# US 2019/0376131 A1 · Compositions and methods for detection of hepatitis a virus nucleic acid

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- Number: US 2019/0376131 A1
- Document ID: US20190376131A1
- Status: Published application
- Kind: A1
- Application number: 16/546,749
- Filed: 2019-08-21
- Published: 2019-12-12
- Earliest claimed: 2004-07-13
- Assignees: Gen-Probe Incorporated
- Applicants: Gen-Probe Incorporated
- Inventors: James D. CARLSON; Steven T. BRENTANO
- Web page: https://patentgrep.com/patent/US20190376131A1

## CPC

- C12Q 1/6865: Promoter-based amplification, e.g. nucleic acid sequence amplification [NASBA], self-sustained sequence replication [3SR] or transcription-based amplification system [TAS]
- C12Q 1/706: {for hepatitis}
- C12Q 2600/158: Expression markers
- C12Q 2600/16: Primer sets for multiplex assays
- Y02A 50/30: Against vector-borne diseases, e.g. mosquito-borne, fly-borne, tick-borne or waterborne diseases whose impact is exacerbated by climate change
- C12Q: MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS (immunoassay G01N33/53); COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
- Y02A: TECHNOLOGIES FOR ADAPTATION TO CLIMATE CHANGE

## Abstract

Nucleic acid oligomeric sequences and in vitro nucleic acid amplification and detection methods for detecting the presence of HAV RNA sequences in samples are disclosed. Kits comprising nucleic acid oligomers for amplifying and detecting HAV nucleic acid sequences are disclosed.

## Claims

### Claim 1

A combination of at least two oligomers for amplifying a HAV target region comprising:
a first oligomer comprising a target-specific sequence of about 24 to 28 nt contained in the sequence of SEQ ID NO:147 that includes at least the sequence of SEQ ID NO:148, and optionally joined at its 5′ end to a promoter sequence, and a second oligomer comprising a target-specific sequence of about 24 to 30 nt, contained in the sequence of SEQ ID NO:157 and that includes at least the sequence of SEQ ID NO:158.

### Claim at position 2

-3. (canceled)

### Claim 4 (depends on 1)

The combination of at least two oligomers of claim 1, wherein the first oligomer comprises a sequence consisting of: SEQ ID NO:31, or SEQ ID NO:32, or comprises a target specific sequence consisting of SEQ ID NO:61 further comprising a promoter sequence attached to its 5′ end, SEQ ID NO:62 further comprising a promoter sequence attached to its 5′ end, or SEQ ID NO:148 further comprising a promoter sequence attached to its 5′ end; and the second oligomer comprises a target specific sequence of SEQ ID NO:89, SEQ ID NO:90, or SEQ ID NO:91.

### Claim at position 4

-8. (canceled)

### Claim 9 (depends on 1)

The combination of at least two oligomers of claim 1, further comprising at least one capture probe oligomer selected from the group consisting of SEQ ID NOS:1 to 7 and SEQ ID NOS:8-14 linked to a moiety that allows it to bind a solid support.

### Claim 10 (depends on 1)

The combination of at least two oligomers of claim 1, further comprising at least one detection probe oligomer comprising a target-specific sequence selected from the group consisting of SEQ ID NO:115; optionally wherein said nucleic acid detection oligomer further comprises a 2′-O-methyl linkages, a chemiluminescent label, an acridinium ester label, a synthetic linker or combinations thereof.

### Claim 11 (depends on 1)

The combination of at least two oligomers according to claim 1, wherein said combination is packaged in a kit.

### Claim 12

A method of detecting the presence of HAV in a sample comprising the steps of:
purifying HAV nucleic acid from other components in a sample containing HAV;
amplifying a HAV target sequence in the purified HAV nucleic acid, or a cDNA made therefrom, by using an in vitro amplification reaction that includes at least two amplification oligomers specific for a selected HAV target region, which include:
a first oligomer comprising a target-specific sequence of about 24 to 28 nt contained in the sequence of SEQ ID NO:147 that includes at least the sequence of SEQ ID NO:148, and optionally joined at its 5′ end to a promoter sequence, and a second oligomer comprising a target-specific sequence of about 24 to 30 nt contained in the sequence of SEQ ID NO:157 and that includes at least the sequence of SEQ ID NO:158;
to produce an amplified product of the selected HAV target region; and
detecting the amplified product.

### Claim 13 (depends on 12)

The method of claim 12, wherein the purifying step contacts the sample with at least one capture probe oligomer selected from the group consisting of SEQ ID NOS:1 to 7 and SEQ ID NOS:8-14 linked to a moiety that allows it to bind a solid support, wherein a target hybridization sequence of said at least one capture probe oligomer hybridizes specifically to a sequence in HAV RNA to form a hybridization complex with the HAV RNA, and can be used with a solid support to separate the HAV RNA from other sample components.

### Claim at position 10

-15. (canceled)

### Claim 16 (depends on 12)

The method of claim 12, wherein the amplifying step amplifies a sequence by using at least two oligomers selected from the group consisting of: SEQ ID NO:31, SEQ ID NO:32, SEQ ID NO:61 further comprising a promoter sequence attached to its 5′ end, SEQ ID NO:62 further comprising a promoter sequence attached to its 5′ end, SEQ ID NO:89, SEQ ID NO:90, SEQ ID NO:91, and SEQ ID NO:148 further comprising a promoter sequence attached to its 5′ end; and wherein the detecting step uses at least one detection probe that hybridizes specifically to the amplified product of the third HAV target region.

### Claim at position 12

-19. (canceled)

### Claim 20 (depends on 12)

The method of claim 12, wherein said detecting step uses a nucleic acid detection oligomer, wherein said nucleic acid detection oligomer comprises a target hybridizing sequence that specifically hybridizes with at least one amplified product generated in said amplifying step; optionally wherein said nucleic acid detection oligomer comprises a target hybridizing region nucleic acid sequence consisting essentially of SEQ ID NO:115; optionally wherein said nucleic acid detection oligomer further comprises a 2′-O-methyl linkages, a chemiluminescent label, an acridinium ester label, a synthetic linker or combinations thereof.

### Claim 21 (depends on 12)

The method of claim 12, wherein the sample is a biological sample collected from a human

### Claim 22 (depends on 21)

The method of claim 21, wherein the sample collected from a human is a plasma sample.

### Claim 23 (depends on 22)

The method of claim 22, wherein the sample is a sample used for the preparation of therapeutic factors isolated from humans.

### Claim 24 (depends on 12)

The method of claim 12, wherein the first oligomer nucleic acid sequence consists of SEQ ID NO:89 and the second oligomer nucleic acid sequence consists of SEQ ID NO:32, and wherein the detecting step uses a detection probe oligomer comprising a nucleic acid sequence consisting of SEQ ID NO:115.

### Claim 25 (depends on 12)

The method of claim 12, wherein the length of the first oligomer target specific sequence is 24 nt or is 26 nt.

### Claim 26 (depends on 12)

The method of claim 12, wherein the length of the second oligomer is 29 nt or 30 nt.

### Claim 27 (depends on 4)

The composition of claim 4, wherein the first oligomer nucleic acid sequence consists of SEQ ID NO:89 and the second oligomer nucleic acid sequence consists of SEQ ID NO:32.

### Claim 28 (depends on 1)

The combination of at least two oligomers of claim 1, wherein the length of the first oligomer target specific sequence is 24 nt.

### Claim 29 (depends on 1)

The combination of at least two oligomers of claim 1, wherein the length of the first oligomer target-specific sequence is 26 nt.

### Claim 30 (depends on 1)

The combination of at least two oligomers of claim 1, wherein the length of the second oligomer is 30 nt.

### Claim 31 (depends on 1)

The combination of at least two oligomers of claim 1, wherein the length of the second oligomer is 29 nt.