence is from a super spreader isolate of SARS.

27. A method of comparing a target nucleic acid with a reference sequence, the method comprising:

(a) hybridizing a sample comprising the target nucleic acid to the array of claim 25;

(b) comparing the hybridization pattern of the two corresponding probes from the first and second probe sets;

(c) assigning a nucleotide in the target sequence as the complement of the interrogation position of the probe having the greater hybridization; and

(d) repeating (b) and (c) by comparing the hybridization pattern of a further two corresponding probes from the first and second probe sets until each nucleotide of interest in the target sequence has been assigned.

28. A method of comparing a target nucleic acid with a reference sequence comprising a predetermined sequence of nucleotides, the method comprising:

(a) hybridizing a sample comprising the target nucleic acid to an array of nucleic acid probes immobilized on a solid support, the array comprising at least four sets of probes,

(1) a first probe set comprising a plurality of probes, each probe comprising a segment of at least nine nucleotides exactly complementary to a subsequence of a reference sequence, the segment including at least one interrogation position complementary to a corresponding nucleotide in the reference sequence,

(2) second, third and fourth probe sets, each set comprising a probe for each interrogation position in the first probe set, each probe comprising a corresponding probe for each probe in the first probe set, the probes in the second, third and fourth probe sets being identical to a sequence comprising the corresponding probe from the first probe set or a subsequence of at least nine nucleotides thereof that includes the interrogation position, except that the interrogation position is occupied by a different nucleotide in each of the four corresponding probes from the four probe sets;

provided the array does not consist of a complete set of probes of a given length, wherein a complete set is all permutations of nucleotides A, C, G and T/U;

wherein the reference sequence is a SARS virus

(b) comparing the relative specific binding of four corresponding probes from the first, second, third and fourth probe sets;

(c) assigning a nucleotide in the target sequence as the complement of the interrogation position of the probe having the greatest specific binding;

(d) repeating (b) and (c) by comparing the relative specific binding of a further four corresponding probes from the first, second, third and fourth probe sets until each nucleotide of interest in the target sequence has been assigned.

29. The method of claim 28 wherein one or more steps of the method are performed in a high throughput assay.