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Confusion Over RNA/NAAT Test

Dec 24, 2008

Dr. Bob,

I donate every year and will continue to do so but hope you will answer this question. Had unprotected oral (giving/receiving with no ejaculation) and protected receptive anal; saw condom afterwards and not broken. Probably only need to test as I am a worried well.

I live in San Francisco and the San Francisco City Clinic and Magnet state that the conclusive window period for RNA/NAAT is 2 weeks and not to take past 4 weeks. Seattle/King County also say the same thing. Since you live in San Fran, what are your thoughts on the NAAT/RNA test? Seems more and more public health services are starting to offer this test to shorten the window? I figured you might know more since you are closer to the organizations proposing the RNA/NAAT test.

Response from Dr. Frascino


There is no doubt the three-month wait for a definitive HIV-antibody test can be three months of hell for those worried about becoming infected. Improvements to HIV screening are attempting to shorten the window period. Some organizations have recommended that six weeks is definitive (see below). The makers of NAAT/RNA have suggested two weeks is conclusive. The majority of regulatory agencies and major HIV/AIDS organizations have not yet adopted this policy or made any change in their published guidelines. No doubt that the SF City Clinic and Magnet have a great deal of experience and I'm not going to take issue with their policy other than to note this type of testing for routine HIV screening is not yet a "standard of care" recommendation. There is no doubt it's a highly sensitive test; however, I have not seen a head-to-head comparison with HIV-antibody testing at three months that convinces me it is as accurate or reliable as the current gold standard. (See below.)

Dr. Bob

NAT Testing Apr 26, 2008


I had a possible exposure to HIV on or around March 19. I made a major mistake by having unprotected sex with a stranger. He later told me he was HIV positive and has since changed his cell phone number, so I was unable to confirm if he was indeed positive nor was I able to get further information about viral load etc.

I waited until April 3rd to get tested. I live in Los Angeles and was fortunate enough to receive free NAT testing. Additionally, I was screened for all STDs. Everything came back negative. The counselor said that I am 100% negative as of March 13 (before the possible exposure) and assured me that I should feel confident about my negative result being conclusive. My question is how good should I feel about the 15 days I waited before getting the NAT test? Do you have any statistics around how long it takes for the virus to present itself?



Response from Dr. Frascino

Hello Eric,

The current testing guidelines still recommend HIV-antibody testing at the three-month mark. Other more sensitive tests are being developed and coming online; however, the formal guidelines have not yet been revised, as we are still gaining information about the sensitivity and specificity of the newer tests. NAT allows us to detect very small amounts of genetic material (DNA or RNA) via a process called amplification, which involves massive copying. In laboratory studies NAT testing reduced the time to viral detection to 12 days. So is your 15-day negative NAT WOO-HOOable? Honestly I don't know. There has not been enough published research for me to make that a definitive statement. I'd still recommend the 3 month antibody test.

Dr. Bob

NAT test Aug 5, 2007

Dr. Bob, some states actually use a nat test along with an antibody test to check subjects for hiv. They take two viles of blood for this. Can you tell me what a nat test checks for ?

Response from Dr. Frascino


Sure. See below.

Dr. Bob

nucleic acid testing May 16, 2006

dr. bob, i'm a 25 year old guy who made a mistake and had brief unprotected insertive anal sex about 5 weeks ago. The guy also had his penis around my anus- but not in. Of course, I'm beating myself up and my anxiety is really kicking up right now. I had an hiv test and std screenings at one week. All negative/non reactive. My anxiety got very bad and my dr. recommended having a nucleic acid test at 3 weeks if that was the case. I found a program at the los angeles gay and lesbian center that offers free diagnostic nat for hiv. I went about 10 days ago and get the results tomorrow. I know you don't recommend this as a means of diagnosis, but I wanted to know what you know of the testing they offer and whether or not it is reliable. also, is the chance for a false positive still high as i believe it is a pooled nat test?

whether or not you answer this, thanks for all your help and support, you've gotten me through a scare once before and hopefully i'm a day away from woohooing again. or at least a woo. you really are an angel.

Response from Dr. Frascino


Yes, I am aware the Gay and Lesbian Center in Los Angeles began offering free nucleic acid amplification testing (NAT). I believe they are the first site in Los Angeles County to do so! By report, this testing assay, which detects actual HIV rather than antibodies to the virus, can give accurate results within three to four weeks, compared to three months for standard HIV-antibody tests, such as ELISA. I do not have specific information about the rate of false-negatives or false-positives for the specific testing assay the center is using. However, chances are the folks at the center would be able to provide you with whatever information has been generated so far. I do believe the general testing assay (NAT) is indeed valid. More information should be available fairly soon if this type of testing becomes more widespread and available. I'll try to keep you posted as reliable information evolves.

Good luck!

Dr. Bob

Three New Assays Approved

May 25, 2007

On May 23, 2007, FDA approved the Procleix Ultrio Assay on the fully automated Procleix TIGRIS system manufactured by Gen-Probe Inc., of San Diego, California, and marketed by Chiron Corporation. This is a fully automated qualitative in vitro nucleic acid test (NAT) to screen for human immunodeficiency virus type 1 (HIV-1) and hepatitis C virus (HCV) RNA in donated blood from donors of whole blood, blood components, or source plasma. It is also licensed to screen individual organ donations from living donors, heart-beating organ donors, and cadaveric (non-heart-beating) organ donors. The capability of full automation will reduce human error and accelerate blood screening, enhancing blood safety.

On May 11, 2007, FDA granted marketing approval to two HIV-1 PCR assays for use in managing the treatment HIV infection.

The Abbott RealTime HIV-1 Assay, made by ABBOTT Molecular, Inc., is an in vitro reverse transcription-polymerase chain reaction (RT-PCR) assay for the quantitation of Human Immunodeficiency Virus type 1 (HIV-1) on the automated m2000 System in human plasma from HIV-1 infected individuals over the range of 40 to 10,000,000 copies/mL. The Abbott RealTime HIV-1 assay is intended for use in conjunction with clinical presentation and other laboratory markers for disease prognosis and for use as an aid in assessing viral response to antiretroviral treatment as measured by changes in plasma HIV-1 RNA levels. (Product label)

The COBAS AmpliPrep/COBAS TaqMan HIV-1 Test, made by Roche Diagnostics is an automated PCR test, indicated for the quantitation of Human Immunodeficiency Virus Type 1 (HIV-1) nucleic acid in human plasma (viral load) for use in conjunction with clinical presentation and other laboratory markers. The test is intended for use in conjunction with clinical presentation and other laboratory markers of disease progress for the clinical management of HIV-1 infected patients. It can be used to assess patient prognosis by measuring the baseline HIV-1 RNA level or to monitor the effects of antiretroviral therapy by measuring changes in plasma HIV-1 RNA levels during the course of antiretroviral treatment. (Product label)

Neither the Abbott RealTime nor the COBAS AmpliPrep/COBAS TaqMan HIV-1 assay is intended to be used as a donor screening test for HIV-1 or as a diagnostic test to confirm the presence of HIV-1 infection.

blood donation and notification May 18, 2006

Hey doc, Just wanted to say before i ask my question, that you provide a wonderful service and should be commended for your expertise and sacrifice. My question is this: About two weeks ago, i donated blood. I dont consider myself at risk, and i answered all questions honestly. Anyway, the other day, i called the blood bank to see if and when i could donate again. The woman on the phone gave me a date and the conversation ended. (I must admit that i had two motives in makeing this call. I would like to donate again, but i also wanted to know the status of my blood) Would the womans prompt response of my eligibility date mean that my blood has been approved for use?(I gave her my blood number, name, and date of birth) Finally, if my blood tested positive for anything, how long would it be until i was contacted about it? Lastly, how would the red cross notify me of any possible condition? (mail, telephone, etc.) Thank you for all of your help in this matter.

Response from Dr. Frascino


If you don't consider yourself at risk and answered all the questions honestly, I don't understand why you had a second motive for your call.

If, on the other hand, you have cause to be even slightly concerned that you may be HIV positive and decided to give blood anyway because you "wanted to know the status of my blood," that is unconscionable and immoral and you should be ashamed of yourself. Since I strongly hope this is not the case, I'll simply advise you that since you do not consider yourself at risk and answered all the questions honestly, you have absolutely nothing to worry about. Right?

Dr. Bob

why don't you ever recommend the RNA tests? Jul 31, 2008

Dear Dr Frascino, Thanks for answering my previous question. When I'm not so poor, I will make a donation to your fantastic organisation. My question to you is simply this: why do you only ever recommend the HIV antibody test (which necessitates a 3 month wait post-exposure)? I've been tested several times here in San Francisco and they have always given me the new RNA test - which they tell me can detect the virus with 100% accuracy only 10 days post-exposure. Is this because you think the RNA test is less accurate than the traditional antibody test, or is it the case that this test is not available countrywide and you want to recommend a test everyone can obtain access to?


Response from Dr. Frascino


Thanks for your question. It's one that comes up quite often. There are several reasons for recommending HIV-antibody tests over RNA-PCR tests for diagnostic purposes.

1. HIV-antibody tests are FDA approved for diagnosing HIV disease. PCR tests (RNA and DNA) are not. Large epidemiological studies have been conducted to verify validity, sensitivity and specificity of HIV-antibody tests. The false-negative/false-positive percentage is acceptably low, particularly when combining a Western Blot test for confirmation of positive ELISA/EIA/rapid tests.

2. PCR-RNA has a risk of false-positive results. Getting a false-positive result when screening for a condition as catastrophic as HIV can lead to significant anxiety. Just check the archives for a number of testimonials that provide concrete examples of this. (Or, just imagine if it happened to you!) RNA tests were not designed (or approved) for routine HIV screening and diagnosis. HIV PCR RNA tests are used to monitor how much HIV is growing (how rapidly HIV is replicating). It is very possible to be HIV infected but have an "undetectable" PCR-RNA if someone is on antiretroviral therapy (PEP, for instance). This could lead to confusion: The person tested might think he is HIV negative when in reality he is HIV positive but at the same time RNA undetectable.

3. Availability and cost. PCR-RNA testing is very costly and not available worldwide. My comments on this site are read throughout the cyber-universe.

Finally, I should mention I recommend quantitative PCR RNA and qualitative PCR DNA tests. Lots of them! However, I recommend them for specific purposes and routine HIV screening is not one of them.

Hope that helps.

Dr. Bob

On the testing window, with a BUTT! Oct 3, 2006

Hey Mr. Sexy man,

I am one of the 10000000 aussies who worship you - the one who gave head to the sheila and was freaking out about it. This is a question on the testing window - a specific one. The question is coming up more and more often - I want to see if I am the one who manages to get a "different" answer. Would you consider conclusive a negative 4th generation DUO P24/antibodies test done after seven weeks, after a low-risk exposure? (Giving a woman head).

You wrote before that "not everybody have access to those 4th generation tests, but everybody has access to my forums". I respect the fact that you might not want to publish a "yes" even if you thought that "yes" was indeed the answer. So, here's the deal: I will interpret a non-answer as a "well, yes, but I am not gonna say that in a WWW forum everybody can access".

It just means that I will do a (possibly unnecessary) 12 week test just to get your Woooo hoooo!!! But that's OK :-D


My previopus message started with: "Hey Mr. Sexy man, I am one of the 10000000"

I was stupid enough to SIGN IT!!! Please delete my signature at the bottom of the message if you decide to publish it!!!

(Unsigned this time)

Response from Dr. Frascino

G'day Mate,

10,000,000 Aussies worship me??? Yikes, that's a whole lot of Oz-love coming my way. Guess I better stock up on the economy size condom multi-packs!

The general rule is that HIV-antibody testing prior to three months is not considered definitive or conclusive. I still agree with that. However, that said, I also still agree with my previously published opinion on the SYDSEX recommendation. I'll repost that below. So, as you can see, no, you did not get a "different" answer. In fact, you got exactly the same answer.

And don't worry, John Howard, we would never publish your name or signature. Ooops.

Dr. Bob

bobby can i get back on the Jobby?

Sep 26, 2006

hello bobby!!. I am yet another aussie, (actually i am a pom who came here for a holiday and decided to never go back to england), yes i am also one who likes to wear their cossies in an alluring fashion on Manly beach. However i am not another worry wort well not until recently anyway, i think reading that post from that other aussie who questioned the reliability of sydney sexual health clinics Six week TESTS put me in a spot of bother. You said that one should be quite confident in the reliability of those tests, anyhooo i am not a worrier rather an arguer i argued my way into another test at SydSexHealth at post 7.5 weeks they also threw in a DNA PCR test for good measure. it WAS negative whoopty f****g do i thought until i was reminded once agian of your universal recommendation for no test being reliable before 3 months. in a state of disdain i once again called up the nurses at SydSexHealth they raher politely told me to never come back again especially after my negative pcr. My question to you bob is this?? Am i kool, i mean offcourse i am kool in the paddington street sense..i dress allright have a trendy hair do etc etc do 150 push ups a day. BUT am i kool in the hiv sense? DO I NEED FURTHER TESTING?!!!!?? I really just want to believe these sydney std docs and go on minding my own businesss spending lazy summer afternoons listening to Maddonna while i work on my suntan on the beach because it has been rather hot here..also i wouldnt mind having sex again not worrying that i might give someone hiv so bobby can i get back on the jobby, Im sure you now what i mean? ;-)

love ya lots xoxoxo....johnno

Response from Dr. Frascino

Hey Johnno,

Paddington address, trendy hair, 150 pushups a day, cossie up the crack, Madonna on Manly Beach . . . yeah OK, you would qualify as Aussie-Boy Kewl, if it weren't for that wowser worrywart look on your mug. That is so un-kewl it makes you look like a cross between John Howard and Dick Cheney. I much prefer your whoopty f***ing do look.

The advice I gave Banana Bender hasn't changed. (See below.) Do I think you need to spoil your kewl look with worrywart wrinkles? Nope. Can Johnno get back to Jobbo? Absoluto!

Stay well, Mate.

Dr. Bobbo

c'mon mate please help

Aug 30, 2006

oh cmon doc,,,i really need ur help...this is my 3rd time unemployed so im unable to make a just a student!!!...well i live in sydney australia...and i had a six week test done at sydney sexual health centre it was negative ,,,the DOCTORS at SYDSEX said ur result is conclusive and definitive..i argued with them quoting ur website ,,,they replied back that the internet is full of trash,,,,and that the modern tests in sydney are conclusive after six than i went to a reputable doctor near oxford street,,,,he said yep after six weeks ur fine,,and that he wouldnt get anoher test.....please answer me ,,,i really need ur help ....ive been traumatised ...all this conflicting information!!!!.......the HIV hotline in sydney also says six weeks is fine with modern aussie tests....and mind u this is SYDNEY,,,a first class city where hiv has been around since day one.....but i stlll dont believe this six week crap...but they wont even retest me...... what the hell should i do bob!!!!...i really need ur opinion mate ,,please answer me this time...whats the matter u'VE lost love for us aussie boys?? me ,,us aussies have lost no love for u...

cheers - RAT

Response from Dr. Frascino

G'day RAT,

Moi? Lose the love for spunky Aussie jackaroos??? No way, mate! I'm well aware of SYDSEX's recommendations. I'm also aware other countries' guidelines state six months in their guidelines. And there are some physicians who put the window period out to one year and beyond! The three-month guideline is the most universally accepted and I still believe, based on all the epidemiological studies, it's the most reasonable universally. Yes, it may be somewhat conservative in light of the improvements made in HIV screening (3rd and 4th generation assays, etc.); however, not everyone worldwide has access to these newer tests, but everyone does have access to what I post here. Also, no matter how good the test assays may be, there is still host variability. That means not everyone's immune system behaves in exactly the same manner. Some may take longer to produce detectable levels of anti-HIV antibodies for a wide variety of reasons. Consequently, my recommendation, at least for now, remains that tests taken prior to three months are not considered to be definitive and conclusive. That said, I'm quite confident the six-week test in Sydney is indeed accurate, and I would not argue with their recommendations for folks getting tested there; although, there are extenuating circumstances in which I personally would extend the testing period (hep C coinfection, significant occupational exposures, etc.). Finally, the option to retest is always open to you, although you may need to pay for the test yourself, if your health plan refuses to cover it. OK, banana bender, are we mates again? As always my affection for you guys stands out like a shag on a rock. By the way, some Oz organizations would even like to shorten the six weeks window! See below.

Ciao bella,

Dr. Bob

Window period. Aussie policy.

Jun 13, 2006

Hi Dr Bob.

Just thought I'd share this with your readers. This is the current policy from ANCARD (Australian National Council of AIDs and Related Diseases). The passage below was taken from the 'Clinical Screening and Case Detection' section. Where there is reasonable concern about the risk of HIV infection, a patient with a negative test result should be retested one to three months after exposure or a specific event, and retested if there are clinical signs or symptoms. The seroconversion window period ranges from two to six weeks after infection (Schreiber et al., 1996). To identify very early infection, p24 antigen or nucleic acid amplification testing may be carried out. I found another officaial Aussie site that also suggested that when using current testing methods, one month is adeqaute to allow for detectable antibody production. I see that your 'New York Health Department' site also concedes that one month is ample time in almost all cases of seroconversion. Hope this helps ease the minds of some WW's out there.

Response from Dr. Frascino

G'day Mate,

Thanks for the information!

Dr. Bob

we need ur opinion on this dr bob
HIV worried well

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