Viruses associated with immunodeficiency and enteropathy and methods using same

A method of detecting acquired immune deficiency syndrome (AIDS) and/or AIDS progression in a subject, said method comprising:

• a) synthesizing cDNA from RNA by a biological sample obtained from as subject;
• and
• b) detecting if present in the sample one or more target nucleotide sequences that specifically hybridize wider stringent conditions to one or more polynucleotides having at least 70% sequence identity with any one of SEQ ID NO:1-107 by a PCR assay selected from the group consisting of a real time PCR assay and a nested PCR assay;
• and
• determining the magnitude of difference between the level of said one or more target nucleotide sequences in said subject relative to the level of said one or more target nucleotide sequences from a control subject whereby an increase in the level of said one or more target nucleotide sequences in said subject, relative to the level of the one or more target nucleotide sequences from a control subject, indicates AIDS and/or AIDS progression in said subject.

A method of diagnosing, or providing a prognostic indicator of, immunodeficiency and/or enteropathy in a subject, said method comprising:

• providing at least one biological sample from the subject;
• subjecting RNA if present from the at least one biological sample to synthesis of cDNA comprising one or more target nucleotide sequences that specifically hybridize under stringent conditions to one or more of polynucleotides having a sequence that is at least 70% identical to the sequence of a polynucleotide selected from the group consisting of SEQ ID NO:1-107;
• detecting said one or more target nucleotide sequences by a PCR assay selected from the group consisting of a real time PCR assay and a nested PCR assay;
• and
• determining the magnitude of difference between the level of said one or more target nucleotide sequences in said subject relative to the level of one more target nucleotide sequences from a control subject wherein the detection of an increase in the level of said one or more target nucleotide sequences in said subject, relative to the level of one or more target nucleotide sequences from a control subject, indicates the presence of, or the propensity to develop, immunodeficiency and/or enteropathy in said subject.

A method of identifying a therapeutic agent for treating immunodeficiency and/or enteropathy in a subject, said method comprising:

• providing a first sample from the subject prior to administration of a candidate therapeutic agent;
• administering a therapeutically effective amount of the candidate therapeutic agent to the subject;
• providing a second sample from the subject after the administering the candidate therapeutic agent;
• detecting in the first sample by a first PCR assay one or more target polynucleotides that specifically hybridize under stringent conditions to one or more polynucleotides having a sequence that is at least 70% identical to the sequence of a polynucleotide selected from the group consisting of SEQ ID NO:
• 1-107;
• detecting in the second sample by a second PCR assay the one or more target polynucleotides, wherein the detection of a decrease in the level of said one or more target nucleotide sequences in said second sample, relative to the level of the one or more target nucleotide sequences from said first sample, identifies said candidate agent as said therapeutic agent.