Patent

1. A method for specifically detecting M. genitalium nucleic acid including clinical isolate M. genitalium nucleic acid in a clinical sample, comprising:

(a) amplifying a nucleic acid sequence comprising a fragment of SEQ ID NO: 1, wherein said fragment of SEQ ID NO: 1 is at least 25 consecutive nucleotides of SEQ ID NO: 1, by contacting said sample with forward and reverse primers, to produce the amplified nucleic acid sequence;

wherein said forward primer binds to a target site located between nucleotide residue 41 and nucleotide residue 125 of the nucleic acid strand complementary to SEQ ID NO: 48; and

wherein said reverse primer binds to a target site located between nucleotide residue 197 and nucleotide 350 of SEQ ID NO: 48;

(b) detecting the amplified nucleic acid sequence; and

(c) detecting specifically M. genitalium nucleic acid including M. genitalium nucleic acid from clinical isolates in the clinical sample, based on the presence of said amplified nucleic acid sequence.

2. The method according to claim 1 , wherein said forward and reverse oligonucleotide primers are at least 20 nucleotides long.

3. The method according to claim 1 , wherein said detecting step comprises:

(a) contacting said amplified nucleic acid sequence with a probe, wherein the probe binds to a target site within said amplified nucleic acid sequence, or the complement thereof; and

(b) detecting binding of said probe to said amplified nucleic acid sequence.

4. The method according to claim 3 , wherein the probe binds to a target site located between nucleotide residues 55 and 100 of the nucleic acid strand complementary to SEQ ID NO: 1.

5. The method according to claim 3 , wherein said probe is at least 15 nucleotides long and up to 50 nucleotides long.

6. The method according to claim 5 , wherein the probe comprises the nucleic acid sequence of SEQ ID NO: 3, or a fragment thereof having at least 15 nucleotides.

7. An in vitro method for quantitating specifically M. genitalium pathogen load including clinical M. genitalium isolates in a clinical sample, comprising:

(a) amplifying a nucleic acid sequence comprising a fragment of SEQ ID NO:1, wherein said fragment of SEQ ID NO: 1 is at least 25 consecutive nucleotides of SEQ ID NO:1, by contacting the clinical sample and a reference sample having a predetermined known M. genitalium pathogen load with forward and reverse primers,

wherein said forward primer binds to a target site located between nucleotide residue 41 and nucleotide residue 125 of the nucleic acid stand complementary to SEQ ID NO: 48; and wherein said reverse primer binds to a target site located between nucleotide residue 197 and nucleotide 350 of SEQ ID NO: 48;

(b) detecting the amplified nucleic acid sequence in the clinical sample and in the reference sample; and

(c) determining the quantity of the amplified nucleic acid sequence in the clinical sample and in the reference sample as indicative of the quantity of the M. genitalium nucleic acid in the clinical sample and in the reference sample; and

(d) comparing the quantity of M. genitalium nucleic acid detected in the clinical sample with the quantity of M. genitalium nucleic acid detected in the reference sample;

and thereby quantitating specifically M. genitalium pathogen load including clinical M. genitalium isolates in the clinical sample.

8. An in vitro method for determining the efficacy of a drug against M. genitalium and M. genitalium clinical isolates over the course of a period of drug therapy, comprising:

(a) amplifying a nucleic acid sequence comprising a fragment of SEQ ID NO:1, wherein said fragment of SEQ ID NO: 1 is at least 25 consecutive nucleotides of SEQ ID NO:1, by contacting a first clinical sample obtained at a first time point within or prior to the period of drug therapy and a second clinical sample obtained at a later time point within the period of drug therapy with forward and reverse primers,

wherein said forward primer binds to a target site located between nucleotide residue 41 and nucleotide 125 of the nucleic acid strand complementary to SEQ ID NO: 48; and

wherein said reverse primer binds to a target site located between nucleotide residue 197 and nucleotide 350 of SEQ ID NO: 48;

(b) detecting the amplified nucleic acid sequence in the first and second clinical sample;

(c) determining the quantity of the amplified nucleic acid sequence in the first and second clinical sample as indicative of the quantity of M. genitalium nucleic acid and M. genitalium clinical isolate nucleic acid in the first and second clinical sample; and

(d) comparing the quantity of M. genitalium nucleic acid and M. genitalium clinical isolate nucleic acid detected in the first clinical sample with the quantity of M. genitalium nucleic acid and M. genitalium clinical isolate nucleic acid detected in the second clinical samples, wherein a decrease in the quantity of M. genitalium nucleic acid and M. genitalium clinical isolate nucleic acid detected in the second clinical samples as compared to the first clinical sample indicates that the drug has been effective against M. genitalium and M. genitalium clinical isolate nucleic acid over the course of the period of drug therapy, whereas an increase in the quantity of M. genitalium nucleic acid and M. genitalium clinical isolate nucleic acid detected in the second clinical samples as compared to the first clinical sample indicates that the drug has been ineffective against M. genitalium over the course of the period of drug therapy;

and thereby determining drug efficacy against M. genitalium and M. genitalium clinical isolates over the course of the period of drug therapy.

9. An in vitro method for detecting and/or monitoring the development of resistance of M. genitalium over the course of a period of drug therapy, comprising:

(a) amplifying a nucleic acid sequence comprising a fragment of SEQ ID NO:1, wherein said fragment of SEQ ID NO: 1 is at least 25 consecutive nucleotides of SEQ ID NO:1, by contacting a first clinical sample obtained at a first time point within or prior to the exposure of M. genitalium to the drug and a second clinical sample obtained at a later time point following exposure of M. genitalium to the drug with forward and reverse primers,

wherein said forward primer binds to a target site located between nucleotide residue 41 and nucleotide 125 of the nucleic acid strand complementary to SEQ ID NO: 48; and

wherein said reverse primer binds to a target site located between nucleotide residue 197 and nucleotide 350 of SEQ ID NO: 48;

(b) detecting the amplified nucleic acid sequence in the first and second clinical sample;

(c) determining the quantity of the amplified nucleic acid sequence in the first and second clinical sample as indicative of the quantity of M. genitalium nucleic acid in the first and second clinical sample; and

(d) comparing the quantity of M. genitalium nucleic acid detected in the first clinical sample with the quantity of M. genitalium nucleic acid detected in the second clinical samples;

wherein the absence of a reduction in the quantity of M. genitalium nucleic acid in the second clinical samples as compared to the first clinical sample, or an increase in the quantity of M. genitalium nucleic acid in the second clinical samples as compared to the first clinical sample, indicates that the M. genitalium have developed resistance to the drug.

10. The method according to claim 3 , wherein said probe is at least 15 nucleotides long and up to 20 nucleotides long.

11. The method according to claim 4 , wherein said probe binds to a target site located between nucleotide residues 60 and 90 of the nucleic acid strand complementary to SEQ ID NO: 1.

12. The method according to claim 4 , wherein said probe binds to a target site located between nucleotide residues 65 and 85 of the nucleic acid strand complementary to SEQ ID NO: 1.

13. The method according to claim 3 , wherein said probe comprises the nucleic acid sequence of SEQ ID NO: 3.

14. The method according to claim 1 , wherein said fragment of SEQ ID NO: 1 is at least 100 consecutive nucleotides of SEQ ID NO: 1 or at least 200 consecutive nucleotides of SEQ ID NO: 1.

15. The method according to claim 1 , wherein said fragment of SEQ ID NO: 1 is up to 275 consecutive nucleotides of SEQ ID NO: 1.

16. The method according to claim 2 , wherein said forward primer and/or said reverse primer is between 25-30 nucleotides long.

17. The method according to claim 2 , wherein said forward primer and/or said reverse primer is between 45-55 nucleotides long.

18. The method according to claim 1 , wherein said forward primer binds to a target site located between nucleotide residues 1-18 of a nucleic acid strand complementary to SEQ ID NO: 1, and said reverse primer binds to a target site located between nucleotide residues 214-240 of SEQ ID NO: 1.

19. The method according to claim 1 , wherein the forward primer target site is located between nucleotide residue 76 and nucleotide residue 125 of a nucleic acid strand complementary to SEQ ID NO: 48.

20. The method according to claim 19 , wherein the forward primer target site is located between nucleotide residue 81 and nucleotide residue 120 of a nucleic acid strand complementary to SEQ ID NO: 48.

21. The method according to claim 19 , wherein the forward primer target site is located between nucleotide residue 86 and nucleotide residue 120 of a nucleic acid strand complementary to SEQ ID NO: 48.

22. The method according to claim 1 , wherein said forward primer binds to a target site that comprises nucleotide residues 101-118 of a nucleic acid strand complementary to SEQ ID NO: 48.

23. The method according to claim 1 , wherein said forward primer binds to a target site located from nucleotide residue 90 to nucleotide residue 118 of a nucleic acid strand complementary to SEQ ID NO: 48.

24. The method according to claim 1 , wherein the forward primer target site is located between nucleotide residue 41 and nucleotide residue 101 of a nucleic acid strand complementary to SEQ ID NO: 48.

25. The method according to claim 24 , wherein the forward primer target site is located between nucleotide residue 46 and nucleotide residue 101 of a nucleic acid strand complementary to SEQ ID NO: 48.

26. The method according to claim 1 , wherein said forward primer binds to a target site located from nucleotide residue 48 to nucleotide residue 100 of a nucleic acid strand complementary to SEQ ID NO: 48.

27. The method according to claim 1 , wherein said forward primer comprises a nucleic acid sequence having at least 90% sequence identity to a nucleic acid sequence selected from SEQ ID NOs: 4, 8, 10, or 31.

28. The method according to claim 1 , wherein said forward primer comprises a nucleic acid selected from SEQ ID NOs: 4, 8, 10, and 31.

29. The method according to claim 1 , wherein said forward primer comprises a nucleic acid sequence selected from SEQ ID NOs: 4, 8, and 31, or at least 27 consecutive nucleotides of SEQ ID NOs: 4, 8, or 31.

30. The method according to claim 1 , wherein said reverse primer binds to a target site located between nucleotide residue 197 and nucleotide residue 297 of SEQ ID NO: 48.

31. The method according to claim 1 , wherein said reverse primer binds to a target site located between nucleotide residue 198 and nucleotide residue 247 of SEQ ID NO: 48.

32. The method according to claim 1 , wherein said reverse primer binds to a target site located between nucleotide residue 248 and nucleotide residue 350 of SEQ ID NO: 48.

33. The method according to claim 1 , wherein the reverse primer target site is located from nucleotide residue 298 to nucleotide residue 347 of SEQ ID NO: 48.

34. The method according to claim 1 , wherein said reverse primer binds to a target site located between nucleotide residue 300 and nucleotide residue 350 of SEQ ID NO: 48.

35. The method according to claim 1 , wherein the reverse primer target site is located between nucleotide residue 310 and nucleotide residue 345 of SEQ ID NO: 48.

36. The method according to claim 1 , wherein the reverse primer target site is located from nucleotide residue 314 and nucleotide residue 340 of SEQ ID NO: 48.

37. The method according to claim 1 , wherein said reverse primer comprises a nucleic acid sequence having at least 90% sequence identity to a nucleic acid sequence selected from SEQ ID NOs: 5, 26, and 28.

38. The method according to claim 1 , wherein said reverse primer comprises a nucleic acid sequence selected from SEQ ID NOs: 5, 26, and 28.

39. The method according to claim 1 , wherein said reverse primer comprises the nucleic acid sequence of SEQ ID NO: 5, or at least 25 consecutive nucleotides of SEQ ID NO: 5.

40. The method according to claim 1 , wherein said forward primer comprises a nucleic acid sequence having at least 90% sequence identity to a nucleic acid sequence selected from SEQ ID NOs: 4, 8, 10, and 31, and wherein said reverse primer comprises a nucleic acid sequence having 90% sequence identity to a nucleic acid sequence selected from SEQ ID NOs: 5, 26, and 28.

41. The method according to claim 1 , wherein said forward primer comprises a nucleic acid sequence selected from SEQ ID NOs: 4, 8, 10, and 31, and wherein said reverse primer comprises a nucleic acid sequence selected from SEQ ID NOs: 5, 26, and 28.

42. The method according to claim 1 , wherein said forward primer comprises a nucleic acid sequence selected from SEQ ID NOs: 4, 8, and 31, and wherein said reverse primer comprises the nucleic acid sequence of SEQ ID NO: 5.

43. The method according to claim 7 , wherein said forward and reverse oligonucleotide primers are at least 20 nucleotides long.

44. The method according to claim 7 , wherein said detecting step comprises:

(a) contacting said amplified nucleic acid sequence with a probe, wherein the probe binds to a target site within said amplified nucleic acid sequence, or the complement thereof; and

(b) detecting binding of said probe to said amplified nucleic acid sequence.

45. The method according to claim 44 , wherein the probe binds to a target site located between nucleotide residues 55 and 100 of the nucleic acid strand complementary to SEQ ID NO: 1.

46. The method according to claim 44 , wherein said probe is at least 15 nucleotides long and up to 50 nucleotides long.

47. The method according to claim 46 , wherein the probe comprises the nucleic acid sequence of SEQ ID NO: 3, or a fragment thereof having at least 15 nucleotides.

48. The method according to claim 44 , wherein said probe is at least 15 nucleotides long and up to 20 nucleotides long.

49. The method according to claim 45 , wherein said probe binds to a target site located between nucleotide residues 60 and 90 of the nucleic acid strand complementary to SEQ ID NO: 1.

50. The method according to claim 45 , wherein said probe binds to a target site located between nucleotide residues 65 and 85 of the nucleic acid strand complementary to SEQ ID NO: 1.

51. The method according to claim 44 , wherein said probe comprises the nucleic acid sequence of SEQ ID NO: 3.

52. The method according to claim 7 , wherein said fragment of SEQ ID NO: 1 is at least 100 consecutive nucleotides of SEQ ID NO: 1 or at least 200 consecutive nucleotides of SEQ ID NO: 1.

53. The method according to claim 7 , wherein said fragment of SEQ ID NO: 1 is up to 275 consecutive nucleotides of SEQ ID NO: 1.

54. The method according to claim 43 , wherein said forward primer and/or said reverse oligonucleotide primer is between 25-30 nucleotides long.

55. The method according to claim 43 , wherein said forward primer and/or said reverse oligonucleotide primer is between 45-55 nucleotides long.

56. The method according to claim 7 , wherein said forward primer binds to a target site located between nucleotide residues 1-18 of a nucleic acid strand complementary to SEQ ID NO: 1, and said reverse primer binds to a target site located between nucleotide residues 214-240 of SEQ ID NO: 1.

57. The method according to claim 7 , wherein the forward primer target site is located between nucleotide residue 76 and nucleotide residue 125 of a nucleic acid strand complementary to SEQ ID NO: 48.

58. The method according to claim 57 , wherein the forward primer target site is located between nucleotide residue 81 and nucleotide residue 120 of a nucleic acid strand complementary to SEQ ID NO: 48.

59. The method according to claim 57 , wherein the forward primer target site is located between nucleotide residue 86 and nucleotide residue 120 of a nucleic acid strand complementary to SEQ ID NO: 48.

60. The method according to claim 7 , wherein said forward primer binds to a target site that comprises nucleotide residues 101-118 of a nucleic acid strand complementary to SEQ ID NO: 48.

61. The method according to claim 7 , wherein said forward primer binds to a target site located from nucleotide residue 90 to nucleotide residue 118 of a nucleic acid strand complementary to SEQ ID NO: 48.

62. The method according to claim 7 , wherein the forward primer target site is located between nucleotide residue 41 and nucleotide residue 101 of a nucleic acid strand complementary to SEQ ID NO: 48.

63. The method according to claim 62 , wherein the forward primer target site is located between nucleotide residue 46 and nucleotide residue 101 of a nucleic acid strand complementary to SEQ ID NO: 48.

64. The method according to claim 7 , wherein said forward primer binds to a target site located from nucleotide residue 48 to nucleotide residue 100 of a nucleic acid strand complementary to SEQ ID NO: 48.

65. The method according to claim 7 , wherein said forward primer comprises a nucleic acid sequence having at least 90% sequence identity to a nucleic acid sequence selected from SEQ ID NOs: 4, 8, 10, or 31.

66. The method according to claim 7 , wherein said forward primer comprises a nucleic acid selected from SEQ ID NOs: 4, 8, 10, and 31.

67. The method according to claim 7 , wherein said forward primer comprises a nucleic acid sequence selected from SEQ ID NOs: 4, 8, and 31, or at least 27 consecutive nucleotides of SEQ ID NOs: 4, 8, or 31.

68. The method according to claim 7 , wherein said reverse primer binds to a target site located between nucleotide residue 197 and nucleotide residue 297 of SEQ ID NO: 48.

69. The method according to claim 7 , wherein said reverse primer binds to a target site located between nucleotide residue 198 and nucleotide residue 247 of SEQ ID NO: 48.

70. The method according to claim 7 , wherein said reverse primer binds to a target site located between nucleotide residue 248 and nucleotide residue 350 of SEQ ID NO: 48.

71. The method according to claim 7 , wherein the reverse primer target site is located from nucleotide residue 298 to nucleotide residue 347 of SEQ ID NO: 48.

72. The method according to claim 7 , wherein said reverse primer binds to a target site located between nucleotide residue 300 and nucleotide residue 350 of SEQ ID NO: 48.

73. The method according to claim 7 , wherein the reverse primer target site is located between nucleotide residue 310 and nucleotide residue 345 of SEQ ID NO: 48.

74. The method according to claim 7 , wherein the reverse primer target site is located from nucleotide residue 314 and nucleotide residue 340 of SEQ ID NO: 48.

75. The method according to claim 7 , wherein said reverse primer comprises a nucleic acid sequence having at least 90% sequence identity to a nucleic acid sequence selected from SEQ ID NOs: 5, 26, and 28.

76. The method according to claim 7 , wherein said reverse primer comprises a nucleic acid sequence selected from SEQ ID NOs: 5, 26, and 28.

77. The method according to claim 7 , wherein said reverse primer comprises the nucleic acid sequence of SEQ ID NO: 5, or at least 25 consecutive nucleotides of SEQ ID NO: 5.

78. The method according to claim 7 , wherein said forward primer comprises a nucleic acid sequence having at least 90% sequence identity to a nucleic acid sequence selected from SEQ ID NOs: 4, 8, 10, and 31, and wherein said reverse primer comprises a nucleic acid sequence having 90% sequence identity to a nucleic acid sequence selected from SEQ ID NOs: 5, 26, and 28.

79. The method according to claim 7 , wherein said forward primer comprises a nucleic acid sequence selected from SEQ ID NOs: 4, 8, 10, and 31, and wherein said reverse primer comprises a nucleic acid sequence selected from SEQ ID NOs: 5, 26, and 28.

80. The method according to claim 7 , wherein said forward primer comprises a nucleic acid sequence selected from SEQ ID NOs: 4, 8, and 31, and wherein said reverse primer comprises the nucleic acid sequence of SEQ ID NO: 5.

81. The method according to claim 8 , wherein said forward and reverse oligonucleotide primers are at least 20 nucleotides long.

82. The method according to claim 8 , wherein said detecting step comprises:

(a) contacting said amplified nucleic acid sequence with a probe, wherein the probe binds to a target site within said amplified nucleic acid sequence, or the complement thereof; and

(b) detecting binding of said probe to said amplified nucleic acid sequence.

83. The method according to claim 82 , wherein the probe binds to a target site located between nucleotide residues 55 and 100 of the nucleic acid strand complementary to SEQ ID NO: 1.

84. The method according to claim 82 , wherein said probe is at least 15 nucleotides long and up to 50 nucleotides long.

85. The method according to claim 84 , wherein the probe comprises the nucleic acid sequence of SEQ ID NO: 3, or a fragment thereof having at least 15 nucleotides.

86. The method according to claim 82 , wherein said probe is at least 15 nucleotides long and up to 20 nucleotides long.

87. The method according to claim 83 , wherein said probe binds to a target site located between nucleotide residues 60 and 90 of the nucleic acid strand complementary to SEQ ID NO: 1.

88. The method according to claim 83 , wherein said probe binds to a target site located between nucleotide residues 65 and 85 of the nucleic acid strand complementary to SEQ ID NO: 1.

89. The method according to claim 82 , wherein said probe comprises the nucleic acid sequence of SEQ ID NO: 3.

90. The method according to claim 8 , wherein said fragment of SEQ ID NO: 1 is at least 100 consecutive nucleotides of SEQ ID NO: 1 or at least 200 consecutive nucleotides of SEQ ID NO: 1.

91. The method according to claim 8 , wherein said fragment of SEQ ID NO: 1 is up to 275 consecutive nucleotides of SEQ ID NO: 1.

92. The method according to claim 81 , wherein said forward primer and/or said reverse oligonucleotide primer is between 25-30 nucleotides long.

93. The method according to claim 81 , wherein said forward primer and/or said reverse oligonucleotide primer is between 45-55 nucleotides long.

94. The method according to claim 8 , wherein said forward primer binds to a target site located between nucleotide residues 1-18 of a nucleic acid strand complementary to SEQ ID NO: 1, and said reverse primer binds to a target site located between nucleotide residues 214-240 of SEQ ID NO: 1.

95. The method according to claim 8 , wherein the forward primer target site is located between nucleotide residue 76 and nucleotide residue 125 of a nucleic acid strand complementary to SEQ ID NO: 48.

96. The method according to claim 95 , wherein the forward primer target site is located between nucleotide residue 81 and nucleotide residue 120 of a nucleic acid strand complementary to SEQ ID NO: 48.

97. The method according to claim 95 , wherein the forward primer target site is located between nucleotide residue 86 and nucleotide residue 120 of a nucleic acid strand complementary to SEQ ID NO: 48.

98. The method according to claim 8 , wherein said forward primer binds to a target site that comprises nucleotide residues 101-118 of a nucleic acid strand complementary to SEQ ID NO: 48.

99. The method according to claim 8 , wherein said forward primer binds to a target site located from nucleotide residue 90 to nucleotide residue 118 of a nucleic acid strand complementary to SEQ ID NO: 48.

100. The method according to claim 8 , wherein the forward primer target site is located between nucleotide residue 41 and nucleotide residue 101 of a nucleic acid strand complementary to SEQ ID NO: 48.

101. The method according to claim 100 , wherein the forward primer target site is located between nucleotide residue 46 and nucleotide residue 101 of a nucleic acid strand complementary to SEQ ID NO: 48.

102. The method according to claim 8 , wherein said forward primer binds to a target site located from nucleotide residue 48 to nucleotide residue 100 of a nucleic acid strand complementary to SEQ ID NO: 48.

103. The method according to claim 8 , wherein said forward primer comprises a nucleic acid sequence having at least 90% sequence identity to a nucleic acid sequence selected from SEQ ID NOs: 4, 8, 10, or 31.

104. The method according to claim 8 , wherein said forward primer comprises a nucleic acid selected from SEQ ID NOs: 4, 8, 10, and 31.

105. The method according to claim 8 , wherein said forward primer comprises a nucleic acid sequence selected from SEQ ID NOs: 4, 8, and 31, or at least 27 consecutive nucleotides of SEQ ID NOs: 4, 8, or 31.

106. The method according to claim 8 , wherein said reverse primer binds to a target site located between nucleotide residue 197 and nucleotide residue 297 of SEQ ID NO: 48.

107. The method according to claim 8 , wherein said reverse primer binds to a target site located between nucleotide residue 198 and nucleotide residue 247 of SEQ ID NO: 48.

108. The method according to claim 8 , wherein said reverse primer binds to a target site located between nucleotide residue 248 and nucleotide residue 350 of SEQ ID NO: 48.

109. The method according to claim 8 , wherein the reverse primer target site is located from nucleotide residue 298 to nucleotide residue 347 of SEQ ID NO: 48.

110. The method according to claim 8 , wherein said reverse primer binds to a target site located between nucleotide residue 300 and nucleotide residue 350 of SEQ ID NO: 48.

111. The method according to claim 8 , wherein the reverse primer target site is located between nucleotide residue 310 and nucleotide residue 345 of SEQ ID NO: 48.

112. The method according to claim 8 , wherein the reverse primer target site is located from nucleotide residue 314 and nucleotide residue 340 of SEQ ID NO: 48.

113. The method according to claim 8 , wherein said reverse primer comprises a nucleic acid sequence having at least 90% sequence identity to a nucleic acid sequence selected from SEQ ID NOs: 5, 26, and 28.

114. The method according to claim 8 , wherein said reverse primer comprises a nucleic acid sequence selected from SEQ ID NOs: 5, 26, and 28.

115. The method according to claim 8 , wherein said reverse primer comprises the nucleic acid sequence of SEQ ID NO: 5, or at least 25 consecutive nucleotides of SEQ ID NO: 5.

116. The method according to claim 8 , wherein said forward primer comprises a nucleic acid sequence having at least 90% sequence identity to a nucleic acid sequence selected from SEQ ID NOs: 4, 8, 10, and 31, and wherein said reverse primer comprises a nucleic acid sequence having 90% sequence identity to a nucleic acid sequence selected from SEQ ID NOs: 5, 26, and 28.

117. The method according to claim 8 , wherein said forward primer comprises a nucleic acid sequence selected from SEQ ID NOs: 4, 8, 10, and 31, and wherein said reverse primer comprises a nucleic acid sequence selected from SEQ ID NOs: 5, 26, and 28.

118. The method according to claim 8 , wherein said forward primer comprises a nucleic acid sequence selected from SEQ ID NOs: 4, 8, and 31, and wherein said reverse primer comprises the nucleic acid sequence of SEQ ID NO: 5.

119. The method according to claim 9 , wherein said forward and reverse oligonucleotide primers are at least 20 nucleotides long.

120. The method according to claim 9 , wherein said detecting step comprises:

(a) contacting said amplified nucleic acid sequence with a probe, wherein the probe binds to a target site within said amplified nucleic acid sequence, or the complement thereof; and

(b) detecting binding of said probe to said amplified nucleic acid sequence.

121. The method according to claim 120 , wherein the probe binds to a target site located between nucleotide residues 55 and 100 of the nucleic acid strand complementary to SEQ ID NO: 1.

122. The method according to claim 120 , wherein said probe is at least 15 nucleotides long and up to 50 nucleotides long.

123. The method according to claim 122 , wherein the probe comprises the nucleic acid sequence of SEQ ID NO: 3, or a fragment thereof having at least 15 nucleotides.

124. The method according to claim 120 , wherein said probe is at least 15 nucleotides long and up to 20 nucleotides long.

125. The method according to claim 121 , wherein said probe binds to a target site located between nucleotide residues 60 and 90 of the nucleic acid strand complementary to SEQ ID NO: 1.

126. The method according to claim 121 , wherein said probe binds to a target site located between nucleotide residues 65 and 85 of the nucleic acid strand complementary to SEQ ID NO: 1.

127. The method according to claim 120 , wherein said probe comprises the nucleic acid sequence of SEQ ID NO: 3.

128. The method according to claim 9 , wherein said fragment of SEQ ID NO: 1 is at least 100 consecutive nucleotides of SEQ ID NO: 1 or at least 200 consecutive nucleotides of SEQ ID NO: 1.

129. The method according to claim 9 , wherein said fragment of SEQ ID NO: 1 is up to 275 consecutive nucleotides of SEQ ID NO: 1.

130. The method according to claim 119 , wherein said forward primer and/or said reverse oligonucleotide primer is between 25-30 nucleotides long.

131. The method according to claim 119 , wherein said forward primer and/or said reverse oligonucleotide primer is between 45-55 nucleotides long.

132. The method according to claim 9 , wherein said forward primer binds to a target site located between nucleotide residues 1-18 of a nucleic acid strand complementary to SEQ ID NO: 1, and said reverse primer binds to a target site located between nucleotide residues 214-240 of SEQ ID NO: 1.

133. The method according to claim 9 , wherein the forward primer target site is located between nucleotide residue 76 and nucleotide residue 125 of a nucleic acid strand complementary to SEQ ID NO: 48.

134. The method according to claim 133 , wherein the forward primer target site is located between nucleotide residue 81 and nucleotide residue 120 of a nucleic acid strand complementary to SEQ ID NO: 48.

135. The method according to claim 133 , wherein the forward primer target site is located between nucleotide residue 86 and nucleotide residue 120 of a nucleic acid strand complementary to SEQ ID NO: 48.

136. The method according to claim 9 , wherein said forward primer binds to a target site that comprises nucleotide residues 101-118 of a nucleic acid strand complementary to SEQ ID NO: 48.

137. The method according to claim 9 , wherein said forward primer binds to a target site located from nucleotide residue 90 to nucleotide residue 118 of a nucleic acid strand complementary to SEQ ID NO: 48.

138. The method according to claim 9 , wherein the forward primer target site is located between nucleotide residue 41 and nucleotide residue 101 of a nucleic acid strand complementary to SEQ ID NO: 48.

139. The method according to claim 138 , wherein the forward primer target site is located between nucleotide residue 46 and nucleotide residue 101 of a nucleic acid strand complementary to SEQ ID NO: 48.

140. The method according to claim 9 , wherein said forward primer binds to a target site located from nucleotide residue 48 to nucleotide residue 100 of a nucleic acid strand complementary to SEQ ID NO: 48.

141. The method according to claim 9 , wherein said forward primer comprises a nucleic acid sequence having at least 90% sequence identity to a nucleic acid sequence selected from SEQ ID NOs: 4, 8, 10, or 31.

142. The method according to claim 9 , wherein said forward primer comprises a nucleic acid selected from SEQ ID NOs: 4, 8, 10, and 31.

143. The method according to claim 9 , wherein said forward primer comprises a nucleic acid sequence selected from SEQ ID NOs: 4, 8, and 31, or at least 27 consecutive nucleotides of SEQ ID NOs: 4, 8, or 31.

144. The method according to claim 9 , wherein said reverse primer binds to a target site located between nucleotide residue 197 and nucleotide residue 297 of SEQ ID NO: 48.

145. The method according to claim 9 , wherein said reverse primer binds to a target site located between nucleotide residue 198 and nucleotide residue 247 of SEQ ID NO: 48.

146. The method according to claim 9 , wherein said reverse primer binds to a target site located between nucleotide residue 248 and nucleotide residue 350 of SEQ ID NO: 48.

147. The method according to claim 9 , wherein the reverse primer target site is located from nucleotide residue 298 to nucleotide residue 347 of SEQ ID NO: 48.

148. The method according to claim 9 , wherein said reverse primer binds to a target site located between nucleotide residue 300 and nucleotide residue 350 of SEQ ID NO: 48.

149. The method according to claim 9 , wherein the reverse primer target site is located between nucleotide residue 310 and nucleotide residue 345 of SEQ ID NO: 48.

150. The method according to claim 9 , wherein the reverse primer target site is located from nucleotide residue 314 and nucleotide residue 340 of SEQ ID NO: 48.

151. The method according to claim 9 , wherein said reverse primer comprises a nucleic acid sequence having at least 90% sequence identity to a nucleic acid sequence selected from SEQ ID NOs: 5, 26, and 28.

152. The method according to claim 9 , wherein said reverse primer comprises a nucleic acid sequence selected from SEQ ID NOs: 5, 26, and 28.

153. The method according to claim 9 , wherein said reverse primer comprises the nucleic acid sequence of SEQ ID NO: 5, or at least 25 consecutive nucleotides of SEQ ID NO: 5.

154. The method according to claim 9 , wherein said forward primer comprises a nucleic acid sequence having at least 90% sequence identity to a nucleic acid sequence selected from SEQ ID NOs: 4, 8, 10, and 31, and wherein said reverse primer comprises a nucleic acid sequence having 90% sequence identity to a nucleic acid sequence selected from SEQ ID NOs: 5, 26, and 28.

155. The method according to claim 9 , wherein said forward primer comprises a nucleic acid sequence selected from SEQ ID NOs: 4, 8, 10, and 31, and wherein said reverse primer comprises a nucleic acid sequence selected from SEQ ID NOs: 5, 26, and 28.

156. The method according to claim 9 , wherein said forward primer comprises a nucleic acid sequence selected from SEQ ID NOs: 4, 8, and 31, and wherein said reverse primer comprises the nucleic acid sequence of SEQ ID NO: 5.