Though I don’t have a musical bone in my body, I’ve been thinking recently about how to code statistical data about people into melodies. Now I find that there’s a whole industry out there of people who are turning DNA into music. If you know anything about your own DNA, you can plug your genes into a programme a play yourself. So maybe I do have music in my bones after all.

One of the people who has been working on this is a young composer in the States, Alexandra Pajak. She’s been busy setting the HIV genome to music. Here’s what she says about her project, courtesy of Bertalan Meskó at ScienceRoll

Sounds of HIV is a musical translation of the genetic code of HIV, the Human Immunodeficiency Virus. Every segment of the virus is assigned music pitches that correspond to the segment’s scientific properties. In this way, the sounds reflect the true nature of the virus. When listening from beginning to end, the listener hears the entire genome of HIV.

In English, the nucleotides Adenine, Cytosine, Uracil/Thymine, and Guanine are abbreviated with the letters A, C, T, and G. Since A, C, and G are also musical pitches in the Western melodic scale, these pitches were assigned to the matching nucleotides. To form two perfect fifths (C-G and D-A), “D” was arbitrarily assigned to musically represent Uracil. I assigned the pitches of the A minor scale to the amino acids based on their level of attraction to water.

Question: would HIV sound different in a setting like Bali, which uses the seven-tone pelog scale?

Illustration by Wendy Stephenson

On individual measures that are often indicators of women’s ability to make their own choices and decisions — educational level, for example, we see a strong correlation too, both at the national level:

and at the household level:

So, in countries where women are more equal to men on measures of workforce and political participation as well as education, there’s more HIV than in countries where women are more constrained. In countries where women are more educated, there’s more HIV. Within countries, more educated women are more likely to be infected with HIV.

Multiple concurrent partnerships: we’re crap at defining them, and therefore at measuring them. The imporant issue is simply: how likely is an infected person to be having sex with an uninfected person in the relatively short periods when viral load is high? These periods are more frequent where other STIs (and especially HSV2) are high. But the highest viraemia is right after someone first becomes infected. So anyone who has several partners in the two of three month window in which they themselves were infected are most likely to pass on the virus to others. If enough people (men AND women — it has to work on both sides of the equation in a heterosexual epidemic) have multiple partners in that time, you have the potential for a hyper-epidmic. Without it, you don’t.

Here are data from the first round of national surveys of HIV-related risk, way back in 1989-1991. The dark bars are people who reported that they had more than one REGULAR partner in the previous year. I.e. more than one person to whom they were married and with whom they had been having sex on an ongoing basis for a year or more. You can see that there’s something of a difference between countries in Africa and those elsewhere.

For your interest, I’ve also put in what people think their partners do. In almost every case, men report fewer partners than their wives think they have. I.e., women think men are pigs. And women report more partners than their husbands think they have. Men labour under the illusion that women are angels.

Ho hum.

Not wanting to be always the purveyor of bad news, I was looking forward to today’s results from the Pro2000 microbicide studies. After hopeful results in an earlier trial, I’d convinced myself the gel would prevent HIV. But it doesn’t.

It’s very depressing news from a huge, well designed and well managed study of over 9,000 women across four countries. I’m fond of saying that if you torture the statistics enough they will confess to anything (as we saw in the recent vaccine trial in northern Thailand.) But however badly you twist the arms of this study, they’re not going to scream success. For the record:

* If you exclude the women who got pregnant or stayed in the trial more than the planned period of one year, there were 130 new infections among those who used the microbicide gel, and 123 in those who used the identical-feeling placebo. Calculated as new infections per 100 woman-years of exposure, that’s 4.5 for the gel and 4.3 for the placebo, making the microbicide 5% more risky. The statisticians are 95% sure that the true effect of the microbicide is somewhere between decreasing risk by18 % or increasing it by 34 %. In other words, we can’t make any claims at all that the product works.

* If you don’t exclude people who got pregnant and look at everyone in the trial for as long as they were enrolled, you get 145 new infections with the microbicide versus 143 without: 4.6 new infections per 100 years of exposure in both. No difference. None. The true effect using this analysis is somewhere between reducing the risk of HIV infection by 21% and increasing it by 26%.

* The researchers also looked at whether women who used the gel consistently were less likely to get infected than those who didn’t. They weren’t.

It is hard to measure consistent use of microbicides in these studies, but researchers compared three sources of information: what all participants reported during study visits, whether all participants brought back used applicators, and what a sub-sample of women recorded in their detailed sex diaries. All point in the same direction: around 90% of women used the gel most of the time. That in itself might be counted a triumph compared to some earlier studies. It means that if we could find something that actually works, women would be quite likely to want to use it. All eyes will now be on the CAPRISA study which is testing a vaginal gel that has antiretorvirals embedded in it.

For my own part, I’m feeling somewhat sheepish as well as disappointed. When the results of an earlier, smaller trial of Pro2000 microbicide showed that it reduced infection by 30%, I was dismissive, bordering on rude, about the tyranny of the statisticians who said the results were “not significant”, and that we needed more research before acting.

I remain impatient with scientists who want to delay any action until we have perfect data. In the field of public health we are often obliged to do the best we can with what we have; as long as policy-makers are prepared to change their approach as the data improve we can save valuable time and lives. But in this case, the caution was well placed. Mea culpa.

Once again, it is worth drawing attention to the most basic fact in this research: 30 years into the epidemic, in a population that had safe sex counselling up the wazoo as well as universal access to condoms and other services such as STI treatment, more than four in 100 women are still getting infected with HIV. Pro2000 may not work, but just urging people to use condoms doesn’t, either. We need to keep looking for something that does.

Unlike the United States, the UK has bothered to track HIV infection among large, representative samples of drug injectors (both current injectors and those in methadone and other treatment programmes) since close to the start of the epidemic. Part of this effort involved testing anonymous samples of left over blood for HIV — the samples were usually taken from treatment or diagnostic purposes and are stripped of all but the most basic demographic and risk information (age, sex, length of time injecting, recent needle sharing) before being tested with HIV. The results, shown separately for London and the rest of England and Wales are shown below.

(Click to enlarge)

Yes, prevalence for the whole of England and Wales (including London — Scotland has its own system and reports separately) has risen by over 77% in the last decade. But still, fewer than one injector in 60 is infected with HIV. If you draw the graph using a normal percentage scale, you’ll see something close to the true level of infection — still too high, of course, but not exactly an overwhelming prevention failure when compared with data from any city or country that doesn’t have needle exchanges. The graph compares what happened in the UK with what happened in Jakarta, just because I happened to have the Indonesian data handy. But it would look just the same with data from Bangkok or Moscow or even New York in the years before the city (with no help from the federal government) began to hand out needles.

(Click to enlarge)

Since I’m just a numbers nerd and obviously don’t have a great visual imagination, perhaps someone could help me out here: how can you conclude from these pictures that safe injecting programmes fail to prevent HIV?

Does this signal a new wave of common sense in HIV prevention in the United States? That’s certainly what we expected when Obama was elected. During his campaign, for example, he recognised that sterile needle programmes cut HIV infection among injectors, saving lives and money, and pledged to end a ban on funding those programmes from federal coffers. So cities such as his home town of Chicago, pictured in the map below, will now be able to use central money to provide clean needles to the inner city injectors that need them most. As long as they set up in one of the grey spaces. In the cemetary, in other words.

(Click to enlarge)

On this fantastic map, which comes from Yale University’s Dr. Russell Barbour by way of Stop the Drug War, the red areas are the parts of town where it would be illegal to operate a federally funded needle exchange under new rules proposed by Congress. The Drug War Chronicle provides an interesting history of the needle exchange shenannigans. Essentially, Obama did not remove the ban from a budget bill because he thinks policy shouldn’t be made through sub-clauses in budget bills. Democrats on the committee discussing the bill disagreed, and dropped the ban. Then Republicans, not willing to give up the idea that the availability of clean needles would have us all racing to start shooting up smack, decided to protect the innocent by forbidding needle programmes within 1,000 feet of “a public or private day care centre, elementary school, vocational school, secondary school, college, junior college, or university, or any public swimming pool, park, playground, video arcade, or youth centre, or an event sponsored by any such entity”. That’s the red bits on the map of Chicago above. Here’s Dr, Barbour’s map of needle exchange exclusion zones in San Francisco:

This is clearly just a way of pulling the rug from under any effort to increase access to clean needles. We’ve come to expect this kind of implaccable opposition from conservative Drug Warriors in the United States. We used to expect the Brits to be more rational about their drug policy, and the UK has, thank God, held on to its policy of providing clean fits for anyone that needs them. But with the sacking of the government’s independent advisor on drugs David Nutt for repeating his independent advice after the government chose to ignore it, I’m not so sure.

I’m not even going to wade in here about whether or not idependent scientific advisers to government should shut up after their advice is ignored, but I will commend to you a wonderful paper by Dr Nutt on the dangers of Equasy, (pdf) an irrational addiction to horse riding. This has been seized on by many who have not read it as an example of his inappropriate analyses. Irony, where art thou?

The US Drug Warriors also joyously seized on the latest round of anonymous surveillance of HIV among drug injectors in Britain, sending out an e-mail crowing about rising rates of HIV and drawing a link between that and the fact that the UK was the first country in the world to have national injection safety programmes. My next post will put those rather one-eyed claims into perspective.

AIDS activists need to change not only their tune but their name. What we need is HIV activism, not AIDS activism. Because with the treatments that are now widely available in Western Europe and North America, AIDS is vanishing fast. While it continues to kill millions of people in Sub-Saharan Africa, where two thirds of people with HIV live, in most industrial countries it now kills a few hundred people a year at most. As long as treatment is available and effective, AIDS will remain largely a thing of the past in the rich world. But if drug-resistant strains develop and spread — and there is a real possibility they will — we’ll be back to the carnage of the late 1980s and early 1990s. Only very much worse, because there are so many more people now living with HIV in the West. And there are more people living with HIV in part because people aren’t dying of AIDS any more (a good thing) and in part because we are doing so very badly at prevention (definitely not a good thing). Brand new HIV infections are on the rise again among gay men in Germany, the US, the UK, Australia, Canada, Spain, Switzerland, the Netherlands — just about everywhere we’ve can measure it. That really is shocking.

Does it seem churlish, then, for me to be criticising the new prevention campaign in Germany? Some respondents to a comment I wrote in The Guardian think so. But I’m critical precisely because we need more good prevention that addresses local realities. The local realities in Germany are:

1) we are already effectively preventing AIDS, through treatment
2) we are failing to prevent HIV
3) the vast majority of the sexual transmission of HIV happens between men in anal sex

What Germany needs is campaigns to encourage gay men to avoid an inconvenient life-long infection (HIV) that is expensive to treat and can be most easily prevented by using condoms in sex. That is not what Malawi or Washington DC or Buenos Aires need, but it IS what Germany needs. What the Das Comitee ad gives the German public is a campaign to encourage heterosexual women to avoid a killer disease that in their local reality barely exists. “Shock value” is all very well, but if you are shocking the wrong people about the wrong things, you’re not going to prevent many HIV infections. And that’s what we need to do, now more than ever.

Michael tells the story more patiently than I’d be able to. As several people pointed out, including Dharmawan, Willem and Catherine. Read. Really, please read. What Michael doesn’t say is that Indonesia has pocketed more than US$ 400 million in foreign taxpayers’ money to deal with HIV so far, and has another US$ 130 million from the Global Fund on the table. And it can’t even assure treatment in the big, well-funded, teaching hospitals designated to provide ARVs. No need to point out that treatment is the EASY bit, the big, politically popular success story. People need it because we fail so badly on the cheaper, easier prevention services, like making sure that kids who inject heroin in Indonesia don’t also inject HIV. If it doesn’t make you angry that we’re using your money so badly (if you’re a European or North American tax payer) or serving your needs so poorly (kalau seandenya anda orang Indonesia, apalagi orang Indonesia yang terinfeksi HIV…), this blog’s no place for you.

The oldest know tissue sample containing HIV dates from 1959 — it comes from Congo and was described in (wicked, pay-per-view) Nature in 1998. Scientists have since compared different strains of the virus and guesstimated from the divergence between them (and from comparison with the related monkey-version of the virus SIV) when HIV first emerged. They put the date in the early 1930s. Now another sample has emerged, also from Congo, from a woman who died in 1960. Comparison between this and the 1959 sample has turned the clock back three decades. Analysts of the new old sample now say they think HIV emerged around 1900.

Should that change how we think about HIV? Not really. It is a virus that emerged in the forests of Congo at a time when Leopold, King of the Belgians, was wreaking his uber-hypocritical havoc in the region. (Anyone with the slightest interest in the cynical pursuit of personal enrichment would do well to read Adam Hochschild’s King Leopold’s Ghost. It turns out that political lobbying by foreign powers in Washington is as old as HIV.) Leopold’s oversized ego was blown up with rubber tapped from the forests — tappers were sent in large numbers into areas that had not previously been much visited, and it is probably this that allowed the virus to cross from simians to humans. They then carried their wares back to cities and had sex, and so began the spread of HIV. Belgians were not, however, very efficient colonists. Infrastructure in Congo remains poor to this day, population density is relatively low and travel is difficult. Not surprising then, that the virus was slow to emerge. Not surprising, either, that when it did filter out, it did not begin to spread in earnest until it found its way into pools of people who had a high turnover of partners and relatively risky sexual practices. In other words, gay men celebrating their sexual emancipation in the bars and bathhouses of the west.

No coincidence either that in the African epidemic, where HIV is spread largely in unprotected sex between men and women who each have more than one partner on the go in any two or three month period, the virus spread fastest in the countries with the best infrastructure — South Africa, Botswana and (until the recent meltdown) Zimbabwe. The possibility that HIV existed at low levels in other countries long before it reached a critical mass makes me think twice about early accounts of untreatable patients. Check out, for example, Paul Theroux’s account of his work in a leper colony in Malawi, published in Granta 48. If AIDS wasn’t described in Africa until it had been identified in San Francisco, it was probably because it went unnoticed against a background thick with mysterious bugs and early death.

How is it that people get so uptight about these simple facts? To judge from some of the early readers’ comments on the Nature news pages (now also disgracefully charging for content) scientists cannot describe infection in Africa without being called racist. Some samples:

“HIV is older than your great-grandparents, uh-huh! And I’ll bet that the US bio weapons effort is just ecstatic about this deflection. So now these members of science play to the bio-jackboot population controllers with this ‘revelation’ that those sex-crazed Africans of course just couldn’t stop themselves from pulling chimpanzees (I thought the original scientific theory was “green monkeys”) out of the trees for a quickie. ”

“This is one of the most stupid discovery I have ever heard. You will blame every single human plague on Africa, This is against all the Theories of evolutionary biology where The descents of the people that lived in the area might have developed a kind of resistance instead of being vulnerable to a new strain of the Virus. This is very disturbing, what about all the Slaves you moved around to the Western Hemisphere? What about all the sailors and rapist colonial administrator? How come they did not bring it back to Europe and spread it all over Europe? Please stop insulting our intelligence.”

All I can say is, with intelligence like that…

One of the interesting things about this paper was the forensic epidemiology work it describes. The sample was pretty mashed up, but new technology allowed useable bits of virus to be extracted from abused tissue locked up in paraffin. For those of you who can’t access the Nature story about the paper (beautifully written by Heidi Ledford) here’s a taste. It includes a quote from Mike Worobey, who led the research, which illustrates the mash-up nicely.

The samples had all been treated with harsh chemicals, embedded in paraffin wax and left at room temperature for decades. The acidic chemicals had broken the genome up into small fragments. Formalin, a chemical used to prepare samples for microscopy, had crosslinked nucleic acids with protein. “It’s as if you had a nice pearl necklace of DNA and RNA and protein and you clumped it together, drenched it in glue and then dried it out,” says Worobey.

Robert Ochai, director of the trailblazing AIDS support organisation TASO, has noticed that some of group’s the 23,000 treatment clients are giving up their HIV drugs because they have been “cured” by faith healers, according to a report in The Monitor. Apparently, faith healing has become big business in Uganda.

“Several Pentecostal churches in the country, more so in Kampala, invite the sick, including those with Aids, for spiritual healing. Some churches promise miracles, sometimes in exchange for their patients’ valuables. The most publicised case is of Ms Frances Adroa who claimed last year that she was tricked by pastors of the Universal Church of the Kingdom of God into offering her car to the church. She later sued the pastors after her condition deteriorated and they refused to return her car,” reports Kakaire Kirunda.

Eating in to family finances is bad enough. Deliberately encouraging people to give up life-prolonging therapy is far worse. But the effect on the epidemic as a whole could be catastrophic, too. If a person is on antiretrovirals, it is critical that they stay on them (or, to use the AIDS Inc. jargon, that their “compliance” is high). If they stop taking them for a bit, because they run out, forget, can’t be bothered, feel rotten or whatever, the amount of virus in their blood shoots up. That damages the immune system and makes it more likely that they’ll get sick, it increases the likelihood that the virus will mutate into drug-resistant forms, and it makes it much, much more likely that they’ll pass their infection on if they have unprotected sex.

Partly because of the extraordinary level of support provided by organisations like TASO, compliance among Ugandans on ARVs is very high. Undermining it in the name of God and Mamon is beyond cynical, it is downright wicked. In this regard, the “faith healers” are no better than witch doctors or traditional healers who sell expensive herbal cures for AIDS.

For an insight into the complicated relationship between traditional beliefs, modern medicine and faith, I urge you to read Johnny Steinberg’s book Sizwe’s Test, to be published soon in the UK under the less interesting title Three Letter Plague. He’s writing about South Africa rather than Uganda but he does so with depth of feeling and great humanity. It’s thought-provoking, and a lovely read.

One of my favourites on this list is Nigeria’s Ato nai ise – “Five and three” (5 + 3 = 8, and “eight” sounds like “AIDS”). I like this for a completely off-topic reason: young Chinese often sign off text messages and e-mails with “88″. In Mandarin, 8 is “ba”, so 88 is “ba ba”, enough like English “bye bye” to make it a quick and cheery farewell.

Back on topic of not being able to talk directly about HIV and the things that spread it, I was at first disappointed by the mealy-mouthed HIV policy trotted out by Zimbabwean opposition party Movement for Democratic Change. If you were playing AIDS bingo, you’d have a full house in no time; it’s chock full of all the usual jargon: empowerment, expanded multi-sectoral responses, gender equity, mobilising stakeholders etc etc. Precious little about sex, nothing at all about the tut-tut issues of intergenerational or same sex relations.

Having said that, the fluffy language does hide some sensible policies: Better services for sex workers, including STI care services. Stronger action on sexual abuse, including for children. More efforts to promote condoms. Compulsory licensing. Spousal housing for public sector workers. And they are at least brave enough to put on the table the things that would be sensible to do but are still political hot potatoes:

Some policy areas have not been fully resolved, and the MDC will continue to ensure informed public debate and dialogue on issues such as partner notification, shared confidentiality, reproductive health education for adolescents, commercial sex workers and prisoners, and the promotion of gender equality in a manner that respects social norms, but that also confronts those that are leading to the spread of the disease impeding its management.

I think that last sentence means: stop men behaving like pigs without turning women into harridans, but I can’t be sure. I think we may need better euphemisms.