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DNA PCR Testing Question?
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DNA PCR Testing Question?

Doc,

I have been searching online for more info regarding DNA PCR Testing of HIV.  Across the boards I have seen a negative consenus on using this test for low risk exposures.

What would be the right time window to take a DNA PCR test?   The test looks for HIV virus DNA, so wouldn't be more accurate earlier than anti-body.  Isn't the DNA present regardless of antibodies?

My concerns are over a 1 time unprotected vaginal sex encounter with a female friend of mine (she said she does not have HIV, she had sex 1 other time only,  unprotected though, between her last HIV test (neg)).  At 40 days (5 weeks,5 days) I could not deal with the stress anymore and took a anti-body test and DNA PCR test (labcorp test from www.areuatrisk.com) and both were negatvie.  I have read all of the posts with time to test positive, etc. If seroconversion hadn't happened at 40 days yet, would a PCR negative results still be valid.  The reason why I am posting is at 70 days post exposure I am having some pressure (not necessarily pain) on the left side of my groin (I can't tell if my lymph nodes are swollen) and have had a headache. I really want to move on from this, as I am about to buy my first home and finally start my adult life.  After the negative results I was fine, but once I felt some pressure in my groin, I started to be concerned again.  

If seroconversion hadn't happend yet at the time of the anti-body test, how reliable would the DNA PCR be at 40 days.  Is the false positive rate and cost of the test the real downside to this testing method, but otherwise it is a very good test?  there is not a lot of information online about this testing method - besides people recommending not to take it for the false positive rate.  

Also, would you recommend a retest?
Thanks for all of your help!
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You are well beyond the time frame for use of the PCR test to detect HIV infection and should not have had that test.  The idea is to diagnose infections before antibody develops, typically a few days to 2-3 weeks after exposure--and even then, only in much higher risk situations than yours.  At 40 days (6 weeks) you should have just had a standard abntody test.

You had a low risk exposure that did not warrant testing at all, except as psychological support.  If you have had a negative antibody test at least 6 weeks after the event, you need no further testing.  If you haven't yet had an antibody test and need thereassurance, do it now.  The result will be negative.

HHH, MD
41 Comments
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PCR DNA test are not diagnostic tests. They are not a stand alone test either. There is one PCR test that is a diagnostic test and it's a PCR RNA test. But it too, is not a stand alone test.
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Thanks Doc...why do the testing centers (like LabCorp) offering DNA PCR say to wait 28 days, if by that point in time, its not as useful?  Wouldn't they want to move up the time frame then? The results are still valid post 28 days - as there would be HIV DNA?



FYI - I did have an antibody test at the exact same time (40 days) - which was negative.
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Because the commercial laboratories and the PCR test manufacturers are promoting the test for a differnent purpose than you used it for.  The main use of the test is to monitor the status of someone's ongoing HIV infection, not to diagnose new infections.  For that purpose--which as I said above is not recommended in situations like yours--there is no reason to use PCR beyond ~4 weeks, when the antibody tests are positive.

HHH, MD
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One minor correction to Teak's post. While both PCR tests (RNA and DNA) are NOT recommended for diagnostic purposes, of the two, the one used most for diagnosis is the DNA test. It is used to diagnose newborns if their mom was HIV positive (because a newborn will not produce antibodies soon after birth). The RNA test (which is also called a viral load test) is used in the treatment of people already infected and in treatment for HIV. The DNA test is simply a positive/negative test which can detect very small levels of HIV in a person's system.

As noted also, the PCR tests can show a false positive for several reasons and this is the primary reason they are not recommended (along with their expense).
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Ronnie, you are incorrect.

Gen-Probe Receives FDA Approval for APTIMA(R) HIV-1 RNA Qualitative Assay for Clinical Diagnostic Use

SAN DIEGO, Oct. 5 /PRNewswire-FirstCall/ -- Gen-Probe (Nachrichten) announced today that the U.S. Food and Drug Administration (FDA) has granted marketing approval for the APTIMA(R) HIV-1 RNA qualitative assay. The assay may be used as an aid in the diagnosis of acute and primary HIV-1 infection, and to confirm HIV-1 infection in an individual whose specimen is repeatedly reactive (positive) for HIV-1 antibodies. The assay is the first FDA-approved qualitative nucleic acid test (NAT) for these intended uses.

Gen-Probe expects to launch the assay in November in conjunction with the APTIMA HCV (hepatitis C virus) RNA qualitative assay. Detection of HCV RNA is evidence of active HCV infection. The APTIMA HCV assay may be used to detect HCV RNA in individuals with antibody evidence of HCV infection and evidence of liver disease, individuals suspected to be actively infected with HCV with antibody evidence, and individuals at risk for HCV infection with antibodies to HCV.

"We believe these two new qualitative viral products may fill a small yet important medical niche in the detection of two treatable but potentially life-threatening diseases, especially in light of new CDC guidelines that support increased testing for HIV, and new scientific publications regarding hepatitis C," said Steve Kondor, Gen-Probe's vice president of sales and marketing.

Qualitative assays detect the presence of viral genetic material and give a "yes-no" answer as to whether the target virus is present. In contrast, quantitative assays are used to estimate the amount of genetic material present in a sample. Gen-Probe's new viral products are not approved for quantitative use.

In September, the U.S. Centers for Disease Control and Prevention (CDC) published new recommendations for health care providers that are designed to make voluntary HIV screening a routine part of medical care for all patients aged 13 to 64. The CDC estimated that more than 250,000 Americans are HIV-positive but unaware of their condition, and said that early diagnosis is critical in order for people with HIV to receive life-extending therapy.

A recent article in the journal Hepatology (Vol. 44, No. 2, 2006) illustrated the value of monitoring patients with chronic hepatitis C infection with a highly sensitive nucleic acid test. In the study, independent academic researchers retrospectively tested stored blood samples with an assay identical to the APTIMA HCV RNA qualitative assay. The authors concluded that negative results with this assay were more predictive of sustained virological response (SVR) than were negative results achieved with a less sensitive polymerase chain reaction (PCR)-based assay. According to the authors, SVR is an important endpoint associated with durable eradication of HCV infection and long-term remission, if not cure, of disease.

About Gen-Probe

Gen-Probe Incorporated is a global leader in the development, manufacture and marketing of rapid, accurate and cost-effective nucleic acid tests (NATs) that are used primarily to diagnose human diseases and screen donated human blood. Gen-Probe has more than 20 years of NAT expertise, and received the 2004 National Medal of Technology, America's highest honor for technological innovation, for developing NAT assays for blood screening. Gen-Probe is headquartered in San Diego and employs approximately 900 people. For more information, go to http://www.gen-probe.com/ .

Caution Regarding Forward-Looking Statements

Any statements in this press release about Gen-Probe's expectations, beliefs, plans, objectives, assumptions or future events or performance are not historical facts and are forward-looking statements. These statements are often, but not always, made through the use of words or phrases such as believe, will, expect, anticipate, estimate, intend, plan and would. For example, statements concerning new products, potential regulatory approvals, customer adoption, and results of future R&D studies are all forward-looking statements. Forward-looking statements are not guarantees of performance. They involve known and unknown risks, uncertainties and assumptions that may cause actual results, levels of activity, performance or achievements to differ materially from those expressed or implied by any forward-looking statement. Some of the risks, uncertainties and assumptions that could cause actual results to differ materially from estimates or projections contained in the forward-looking statements include but are not limited to: (i) the risk that new products will not be cleared for marketing in the timeframes we expect, if at all, (ii) the possibility that the market for the sale of our new products, such as our qualitative APTIMA viral products, may not develop as expected, (iii) we may not be able to compete effectively, (iv) we may not be able to maintain our current corporate collaborations and enter into new corporate collaborations or customer contracts, and (v) we are dependent on third parties for the distribution of some of our products. The foregoing describes some, but not all, of the factors that could affect our ability to achieve results described in any forward-looking statements. For additional information about risks and uncertainties we face and a discussion of our financial statements and footnotes, see documents we file with the SEC, including our most recent annual report on Form 10-K and all subsequent periodic reports. We assume no obligation and expressly disclaim any duty to update any forward-looking statement to reflect events or circumstances after the date of this news release or to reflect the occurrence of subsequent events.

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Teak: I stand by my statement:

http://www.medscape.com/viewarticle/448718_8

"Diagnosis of Neonatal HIV Infection

Qualitative DNA PCR assay is the test most often recommended for neonatal diagnosis of HIV infection. However, the sensitivity of the assay during the first month of life is 50%, after which it increases to above 96%.[30] A meta-analysis of 32 studies using DNA amplification by PCR in infants reported 91.6% median sensitivity and 100% median specificity in the early diagnosis of HIV subtype B infection. Improved viral detection was noted for infants older than 1 month.[34] False-positive and false-negative rates of 1.8% were seen. Thus, DNA PCR assay may not definitively diagnose or exclude neonatal HIV infection; it should be followed by a confirmatory PCR test at 30 days of age and then by sequential PCR testing.[34] Reduced assay sensitivity may be seen in non-B viral subtype infections."

Therefore your original statement that PCR DNA tests are not diagnostic tests is false. That was the statement I was referring to.
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You can stand by it all you want, you're incorrect. If you would have looked at the link you posted you would have seen that the information was three years old. The FDA approval date for PCR-RNA was October 5th 2006. A PCR-DNA is NOT approved for a stand alone HIV diagnostic test.
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If PCR DNA test is not a diagnostic test then why is it even on market(in specialized path labs) for sale. Will it be correct to say that these labs are fooling people? Why do pathologists, microbiologists give it a high regard as a diagnostic test calling it extremely sensitive. On the other hand, its PCR RNA which is not a diagnostic test as it is meant to check the viral load and do not deal in YES/NO answer. It's just so confusing and is there anything which is completely believable about HIV infection(from window period to diagnostic tests). When, we talk about 4th generation tests being almost conclusive at 6 weeks, why can't we have a combination of DNA PCR and antibody test at 6 weeks and get more reliable results. I suppose DNA PCR is more sensitive than P24 antigen test. A P24 antigen test sensitivity varies anywhere from 60-80 % and PCR DNA sensitivity is supposed to be 96% after 28 days. This all is just too varied information and can send anyone's head for a spin. There are too many factors which come along with HIV related information(financial gains for test providers, CYA attitude, mixed information regarding window period, testing strategies). Seems everyone is just exploiting fear of HIV and nobody is really bothered to to give correct/complete information varying from window period to testing strategies. seems everyone has an agenda. Superficially, it looks that everyone cares to bring and end to this disease in the world and working hard but if you go by the actions and information present in ground reality...then only God can help...
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173692_tn?1371540094
A PCR-DNA is used on people that have HIV to monitor their viral load.
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The test used to monitor viral load is PCR RNA Quantitative. Teak, really, PCR DNA is used for diagnostic purposes. PCR DNA is a qualitative test and can not quantitate(measure up) the viral load. It just gives a "Yes" or "No" answer. I am no expert and I can not make you forcibly believe but this I honestly believe is the truth from what I have learned.
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O_G it is not an approved as a stand alone diagnostic test.
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"APTIMA(R) HIV-1 RNA Qualitative Assay" - It seems this is also a qualitative test which gives a "Yes" & "No" answer only and do not check upon the viral load. The only difference that I feel that it has from Qualitative DNA PCR is that it checks for virus in free flowing blood plasma whereas the Qual PCR DNA test checks for virus with the cells. I suppose HIV-1 RNA Qualitative is more sensitive as compared to HIV-1 DNA and can detect an infection even quicket. NAT testing is based on similar technology. Whereas, if you go to specialy testing lab and get a DNA PCR test done, they normally ask you to wait at least 2 weeks for reliable results. I think HIV-1 RNA Qualitative PCR even shortens that window.
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Well, yes, indeed a PCR(DNA/RNA)can not be considered conclusive as a stand alone test. It certainly has to be followed by an antibody test as an antibody test is the only gold standard for testing in humans. Again for that, I am not sure if external agendas come into play. Why would NAT testing be considered reliable at 10 days post exposure?? That is also a form of PCR. The blood banks do consider it gold standard...don't they????
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I cannot believe I actually read such detailed and intense posts about the uses and merits of various tests (well, I read part of it anyway), lol. Anyway, while I don't know specifically about HIV, a virus is a virus and I'm sure this is the same... My husband has chronic HBV, and his hepatologist uses a PCR DNA (not RNA), test to measure his viral load.
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173692_tn?1371540094
You get a postive result on any viral infection at the blood center, the unit will be tossed and you'll get a letter from the blood bank. A false positive will also get the unit tossed.
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There is a reasoning for that too and I would like to take a shot at that. Reason your doctor opts for PCR DNA Quantitative test is because viral load is not always detectable in blood plasma as seen in case of HIV RNA(taking into consideration same thing applies for HBV viral load as well). But, once PCR DNA turns positive it remains positive throughout life. The DNA test does not actually look for virus in blood plasma but in the cells. Earlier in the infection, the virus is detectable in free flowing blood till it infects the cells. That's why RNA qualitative can detect it earlier as compared to DNA Qualitative and that is the reason labs prefer to use DNA test after at least 2 weeks have passed post exposure.
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You are right about chances of false positives and the emotional turmil attached with it but what would u make out of a negative PCR test???
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Depending on the time I took the test and the risk if I would retest again at a later day. I certainly would not test after the 13 week period.
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The fact that my link was two years old is irrelevant. The only purpose of a PCR proviral DNA test is for diagnostic purposes. A PCR RNA viral load test is used in the treatment of HIV positive individuals....
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173692_tn?1371540094
Ronnie, stop giving out false information. PCR DNA is not approved for diagnostic purposes. It is not a stand-alone test. PCR RNA is an approved diagnostic test, but it is not a stand-alone test. You show me on article that states PCR DNA is an approved diagnostic test.
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Well, in that case only "APTIMA(R) HIV-1 RNA Qualitative Assay" is FDA approved and not any other PCR RNA also.

That way more than 3/4th of the tests used in the world are not F.D.A approved. Wouldn't you be of the view that FDA approval also got a lot to do with PR BS. I can not comprehend food and drug administration comparing the accuracy rates of 2 PCR tests over a million samples to come up with a clear cut conclusion about which 1 is better and so it should be approved. I know this issue takes the discussion further away from the main topic but what is the basis of approval. Man, I seriously have many issues. I think I just added "trust" to the list. We probably got to check who is a major stock holder in this company and what are his associations in the "u know where".
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o_g, don't start the conspiracy theories. They got FDA approval because they filed for it to be a diagnostic test and provided their studies.
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I think I deserved that comment from you Teak. I am just not a happy person anymore. Me suX!!!!!!
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173692_tn?1371540094
ROFL, you don't suck. Well maybe, I don't care. :)
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Me sux = "i am screwed in the head"/ "not thinking right" (in that sense :(). Damn, what the hell was I thinking writing that. For a min, didn't realize this was a "sexually" TD forum. Indeed straight I am man..
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Teak: You did not read my post. Your original quote which I was referring to was the following: "PCR DNA test are not diagnostic tests." That statement you made is simply not accurate. The PCR DNA test, whether FDA approved or not has only one puspose, and that is for diagnosis of HIV. It is not a viral load test like the PCR RNA viral load test is, it is a test that tells you whether HIV was detected or not detected. That is a diagnostic test. Now, if you are discussing FDA approval, which is not something I brought up, then go ahead. That was not what I had responded to.
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173692_tn?1371540094
There you go talking about something you don't know anything about.

Now here is someone that does know what he's talking about in reference to PCR DNA tests.

Because the commercial laboratories and the PCR test manufacturers are promoting the test for a differnent purpose than you used it for. The main use of the test is to monitor the status of someone's ongoing HIV infection, not to diagnose new infections. For that purpose--which as I said above is not recommended in situations like yours--there is no reason to use PCR beyond ~4 weeks, when the antibody tests are positive.

HHH, MD
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Teak: The test that is used for treatment of HIV positive individuals to monitor their disease status is the PCR RNA viral load test. This test is used for treatment because it measures the LEVEL of virus in a person's system. That is the test used routinely in HIV treatment settings. The PCR proviral DNA test is not a viral load test so it has no use in HIV treatment monitoring as the PCR RNA viral load test does (since it is already known that hte patients are HIV+). The PCR proviral DNA test is a diagnostic test that simply tells whether HIV was detected or not (there is no viral load reporting in this test). The PCR proviral DNA test is used for, amongst other things to:

Test newborns for HIV
Test rape victims for HIV infection very soon after the rape in many states
Test actors in the american adult entertainment industry for HIV

Both types of PCR tests can be used for diagnosis, but the only purpose of the PCR proviral DNA test is for diagnostic purposes (and for testing blood donations).
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173692_tn?1371540094
Ronnie the **** you are dish out here is the same reason you got a timeout on AidsMeds. False Information. Lets let the ww read your posts on AidsMeds and let them see if you are qualified to give out any advice.
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173692_tn?1371540094
http://forums.poz.com/index.php?topic=1794.msg29933#msg29933
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So what if Ronnie may be giving out wrong info.  Who are you to try to control what people say?  You may be able to do it on aidsmeds, but not here.  Just because you have hiv does not make you an expert.  As a matter of fact I would say the opposite.  
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Teak seems to be confusing the PCR RNA viral load test which is used routinely for monitoring HIV+ patients in treatment versus the PCR proviral DNA test which is used for HIV diagnostic purposes only as it has no role in treatment monitoring. Note that I am not making a comment on the reliability of these tests, just the difference between the two types of tests.

Below is a link to the AEGIS site which gives a basic explanation of the PCR RNA test:

http://ww1.aegis.org/factshts/network/simple/viral.html

"Viral load tests measure what's called HIV RNA. RNA is the part of HIV that knows how to make more virus. There are several different viral load tests. These tests were approved by the FDA for use in checking the health of people with HIV, to see if they may be at risk for getting sick. These tests are also approved for checking the effects of anti-HIV drugs, to see if they are working against the virus.

The results of each of these tests can be a little different, so doctors advise that people stick to the same type of test once they start using viral load testing. In this fact sheet all the viral load numbers from studies are based on what the result would be using the PCR test, as this is the most widely available test at the moment.

The website below discusses PCR proviral DNA tests. As noted, these tests attempt to detect whether HIV is present or not, they do not measure viral load:

http://www.uhl.uiowa.edu/newsroom/hotline/archives/1995/hivpcr.xml

"The UHL HIV-1 proviral DNA PCR test will reproducibly detect as few as 10 copies of HIV-1 DNA in a PCR reaction. Each PCR reaction tests 2.5 microliters of processed specimen, which is equivalent to about 30 microliters of unprocessed whole blood.

To date, 71 patient specimens have been tested at the UHL for HIV-1 proviral DNA. Eleven (15.5%) were positive for HIV proviral DNA. Strict adherence to protocol, including quality assurance and quality control guidelines, helps to insure that test results are extremely reliable for the intended uses."

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173692_tn?1371540094
Now go back to the link you provided and reread it. It doesn't mention diagnostic at all. It states, monitoring a health of someone with HIV,viral load.
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Teak: If you are talking about the PCR RNA viral load test then you are right as it does measure viral load. Summary:

PCR RNA viral load test - A test used in the treatment of HIV+ people. This test can also be used for diagnosis, but is almost uniformly used in treatment settings.

PCR proviral DNA test - A test used to determine if a person is infected with HIV or not. It has no use in treatment of HIV+ people because it is already known whether these people have HIV or not.
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173692_tn?1371540094
That's what I said to you. The PCR DNA is not a diagnostic test; it is used for people that have HIV to monitor their viral loads. However PCR RNA can be used for helping in diagnosing HIV but it is not a stand-alone test.
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Teak: This is getting tedious. What you posted is not correct. The PCR RNA viral load test is the only one of the two used for treatment as it measures viral load, which is a key measure needed in treatment of HIV+ people. The PCR proviral DNA test is not used in treatment, its only use is for diagnosis. I think what you are missing is you think that just because a test is not FDA approved for HIV diagnosis, that means the test is not diagnostic in nature. That is not the case. The only use of the PCR proviral DNA test is for diagnosis, whether it is approved for that use by the FDA or not. This is my last post in this thread. If anyone is unsure about what these tests do, just look them up on the web and you will see what I post is accurate.
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173692_tn?1371540094
Ronnie like you did in the other forums. If you would read and comprehend what you've read, then you would be better off. PCR RNA is the only approved PCR dianostic test. PCR DNA in not a dianostic test it is a monitoring test for people that have already been confirmed positive and it's used to monitor their viral load. I get the darn test every three months so don't try to pull your **** on me or anyone else on this forum.

Now post your url's that says different.

05.10.2006 22:10
Gen-Probe Receives FDA Approval for APTIMA(R) HIV-1 RNA Qualitative Assay for Clinical Diagnostic Use

http://www.finanznachrichten.de/nachrichten-2006-10/artikel-7097687.asp

Gen-Probe Receives FDA Approval for APTIMA(R) HIV-1 RNA Qualitative Assay for Clinical Diagnostic Use

PRNewswire - October 5, 2006
Gen-Probe Receives FDA Approval for APTIMA(R) HIV-1 RNA Qualitative Assay for Clinical Diagnostic Use

Gen-Probe
http://www.gen-probe.com/pdfs/pi/500238-ARTRevA.pdf


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Teak: I said my last post was my last in this thread, but I do not appreciate your personal attacks, especially when you are spreading incorrect information. You might get the test regularly, but you are sadly uninformed on which test you are receiving. The viral load test is a PCR RNA test. Sorry, but you do not seem to understand that fact. Please move on and read up on this subject matter instead of spreading false info. Not a single link you have posted has disputed my explanation of the two tests. To the readers here, just look up on google the terms "viral load", hiv, test, PCR and you will see that the test that measures viral load for treatment is the PCR RNA test.
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Teak: Ronnie is indeed correct in calling Proviral DNA PCR a diagnostic test. That indeed is the only purpose of the test. It is not meant to monitor HIV progression and treatment. FDA approved or not is another matter and totally irrelevant to the fact that PCR DNA is only a diagnostic test and serves no other purpose whatsoever. I have to say that it seems you are not completely aware of this test and confusing it with HIV RNA test.
Just trying to help!!!
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Because the commercial laboratories and the PCR test manufacturers are promoting the test for a differnent purpose than you used it for. The main use of the test is to monitor the status of someone's ongoing HIV infection, not to diagnose new infections. For that purpose--which as I said above is not recommended in situations like yours--there is no reason to use PCR beyond ~4 weeks, when the antibody tests are positive.

HHH, MD

o_g, you and ronnie can gave out all the false info you want.  So what you are saying is that Dr.HHH is incorrect in his above statement. But you should advise DR.HHH that he is incorrect.
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A related discussion, DNA PCR at 30 days?... was started.
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Ok don't trust any MD about viral infectionions all they know is how what medication you need to take after you've been infected and they also know there is no cure for HIV. So if you think you've been infected with any virus make sure to get something called PEP within 72 hours of possible contact. Most states don't offfer it cause insurance compnies don't cover the cost and drs don't tell you about it cuz they only do what is covered by insurance. Don't let drs and nurses tell you Its only used for them if they get pricked on the job and you don't deserve it cuz your not 100% sure you were exposed.

Also most drs say to wait 3 months for the regular HIV test and never even tell u about the DNA test again cuz insurance companies don't cover the DNA test and the reason why is cuz it's more expensive. The DNA pcr test is good anytime after 3 weeks and the DNA RNA test at 1-2 weeks.

I went to get tested 2 days after high exposure and the nurse said there was nothing else I can do but wait 3 months and then test again at 6 months but never told me about taking PEP to flush out the virus. How is it that I know about this and a fn nurse that does STD tests for a living has no idea? People r so fn retarded! Don't trust anyone and do what it takes to get answers b4 it's too late!!!    
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check out this link for numbers on where to get PEP www.thebody.com/content/art32456.html
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If want to get tested do the DNA pcr test HIV 1 & 2 then along with an antibody test at the same time. And then repeat the antibody test at 3 months and again at 6 months to be safe.  Don't listen to the dr above that thinks the antibody test is conclusive at 4 weeks cuz it can take up to 3-6 months. Most drs only care about the insurance company they work for and don't give you all the info you need. most Drs also think the PEP is just for them to save themselves those selfish fuks.      
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