IP Library › Granted Patent US 12,428,672
Granted Patent B2
US 12,428,672 · App. 18/442,591 · Granted Sep 30, 2025

Compositions and methods for detecting or quantifying Human Parainfluenza Virus 4

Inventors: Mehrdad Majlessi (Escondido, CA); Pamela Douglass (Kansas City, MO); Daniel Kolk (Ramona, CA)
Assignee: GEN-PROBE INCORPORATED
C12Q1/6811C12Q1/6816C12Q1/6851C12Q1/6853C12Q1/686C12Q1/6876C12Q1/6888C12Q1/701C12Q2600/118C12Q2600/166
View Patent ↗
Loading inventors, assignments & file history…
Monitor This Case
Get email alerts when status or documents change.
Order Certified Copies
Most orders are placed with the USPTO same day — all within 24 business hours.
Order via The Patent Place →
Pre-filled with this patent's details
Quick Facts
Patent No.
US 12,428,672
App. No.
18/442,591
Granted
Sep 30, 2025
Kind
B2
Abstract

Compositions, methods, kits, and uses are provided for detecting or quantifying an Human Parainfluenza virus 1 (HPIV-1), HPIV-2, HPIV-3, and/or HPIV-4 nucleic acid, e.g., using nucleic acid amplification and hybridization assays. In some embodiments, the compositions, methods, kits, and uses target the HN gene of HPIV-1, HPIV-2, and/or HPIV-3 and/or the NP gene of HPIV-4.

Claims (21)

1. A composition comprising at least a first HPIV-4 amplification oligomer and a second HPIV-4 amplification oligomer, wherein:

the first HPIV-4 amplification oligomer and second HPIV-4 amplification oligomer are configured to amplify an HPIV-4 amplicon, wherein the first HPIV-4 amplification oligomer comprises a target-hybridizing region consisting of the sequence of SEQ ID NO: 78 and the second HPIV-4 amplification oligomer comprises a target-hybridizing region consisting of the sequence of SEQ ID NO: 56, and

wherein the composition further comprises a third HPIV-4 oligomer configured to hybridize to the HPIV-4 amplicon, and the third oligomer comprises a chemiluminescent label or a fluorescent label.

2. The composition of claim 1 , wherein the third HPIV-4 oligomer comprises the sequence of SEQ ID NO: 71 or a sequence with one or two mismatches to SEQ ID NO: 71.

3. The composition of claim 2 , wherein the third HPIV-4 oligomer comprises the sequence of SEQ ID NO: 71.

4. The composition of claim 1 , wherein at least one of the first, second, and third HPIV-4 oligomers comprises at least one 5-methylcytosine.

5. A method of detecting HPIV-4 in a sample, comprising:

contacting the sample with at least a first HPIV-4 amplification oligomer and a second HPIV-4 amplification oligomer, wherein the first HPIV-4 amplification oligomer and second HPIV-4 amplification oligomer are configured to amplify an HPIV-4 amplicon, wherein the first HPIV-4 amplification oligomer comprises a target-hybridizing region consisting of the sequence of SEQ ID NO: 78 and the second HPIV-4 amplification oligomer comprises a target-hybridizing region consisting of the sequence of SEQ ID NO: 56,

performing a nucleic acid amplification reaction which produces the HPIV-4 amplicon in the presence of an HPIV-4 nucleic acid, and

detecting the presence or absence of the HPIV-4 amplicon.

6. The method of claim 5 , wherein the nucleic acid amplification reaction comprises PCR with a polymerase with 5′-to-3′ exonuclease activity, and detecting the HPIV-4 amplicon using a probe oligomer comprising a fluorophore and a quencher, wherein exonucleolysis of the probe by the polymerase reduces quenching of fluorescence by the quencher.

7. A reaction mixture for detecting HPIV-4 in a sample, comprising:

(i) at least a first HPIV-4 amplification oligomer and a second HPIV-4 amplification oligomer, wherein the first HPIV-4 amplification oligomer and second HPIV-4 amplification oligomer are configured to amplify an HPIV-4 amplicon, wherein the first HPIV-4 amplification oligomer comprises a target-hybridizing region consisting of the sequence of SEQ ID NO: 78 and the second HPIV-4 amplification oligomer comprises a target-hybridizing region consisting of the sequence of SEQ ID NO: 56, and

(ii) a third HPIV-4 oligomer configured to hybridize to the HPIV-4 amplicon, wherein the third oligomer comprises a detectable chemiluminescent label or a fluorescent label,

wherein the reaction mixture is aqueous or lyophilized.

8. The method of claim 6 , wherein the probe oligomer comprises the sequence of SEQ ID NO: 71 or a sequence with one or two mismatches to SEQ ID NO: 71.

9. The method of claim 8 , wherein the probe oligomer comprises the sequence of SEQ ID NO: 71.

10. The reaction mixture of claim 7 , wherein the reaction mixture further comprises at least one enzyme selected from the group consisting of a DNA polymerase, a reverse transcriptase, and an RNA polymerase.

11. The reaction mixture of claim 7 , wherein the third HPIV-4 oligomer comprises the sequence of SEQ ID NO: 71 or a sequence with one or two mismatches to SEQ ID NO: 71.

12. The reaction mixture of claim 11 , wherein the third HPIV-4 oligomer comprises the sequence of SEQ ID NO: 71.

13. The reaction mixture of claim 7 , wherein at least one of the first, second, and third HPIV-4 oligomers comprises at least one 5-methylcytosine.

Assignments (4)
RELEASE OF SECURITY INTEREST RECORDED AT REEL/FRAME 069172/0436 Recorded Apr 28, 2026
From: BANK OF AMERICA, N.A., AS COLLATERAL AGENT
To: HOLOGIC, INC.; GEN-PROBE INCORPORATED; FAXITRON BIOPTICS, LLC
Reel/Frame 075503/0086 →
SECURITY INTEREST Recorded Apr 8, 2026
From: BIOTHERANOSTICS, INC.; GEN-PROBE INCORPORATED; GEN-PROBE PRODESSE, INC.; CYTYC CORPORATION; SUROS SURGICAL SYSTEMS, INC.; GYNESONICS, INC.; BOLDER SURGICAL, LLC; FAXITRON BIOPTICS, LLC; HEALTH BEACONS, INC.; HOLOGIC, INC.
To: ROYAL BANK OF CANADA, AS COLLATERAL AGENT
Reel/Frame 075462/0440 →
SECURITY INTEREST Recorded Oct 14, 2024
From: HOLOGIC, INC.; GEN-PROBE INCORPORATED; FAXITRON BIOPTICS, LLC
To: BANK OF AMERICA, N.A., AS COLLATERAL AGENT
Reel/Frame 069172/0436 →
ASSIGNMENT OF ASSIGNOR'S INTEREST Recorded Mar 13, 2024
From: MAJLESSI, MEHRDAD; DOUGLAS, PAMELA; KOLK, DANIEL
To: GEN-PROBE INCORPORATED
Reel/Frame 066754/0630 →
Continuity (4)
Division 17072890 · Oct 16, 2020
Division 15934273 · Mar 23, 2018
Provisional Application 62476435 · Mar 24, 2017
Related Publication 20240318230A1 · Sep 26, 2024
References Cited (81)
US 5744299A · Henrickson · 1998 [cited by applicant]
US 6015664A · Henrickson · 2000 [cited by applicant]
US 10844425B2 · Majlessi · 2020 [cited by examiner]
US 12116620B2 · Majlessi · 2024 [cited by examiner]
US 20030050470A1 · An · 2003 [cited by examiner]
US 20040023207A1 · Polansky · 2004 [cited by examiner]
US 20070259337A1 · Hully · 2007 [cited by applicant]
US 20110077170A1 · Lina · 2011 [cited by applicant]
US 20130157874A1 · Dowd · 2013 [cited by applicant]
US 20140127671A1 · Yoo · 2014 [cited by applicant]
US 20240309429A1 · Majlessi · 2024 [cited by examiner]
US 20240318230A1 · Majlessi · 2024 [cited by examiner]
US 20240318231A1 · Majlessi · 2024 [cited by examiner]
CN 101550455 · 2009 [cited by applicant]
CN 101985665 · 2011 [cited by applicant]
CN 102115795 · 2011 [cited by applicant]
CN 104059996 · 2014 [cited by applicant]
CN 104059996A · 2014 [cited by examiner]
CN 105734168 · 2016 [cited by applicant]
EP 1201768 · 2002 [cited by applicant]
JP 2005528891 · 2005 [cited by applicant]
JP 2007129923 · 2007 [cited by applicant]
JP 2009045070 · 2009 [cited by applicant]
JP 2009517087 · 2009 [cited by applicant]
JP 2014505704 · 2014 [cited by applicant]
JP 2015506666 · 2015 [cited by applicant]
RU 2515911 · 2014 [cited by applicant]
WO 9716570 · 1997 [cited by applicant]
WO 2003080638 · 2003 [cited by applicant]
WO 2007064758 · 2007 [cited by applicant]
WO 2007087336 · 2007 [cited by applicant]
WO 2007120120 · 2007 [cited by applicant]
WO 2012106508 · 2012 [cited by applicant]
WO 2013049891 · 2013 [cited by applicant]
WO WO2018175883A1 · 2018 [cited by examiner]
Aguilar et al., 2000. Detection and identification of human parainfluenza viruses 1, 2, 3, and 4 in clinical samples of pediatric patients by multiplex reverse transcription-PCR. Journal of clinical microbiology, 38(3),… [cited by examiner]
CN104059996A_document, Sep. 14, 2014, English Translation of CN104059996A (Year: 2014). [cited by examiner]
Gadberry et al., 2005. Primaclade—a flexible tool to find conserved PCR primers across multiple species. Bioinformatics, 21(7), pp. 1263-1264. (Year: 2005). [cited by examiner]
Genbank Accession No. AB543336—Human parainfluenza virus 4a viral cRNA, complete genome, strain:M-25, submitted by Jan. 23, 2010, retrieved on Jan. 17, 2025 from http://www.ncbi.nlm.nih.gov/nuccore/AB543336). (Year: 201… [cited by examiner]
Genbank Accession No. KF908238—Human parainfluenza virus 4b strain QLD-01, complete genome, submitted by Nov. 26, 2013, retrieved on Jan. 17, 2025 from http://www.ncbi.nlm.nih.gov/nuccore/KF908238). (Year: 2013). [cited by examiner]
Genbank Accession No. NC_021928—Human parainfluenza virus 4a viral cRNA, complete genome, strain: M-25, submitted by Aug. 6, 2013, retrieved on Jan. 17, 2025 from http://www.ncbi.nlm.nih.gov/nuccore/NC_021928). (Year: 2… [cited by examiner]
Jin et al., Epub Apr. 5, 2010. Examination of the specificity of DNA methylation profiling techniques towards 5-methylcytosine and 5-hydroxymethylcytosine. Nucleic Acids Res. Jun. 2010; 8(11), e125, pp. 1-7. (Year: 2010… [cited by examiner]
Ono et al., Synthesis of decadeoxyribonucleotides containing N 6-methyladenine, N 4-methylcytosine, and 5-methylcytosine: recognition and cleavage by restriction endonucleases (nucleosides and nucleotides part 74). Nucl… [cited by examiner]
SantaLucia Jr, John. Physical principles and visual-OMP software for optimal PCR design. PCR Primer Design. Humana Press, 2007: pp. 3-33. (Year: 2007). [cited by examiner]
Wang et al., 2012. A novel duplex real-time PCR for HPIV-4 detects co-circulation of both viral subtypes among ill children during 2008. Journal of clinical virology, 54(1), pp. 83-85. (Year: 2012). [cited by examiner]
Jansen et al., 2011. Development and evaluation of a four-tube real time multiplex PCR assay covering fourteen respiratory viruses, and comparison to its corresponding single target counterparts. Journal of Clinical Vir… [cited by examiner]
Genbank Accession No. M32982—Parainfluenza virus type 4A nucleocapsid (NP) mRNA, complete cds, submitted Aug. 2, 1993, retrieved on May 20, 2025 from http://www.ncbi.nlm.nih.gov/nuccore/M32982). (Year: 1993). [cited by examiner]
Extended European Search Report dated Jan. 25, 2024 from corresponding European Application No. 23199444.3. [cited by applicant]
Prosnyak et al., “Substitution 2-Aminodenine and 5-Methylcytosine for Adenine and Cytosine in Hybridization Probes Increases the Sensitivity of DNA Fingerprinting”, Geonomics, vol. 21, Jan. 1, 1994, pp. 490-494. [cited by applicant]
Notice of Reasons for Rejection as mailed on Aug. 4, 2023, issued in corresponding Japanese Application No. 2022-116624, filed Mar. 23, 2018, 14 pages. [cited by applicant]
Genbank Accession No. M32982, Parainfluenza virus type 4A nucleocapsid (NP) mRNA, complete cds (submitted Aug. 2, 1993, retrieved on Jul. 15, 2023 from http://www.ncbi.nlm.nih.gov/nuccore/M32982). (Year: 1993). [cited by applicant]
Loeffelholz, “Towards Improved Accuracy of Bordetella pertussis Nucleic Acid Amplification Tests,” Journal of Clinical Microbiology, 50(7):2186-2190 (2012). [cited by applicant]
Weimer et al., “Real-time multiplex PCR for simultaneous detection of [cited by applicant]
Almajhdi FN, Hemagglutinin-neuraminidase gene sequence-based reclassification of human parainflenza virus 3 variants. Intervirology, 2015: 58(1):35-40, Epub Jan. 13, 2015. (Year: 2015). [cited by applicant]
Cordey et al., 2009. Simultaneous detection of parainfluenza viruses 1 and 3 by real-time reverse transcription-polymerase chain reaction. Journal of virological methods, 156(1-2), pp. 166-168. (Year: 2009). [cited by applicant]
Genbank Accession No. AB012132 Human respirovirus 3 genomic RNA, complete sequence, viral complementary strand (submitted Mar. 12, 1998, retrieved on Mar. 7, 2023 from http://www.ncbi.nlm.nih.gov/nuccore/AB012132). (Yea… [cited by applicant]
Genbank Accession No. GU732171 Human parainfluenza virus 3 strain BJ/341/109 hemagglutinin-neuraminidase (HN) gene, complete cds (submitted Feb. 10, 2010, retrieved on Sep. 11, 2019 from http://www.ncbi.nlm.nih.gov/nucc… [cited by applicant]
Genbank Accession No. JN089925 Human parainfluenza virus 1 strain Oklahoma/4409/2010 hemagglutinin-neuraminidase mRNA, complete cds (submitted Jun. 7, 2011, retrieved on Sep. 11, 2019 from 2023 from http://www.ncbi.nlm.… [cited by applicant]
Genbank Accession No. KF908238 Human parainfluenza virus 4b strain QLD-01, complete genome (submitted Nov. 26, 2013, retrieved on Sep. 11, 2019 from http://www.ncbi.nlm.nih.gov/nuccore/KF908238. (Year: 2013). [cited by applicant]
Genbank Accession No. NC_001796 Human parainfluenza virus 3, complete genome (submitted Dec. 5, 2000, retrieved on Mar. 7, 2023 from http://www.ncbi.nlm.nih.gov/nuccore/NC_001796). (Year: 2005). [cited by applicant]
Echevarria et al., 1998. Simultaneous detection and identification of human parainfluenza viruses 1, 2, and 3 from clinical samples by multiplex PCR. Journal of Clinical Microbiology, 36(5), pp. 1388-1391. (Yer: 1998). [cited by applicant]
Hu et al. Development of a real-time RT-PCR assay for detection of quantitation of parainfluenza virus 3. J Virol Methods 2005; 130:145-8. (Year: 2005). [cited by applicant]
Jansen et al., Development and evaluation of a four-tube real time multiplex PCR assay covering fourteen respiratory viruses, and comparison to its corresponding single target counterparts. Journal of Clinical Virology.… [cited by applicant]
Ji et al., 2012. Simultaneous detection of human parainfluenza viruses 1, 2, 3 by multiplex real-time reverse transcription-polymerase chain reaction with LNA probes. Chinese Journal of Experimental and Clinical Virolog… [cited by applicant]
Jin et al., Examination of the specificity of DNA methylation profiling techniques towards 5-methylcytosine and 5-hydroxymethylcytosine. Nucleic Acids Res. Jun. 2010; 8(11), e125, pp. 1-7. Epub Apr. 5, 2010. (Year: 2010… [cited by applicant]
Mao et al., 2012. Human parainfluenza virus-associated respiratory tract infection among children and genetic analysis of HPIV-3 strains in Beijing, China (Year: 2012). [cited by applicant]
Ono et al., Synthesis of decadeoxyribonucleotides containing N 6-methyladenine, N 4-methylcytosine and 5-methylcytosine: recogniation of cleavage by restriction endonucleases (nucleosides and nucleotides part 74). Nucle… [cited by applicant]
Ramezannia et al., 2016. Development of a multiplex real-time RT-PCR assay for detection of human parainfluenza viruses in patients with respiratory symptoms. Future Virology, 11(9), pp. 611-617. (Year: 2016). [cited by applicant]
Chakravorty, et al. “Rapid Universal Identification of Bacterial Pathogens from Clinical Cultures by Using a Novel Sloppy Molecular Beacon Melting Temperature Signature Technique,” Journal of Clinical Microbiology, 48(1… [cited by applicant]
Gresham, et al., “Optimized detection of squence variation in heterozygous genomes using DNA microarrays with isothermal-melting probes,” Proceedings of the National Academy of Sciences, 107(4):1482-1487 (2010). [cited by applicant]
Bellau-Pujol et al., “Development of three multiplex RT-PCR assays for the detection of 12 respiratory RNA viruses,” J. Viral. Methods 126:53-63. (2005). [cited by applicant]
Genbank Accession No. AF213352 Human parainfluenza virus 2 hemagglutinin-neuraminidase glycoprotein (H N) mRNA, complete cds (submitted Dec. 8, 1999, retrieved on Sep. 11, 2019 from http://www.ncbi.nlm.nih.gov/nuccore/A… [cited by applicant]
Genbank Accession No. GU732171 Human parainfluenza virus 3 strain BJ/341/09 hemagglutinin-neuraminidase (HN) gene, complete cds (submitted Feb. 10, 2010, retrieved on Sep. 11, 2019 from http://www.ncbi.nlm.nih.gov/nucco… [cited by applicant]
Hu et al., “Rappaport R, et al. Development of a real-time RT-PCR assay for detection and quantitation of parainfluenza virus 3.” J Viral Methods 130:145-148 (2005). [cited by applicant]
Mizuta et al., Detailed genetic analysis of hemagglutinin-neuraminidase glycoprotein gene in human parainfluenza virus type 1 isolates from patients with acute respiratory infection between 2002 and 2009 in Yamagata pre… [cited by applicant]
Mizuta et al., “Molecular evolution of the haemagglutinin-neuraminidase gene in human parainfluenza virus type 3 isolates from children with acute respiratory illness in Yamagata prefecture,” Japan. J Med Microbial. Apr… [cited by applicant]
PCT International Search Report, International Application No. PCT/US2018/024021, Aug. 21, 2018. [cited by applicant]
PCT Invitation to Pay Additional Fees, Partial International Search Report, and Provisional Written Opinion, International Application No. PCT/US2018/024021, Jun. 25, 2018. [cited by applicant]
PCT Written Opinion, International Application No. PCT/US2018/024021, Aug. 21, 2018. [cited by applicant]
Corne, J.M., et al., “A multiplex RT-PCR for the detection of parainfluenza viruses 1-3 in clinical samples,” Journal of Virological Methods 82(1):9-18, 1999. [cited by applicant]
Thiberville, S.D., et al., “The Viral Etiology of an Influenza-like Illness During the 2009 Pandemic,” Journal of Medical Virology 84(7):1071-1079, 2012. [cited by applicant]