Chemistry: molecular biology and microbiology – Measuring or testing process involving enzymes or... – Involving nucleic acid
Reexamination Certificate
1998-01-29
2001-04-10
Whisenant, Ethan (Department: 1655)
Chemistry: molecular biology and microbiology
Measuring or testing process involving enzymes or...
Involving nucleic acid
C435S091200, C536S023100, C536S024300
Reexamination Certificate
active
06214548
ABSTRACT:
FIELD OF THE INVENTION
The present invention relates in general to diagnostic methods and compositions for the intestinal pathogen Cyclospora.
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BACKGROUND OF THE INVENTION
Cyclospora is an emerging human intestinal pathogen (Ortega, et al., 1993, 1994). Since 1979, oocyst-like structures have been detected in the stool of humans with diarrhea (Ashford, 1979). These structures are spherical, 8-10 &mgr;m in diameter, autofluorescent, stain variably with acid-fast techniques, and contain clusters of membrane-bound globules. A variety of workers have referred to this organism as a blue-green alga (cyanobacterium-like body), a fungal spore, a coccidian-like body, and a large cryptosporidium (Long, et al., 1991; Ashford, et al, 1993). In 1993, in vitro sporulation and excystation of these cyanobacterium-like bodies revealed the presence of two sporocysts per oocyst and two sporozoites per sporocyst, leading to re-classification and naming of this organism as a species of the coccidian genus, Cyclospora (Ortega, et al., 1993, 1994).
Increasing numbers of reports suggest that this cyclosporan is an important cause of prolonged diarrheal disease in humans throughout the world (Wurtz, 1994). In one recent study, Cyclospora was found in fecal specimens from 11% of Haitians seropositive for the human immunodeficiency virus who had chronic diarrhea (Pape, et al., 1994). In most of these patients it was the sole pathogen identified and was detected repeatedly. Evidence favoring a role for this organism as a pathogen includes a significant association of oocysts with clinical illness (in absence of other known pathogens), clinical response to antimicrobial therapy, and clearance of organisms coincident with clinical resolution (Page, et al., 1994; Shlim, et al., 1991; Hoge, et al., 1993; Hoge, et al., 1995). Human cyclosporiasis is clinically indistinguishable, however, from cryptosporidiosis, isosporidiosis, giardiasis and microsporidiosis. Epidemiologic data indicate that the human-associated Cyclospora is transmitted by water and by food (Hoge, et al., 1993; Pieniazek, et al., 1996; Centers for Disease Control (CDC), 1996).
Prior to the discoveries disclosed herein, there was no simple way to conclusively diagnose Cyclospora infection in a primate, or to monitor water or food supplies for the presence of Cyclospora.
SUMMARY OF THE INVENTION
In one aspect, the present invention includes a method of detecting the presence of Cyclospora in a sample containing DNA. The method includes identifying, in the sample, the presence of a polynucleotide sequence which (i) is at least about 20 nucleotides in length, (ii) corresponds to a region of SEQ ID NO:2 which contains at least one discrimination position selected from the group consisting of positions at nucleotide numbers 155, 178, 249, 258, 262, 328, 473, 495, 501, 507, 636, 660, 667, 698, 706, 831, 1473, 1579, 1654, 1659, 1664, 1674, 1675, 1684 and 1694, (iii) contains the same nucleotide at such discrimination position as is contained in the corresponding discrimination position in a variant sequence defined by SEQ ID NO:2, and (iv) has a sequence that is greater than about 95% identical with a sequence defined by the corresponding region of SEQ ID NO:2. The presence of such a polynucleotide sequence in the sample indicates the presence of Cyclospora in the sample.
In general embodiments, the polynucleotide has a sequence that is greater than about 97% identical, or greater than about 98i identical, or greater than about 99% identical, or is simply 100% identical, with a sequence defined by the corresponding region of SEQ ID NO:2, such as SEQ ID NO:1.
The identifying may be performed using any of a variety of nucleic acid detection assays, including a hybridization detection assay, such as a hybridization assay performed on a substrate containing a plurality of different-sequence polynucleotide fragments. The diff
Echeverria Peter
Relman David A.
Arwine Elizabeth
Evans Susan T.
Mohr Judy M.
The United States of America as represented by the Secretary of
Whisenant Ethan
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