i am trying to develop a protocol to sequence HIVDR genes. i know that for the RT gene, codons 1-240 have been shown to be most involved in HIVDR . which codons in the Pr gene are most involved in HIVDR so that i don't have to sequence the entire gene?What primers would you recommend i use to amplify this region?
i would appreciate as much detail as possible.
thankyou. Common point mutations are at 10, 20, 24, 30, 32, 33, 36, 46, 47, 48, 50, 53, 54, 63, 71, 73, 77, 82, 84, 88, 90 and 93.
Resistance to protease inhibitors is complex, and usually depends on the accumulation of several different mutations, one after the other. There is often an interplay between mutations that confer resistance but reduce the ability to replicate, and those which increase the ability to replicate without further adding resistance.
Different PIs are likely to select for different mutations.There are also a number of single mutations, such as at 82, 84 and 90 which are regarded as mutations which confer resistance to all PIs.
See this page for more detail of other specific mutations:
http://www.aidsmap.com/cms1032055.asp
No idea about the primers, though. I failed first year biochemistry and haven't been back. Got a job rounding up sheep, which I really enjoy.
You are asking a very technical question. My guess is that a satisfactory answer is more likely to come from reading primary sources such as original peer reviewed research in genetics, virology and pharmacology, rather than secondary sources like my link or very, very tertiary sources like Yahoo Answers.
'Scuse me, gotta go. I've got a wether that keeps trying to break out. You are not going to get your answer to this from this site!! 'MEDS' not 'HIV' - The real killer
Don't believe what the drugs companies tell you.
WITHOUT HAART 'MEDS"
鈥淭hese long-term nonprogressors [Hiv+ people who remained healthy] are a heterogeneous group with respect to viral load and HIV-1 responses鈥one had been treated with antiretroviral agents.鈥?
AIDS Research and Human Retroviruses, 12: 585 (1996)
鈥?Harrer, Thomas, et al, Aids Researchers
NOT ONE USED HAART
鈥淪ubjects: homosexual men in Amsterdam. 鈥淣one of the LTAs [long-term asymptomatics鈥損eople who remained healthy]鈥eceived any antiviral drugs during the study [7 years].鈥?
鈥淭en HIV+ people; 11-15 years infected; non-progressors [i.e., healthy]; maintained stable T-cell counts above 500. 鈥淭hese long-term nonprogressors鈥ll showed the same risk factor (sexual exposure), and all had...virus...and none had been treated with antiretroviral agents.鈥?
AIDS Research and Human Retroviruses, 12: 585 (1996)
鈥?Harrer, Thomas, et al, Aids Researchers
Journal of Infectious Diseases, 171:811 (1995)
鈥?Hogervorst E, et al, Aids Researchers
_________
__________
WITH HAART
鈥溾€hoosing between many of these [HAART] combinations is, therefore, increasingly dependent upon knowledge of antiretroviral toxicities...[which include] myopathy [gross muscle atrophy] (zidovudine [AZT]), neuropathy (stavudine, didanosine, zalcitabine; hepatic steatosis and lactic acidaemia (didanosine, stavudine, zidovudine); and possible also peripheral lipoatrophy and pancreatitis (didanosine)...drug hypersensitivity... lipodystrophy...[including] peripheral fat loss (Presumed lipoatrophy in the face, limbs and buttocks) and central fat accumulation (within the abdomen, breasts and over the dorsocervical spine [so-called buffalo hump]...[and prevalent in] about 50% [of patients] after 12-18 months of therapy...Metabolic features significantly associated with lipodystrophy and protease-inhibitor therapy include hypertriglyceridaemia, hypercholesterolaemia, insulin resistance...and type 2 ...diabetes mellitus. Dyslipidaemia at concentrations associated with increased cardiovascular disease occurs in about 70% of patients. These metabolic abnormalities are more profound in those receiving protease inhibitors...Most cases of diabetes have been identified in recipients of protease inhibitors...Anemia and granulocytopenia affect about 5-10% of patients who receive zidovudine...Virtually all antiretroviral medications can cause nausea, vomiting, or diarrhoea early in therapy...Diarrhea is probably most common with protease inhibitors...Most antiretroviral agents have been associated with hepatic [liver] toxicity...Most protease inhibitors seem to result in increased rates of spontaneous bleeding (bruising, haemarthrosis, and rarely intracranial haemorrhage) in haemophiliacs... 25-35% of patients cannot tolerate [AZT monotherapy] or triple combination therapy for 4 weeks...鈥?
Lancet. 2000 Oct 21;356:1423-0.
鈥?Carr A, Cooper DA, Aids Researchers
BLINDNESS
鈥淭his study was conducted to determine the likelihood of the development of [immune recovery vitritis, IRV], which causes vision loss in AIDS patients with cytomegalovirus (CMV) retinitis, who respond to HAART. We followed 30 HAART-responders鈥ymptomatic IRV developed in 19 (63%) of 30 patients.鈥?
J Infect Dis. 1999 Mar;179(3):697-700
CASTLEMAN'S DISEASE
鈥淩ecently, we observed an unusual cluster of cases of rapidly progressing multicentric Castleman鈥檚 disease. Fever, weakness, generalized enlargement of lymph nodes, and marked polyclonal gammopathy developed in three patients with AIDS...Two of these patients died within one week after the diagnosis, with generalized involvement of the lymphatic system, liver, and bone marrow at autopsy. A fourth patient with AIDS who died equally rapidly after the diagnosis of multicentric Castleman鈥檚 disease had been seen in our hospital 14 months earlier... symptoms鈥tarted after the initiation of highly active antiretroviral therapy in these three patients.鈥?
N Engl J Med. 1999 Jun 17;340(24):1923-4
鈥?Zietz C, et al, Aids Researchers
鈥?Karavellas MP, et al, Aids Researchers
DEATH
鈥溾€f the 70 patients studied, 84% were still alive after the 3-month study period...17 surviving patients (24%) had HAART regimens discontinued due to drug intolerance and 11 (16%) expired [died] during the study period...鈥?
J Pain Symptom Manage. 2001 Jan;21(1):41-51
NERVE DAMAGE
鈥淭he antiretroviral drugs currently licensed in the United Kingdom [June 1996] are zidovudine (azidothymidine [AZT]), zalcitabine (ddC) and didanosine (ddI). All three are nucleoside analogues...All are very toxic. Suppression of bone marrow elements can occur with any of the three, as can peripheral neuropathy [nerve damage].鈥?
Adverse Drug Reaction Bulletin. 1996 Jun;178:675-8.
鈥?Ellis C.J., Leung D., Aids researchers
鈥淎 decrease in mtDNA [DNA of the mitochondria; the energy regulating entities within every cell] content was found in HAART-treated HIV-infected patients with peripheral fat wasting in comparison with subjects in the control cohorts...Lipodystrophy with peripheral fat wasting following treatment with NRTI [Nucleoside Reverse Transcriptase Inhibitor]-containing HAART is associated with a decrease in subcutaneous adipose [under the skin fat] tissue.鈥?
AIDS. 2001;15:1801-9
鈥?Shikuma CM, Hu N, Milne C, et al, Aids Researchers
鈥楾hese drugs are as dangerous as chemotherapy,鈥?
鈥? HIV patients presenting LD [Lipodystrophy, all taking antiretroviral therapy] and 5 HIV non-LD controls participated in the study鈥tructural muscle abnormalities, mitochondrial respiratory chain dysfunction or mtDNA deletions were detected in all HIV lipodystrophic patients. The mitochondrial abnormalities found suggest that mitochondrial dysfunction could play a role in the development of antiretroviral therapy-related lipodystrophy. 鈥?
AIDS. 2001 Sep 7;15(13):1643-51
鈥?Zaera MG, et al, Aids Researchers
鈥淐ombination drug therapy, or the triple-drug 鈥榗ocktail鈥欌€ften provokes severe side effects鈥?鈥楾hese drugs are as dangerous as chemotherapy,鈥?warned Dr. James Kahn, UCSF associate professor of medicine鈥︹€?
鈥?Science Daily, Sep 4, 2001
SEXUAL DIFFICULTIES - Body distortions
鈥淸Chapters in this guide to HIV drugs are entitled Introduction, Appetite loss, Body distortions (lipodystrophy), Bone death and destruction, Cardiac concerns, Diarrhea, Fatigue, Gas and bloating, Hair loss, Headaches, Insulin resistance and diabetes, Kidney stones, Liver toxicity, Muscle aches and pains, Nausea and vomiting, Nightmares, daymares and sleeping difficulties, Pancreatitis, Peripheral neuropathy, Skin problems, Sexual difficulties, The end]鈥?
鈥?A Practical Guide to HIV Drug Side Effects, CATIE, 2002
HEART ATTACKS
鈥淯se of protease inhibitors was strongly associated with the likelihood of having a myocardial infarction [heart attack] and correlated with diabetes mellitus and hyperlipidaemia.鈥?
Lancet. 2002 Nov 30;360(9347)
鈥?Holmberg SD, et al, Aids Researchers |
