# Choice of Ontology

I noticed an interesting phenomenon while reading this paper about a gene therapy that was intended to treat advanced heart failure.

The paper (which documents a Phase I/II study) found an 82% reduction in the risk of cardiac events in the high-dose group vs. the placebo group, with a p-value of 0.048. Weakly significant, but a big effect size.

On the other hand, if you look at the raw numbers you see that some people have a lot of cardiac events, and some have few or none.  If you divide people into “healthy” vs. “unhealthy”, where “unhealthy” people have at least one cardiac event within a year, and “healthy” people don’t, then the placebo group had 7 healthy and 7 unhealthy patients, while the high-dose group had 7 healthy and 2 unhealthy patients.

If you do a one-sided t-test of this, you get a non-significant 0.07 p-value.

And intuitively, it makes sense that 7 out of 14 unhealthy patients vs 7 out of 9 unhealthy patients could very easily be a fluke.

How you frame the problem, what you consider to be an “event” in your probability space, matters. Do you count cardiac events? Mostly healthy vs. mostly unhealthy people? People with no cardiac events vs. people with any cardiac events? (the latter gives you p=0.089).

One way of framing it is that you posit some kind of hierarchical model.  In this case, your risk of having a cardiac event is drawn from a probability distribution which is something like a mixture of two gamma distributions, one with a “low risk” parameter and one with a “high risk” parameter.

You could make a generative model to test the null hypothesis. Under the assumption that the therapy doesn’t work, you could randomly choose the size of the “high risk” vs. “low risk” population, and then for each patient, draw to see whether they’re high risk or low risk, and then draw again (repeatedly) from the appropriate gamma distribution to get their pattern of cardiac events.  Sampling from this can give you the posterior probability distribution of the actual data given the null hypothesis.

You could even make the number of clusters in your mixture, or the cutoffs of the clusters, random variables themselves, and average over different models.  That’s not really eliminating the fact that choice of model matters, it’s just pushing your agnosticism up a meta-level; but it may be general enough to be practically like model-agnosticism (e.g. adding more levels of hierarchy to the model might eventually cease to change the answer to “is this therapy significantly effective?” Note that you’re only getting p-value differences of a few percent even when we’re only tweaking a single parameter.   At some point I should try this empirically and see how much difference added model flexibility actually makes.)

But there’s a basic principle here which I see in a lot of contexts, where the output of a statistical algorithm is dependent on your choice of ontology.  And, I think, your choice of ontology is ultimately dependent on your goals.  Do I want to measure reduction in number of heart attacks or do I want to measure number of people who become heart-attack-free? There can’t be an answer to that question that’s wholly independent of my priorities.  Even averaging over models is essentially saying “over a wide range of possible priority structures, you tend to get answers to your question lying in such-and-such a range.”  It doesn’t mean you couldn’t construct a really weird ontology that would cause the algorithm to spit out something completely different.

# STD Statistics

Meta note: this is a long report on STD epidemiology and risks, made possible by generous crowdfunders. I’m going to post these kinds of research projects on my blog from now on.  I am not a doctor; I’ve just found that it’s hard to find comprehensive syntheses of the medical literature that answer the questions people actually want to know.  Please don’t hesitate to correct me if you find any errors or omissions!

OVERVIEW

 Incidence Age Race Gender Chlamydia 446.6 cases per 100,000 Peaks at age 15-19, at 1852.1 cases per 100,000 rate among blacks 6.4x rate among whites; rate among Hispanics 2.1x rate among whites; rate among Asians 0.61x rate among whites more commonly reported in women (2:1 ratio) because women are more likely to have symptoms HPV genital warts: 194.5 per 100,000 genital seroprevalence: 20-30% Genital warts: peaks at 20-24 for women: 300-900 cases per 100,000 peaks at 25-29 for men: 250-750 cases per 100,000 no difference between races genital warts 4x as common in men as women Trichomoniasis 143 cases per 100,000 (in women) prevalence: 3.1% (in women) increases with age in black women; otherwise uncorrelated prevalence among blacks 10x rate among whites; prevalence among Hispanics and whites equal not studied in men Gonorrhea 106.1 cases per 100,000 Peaks at age 20-24, at 541.6 cases per 100,000 in women, 459.4 cases per 100,000 in men rate among blacks 12.4x rate among whites; rate among Hispanics 1.9x rate among whites; rate among Asians 0.5x rate among whites Equal between genders Herpes/ HSV genital herpes: 96 cases per 100,000 seroprevalence: 16.2% HSV2 Increases with age rate among blacks 3.7x rate among whites; equal among whites and Hispanics 2x as common in women as men HIV 15 cases per 100,000 peaks at ages 20-24 rate among blacks 7.9x rate among whites; rate among Hispanics 3x rate among whites rate among men 4.2x rate among women; 78% of cases are from MSM Syphilis 5.5 cases per 100,000 Peaks age 20-24, at 16.1 cases per 100,000 rate among blacks 5.3x rate among whites; rate among Hispanics 2.0x rate among whites; rate among Asians 0.85x rate among whites 11.4x as common in men as women; 60% of cases are from MSM Hepatitis B 0.9 cases per 100,000 Peaks at age 30-39, at 2 cases per 100,000 no difference between races rate for males 1.7x rate for females
 Per-Partner Transmission Rate Condom Effectiveness Treatability Dangerous sequelae Chlamydia 40% male-to-female, 32% female-to-male high (reduces risk by 60%) [75] high (antibiotics) pelvic inflammatory disease (if untreated) HPV 20% high (reduces risk by 58%) not treatable; preventable with vaccine cervical, oropharyngeal,  anal, and genital cancer Trichomoniasis 60-100% male-to-female, 40-80% female-to-male low? (one study found no effect of condom use on prevalence)[87] high (antibiotics) low birth weight infants Gonorrhea 22% very high (reduces risk by 90%) [75] high (antibiotics) pelvic inflammatory disease (if untreated) Herpes 19% moderate (reduces risk by 30%)[76] genital warts are treatable symptomatically meningitis, encephalitis, Bell’s palsy HIV 40.4%, receptive anal sex; 21.7%, insertive anal sex 28.9%, heterosexual couples high (reduces risk by 80%)[88] moderate (anti-retroviral drugs) AIDS Syphilis 60% high (reduces risk by 60-70%) high (antibiotics) neurosyphilis, cardiac problems Hepatitis B 25%-59% high (reduces risk by 75%) moderate (chronic hepatitis can cause irreversible liver damage, but the vaccine is effective at preventing HBV) cirrhosis, hepatocellular carcinoma

Per-partner transmission rate means “given that you have sex with an infected partner, what is the chance that you’ll get infected?”  By default, these refer to unprotected sex. Many of the studies observe long-term partnerships (e.g. studies of married couples) and the risk of being infected after a long period of time (six months, a year, etc.) Since the time limit varies between studies, these numbers are not strictly comparable.  Clearly, the larger the total number of sex acts, the greater the risk of transmission.

Chlamydia

Symptoms

 Symptom Prevalence in chlamydia patients Common Inflammation of cervix and/or urethra: causes pain while urinating and during sex, abnormal discharge, genital swelling, fever 50% in women, 2% in men Moderate Pelvic inflammatory disease (increases risk of infertility and cancer) Roughly 1% in women. Less likely if chlamydia is treated. Rare Reactive arthritis (causes painful inflammation of the eyes, joints, and genitals). Roughly 0.1%.

Chlamydia causes inflammation of the cervix and/or urethra; one study found that 71% of female patients with chlamydia had cervicitis or urethritis.[18]

In women, chlamydial infection of the cervix is asymptomatic 50-70% of the time; if left untreated it leads to pelvic inflammatory disease in about half of cases.

In men, chlamydia causes inflammation of the urethra about half the time, which sometimes results in symptoms such as burning while urinating, discharge from the penis, testicular pain or swelling, or fever. However, only 2-4% of men infected with chlamydia develop symptoms. [20]

Anal infections cause pain or discharge.

Chlamydia is the primary cause of pelvic inflammatory disease, which can cause infertility in women in 37% of cases in developed countries.  Across 16 studies, an average of 37% of patients diagnosed with pelvic inflammatory disease had chlamydia.  Since asymptomatic chlamydia is often not treated, testing for chlamydia is an effective way to reduce the risk of pelvic inflammatory disease.[21]  Roughly 0.14% of women of reproductive age have been treated for pelvic inflammatory disease.[22]  This yields a (very) roughly 1% chance of getting pelvic inflammatory disease given that one has chlamydia.

Chlamydia can cause reactive arthritis, an autoimmune disease which involves inflammation of the joints, eyes, and genitals.  Reactive arthritis usually develops two to three weeks after an infection. Chlamydia-induced reactive arthritis has an incidence of about 4.6 per 100,000.[23]

Incidence and Risks

 Overall Prevalence 3-5% Male-to-female per-partner transmission rate 40% Female-to-male per-partner transmission rate 32% Per-encounter transmission rate, across sexes 5.85%-0.16% (depending on age) Per-encounter transmission rate with condom, across sexes 0.053%

Chlamydia has a 3-5% population prevalence in both men and women.

It has a single exposure male-to-female transmission rate of 40%, and a single exposure female-to-male transmission rate of 32%.[1]  This refers to the risk that you will get chlamydia given that you have an (unprotected) sex partner who has chlamydia.

In general, single-exposure transmission rates are higher than “per-encounter” or “per-coital-act” transmission rates, because people tend to have more than one sexual encounter with a given partner.

Per-encounter transmission risk declines with age, from 5.85% at age 15 to 0.16% at age 25. One of the most robust epidemiological findings about chlamydia is that it’s more common among younger people.[2]

Estimated per-encounter male-to-female transmission risk for unprotected intercourse was determined to be 0.9%; with a condom it’s 0.053%.[3]

Chlamydia can be transmitted by vaginal, oral, and anal sex.  It can also be passed from a mother to a baby in childbirth.

In a study of men who have sex with men seen at a gay men’s community health center, the prevalence rates of rectal, urethral, and pharyngeal chlamydia were 7.9%, 5.2%, and 1.4% respectively.[4]  Men who have sex with men have higher rates of chlamydia in general than the overall population, at 12.0%.[28]

Detection

Chlamydia is detected by nuclear acid amplification of samples from the cervix, urethra, vaginal swabs, or urine.

A meta-analysis found that pooled sensitivities for LCR (ligase chain reaction), PCR (polymerase chain reaction), gene probe and EIA (enzyme immunoassay) on urine were 96.5%, 85.6%, 92% and 38%, respectively, while on cervical swabs the corresponding sensitivities of PCR, gene probe and EIA were 88.6%, 84% and 65%. Specificities are high, often 100%.[19]

Treatment

Chlamydia is treated with a week-long course of antibiotics, most often azithromycin and doxycycline.  This has a cure rate of 98%.[17]

HPV

Symptoms

 Symptom Prevalence in HPV patients* Common anal intraepithelial neoplasia (MSM) Genital warts (men) Cervical intraepithelial neoplasia Oropharyngeal cancer (women) 70% 20%15-19% 11% Moderate Oropharyngeal cancer (men) Cervical cancer 9.2% 2.4% Rare Genital warts (women) Anal cancer (MSM) Vaginal cancer 0.6% 0.36% 0.23%

*These are back-of-the-envelope calculations, and use the location of HPV most relevant to the disease. For example, for oropharyngeal cancer we take the lifetime risk of oropharyngeal cancer, multiply by the percentage of cases due to HPV, and divide by the prevalence of oral HPV.

There are over 170 types of human papilloma virus, most of which cause no physical symptoms. A subset of HPV types cause papillomas (warts) on the vulva, penis, anus, cervix, or pharynx. Others cause hand or foot warts, and are not sexually transmitted. The “high-risk” HPV types (16, 18, 31, 33, 35, 39, 45, 51, 52, 56, 58, 59, 68, 73, and 82) cause nearly all cases of cervical cancer.

There are about 13,000 cervical cancer cases a year; the incidence of HPV-associated cervical cancer is about 7-10 cases per 100,000 women.[12]  Cervical intraepithelial neoplasia, a precursor to cancer, has a prevalence rate of 4-5% among women receiving cervical cancer screening.[32]  The lifetime risk of developing cervical cancer is 0.65%.[33]

HPV can cause oral and pharyngeal cancer. The incidence of HPV-associated oropharyngeal cancer is about 6.4 per 100,000 in men and 1.4 per 100,000 in women.[34]  HPV causes about 60% of cases of oropharyngeal cancer.[35]  The overall lifetime risk of oropharyngeal cancer is 1.55% for men and 0.67% for women.[33]

HPV can cause anal cancer. The prevalence of anal intraepithelial neoplasia, a precursor to cancer, is 35% among non-HIV-infected men who have sex with men.[14]  The lifetime risk of anal cancer is about 0.2%.[36]  HPV is thought to be associated with 90% of anal cancers.[37]

HPV can cause vaginal cancer. It is thought to be associated with 70% of vaginal cancers.[37]  Vaginal cancer is rare; the lifetime risk is 1/1100.[38]

Low-risk HPV types, i.e. HPV types 6 and 11, cause genital warts. The overall prevalence of genital warts ranges from 0.13% to 0.56%.[13]  Prevalence ranges from 0.13% to 0.16% in women, and 4.1% among heterosexual, sexually active men.[31]

Incidence and Risks

 Vaginal HPV prevalence (women) 26.8% Genital HPV prevalence (men) >20%? Oral HPV prevalence (men) 10.1% Oral HPV prevalence (women) 3.6% Anal HPV prevalence (MSM) 50% Per-partner transmission rate 20% Per-encounter transmission rate 0.2%

The overall prevalence of vaginal HPV in women is 26.8%.[39]

A systematic review of studies of men found prevalences of HPV ranging from 1.3% to 72.9%; a majority found rates of over 20%. [40]

10.1% of men and 3.6% of women have oral HPV infections.[10]

50% of men who have sex with men have anal HPV.[11]

Transmission rates from men to women and women to men are about equal and about 20% per person during a 6-month relationship period.[8] At an average of 4 sexual encounters a week, the per-sex-act transmission rate was roughly 0.2%.

Condom use protects against HPV transmission.  College freshmen women who used condoms consistently had a 37.8% per patient-year incidence of genital HPV, compared to an incidence of 89.3% among those who did not.[15]

Testing

HPV testing is not approved for men, but some healthcare providers may offer anal Pap smears for high-risk men, such as men who have HIV or receive anal sex.

Women are recommended to get a cervical HPV test at the same time they get a Pap smear, every three years.[41]  The HPV test is a DNA amplification test taken from a cervical swab.

Oral HPV testing is commercially available, but the value of the test for predicting oral cancer has not yet been established.  Most people who test positive for salivary HPV will not get oral cancer.

Treatment

Genital warts can be treated with podofilox (an anti-mitotic drug that destroys warts), imiquimod (an immune enhancer), cryotherapy, surgery, or caustic agents.

Cervical cancer is treated with surgery, radiation, and/or chemotherapy.

Asymptomatic HPV is not treated.

The cervical cancer vaccine Gardasil, when administered to young women, has a 94-100% efficacy rate in preventing persistent HPV infections.[16]  (“Young”, because it is most likely to be effective before the onset of sexual activity and thus before exposure to HPV.)  While Gardasil is not as actively promoted for young men, it is also available to men and similarly effective at preventing HPV in men.

Trichomoniasis

Symptoms

 Symptom Prevalence in Trichomoniasis Patients Common Vaginal discharge Odor Swelling Urethritis Dysuria Low birth weight infant 42% (women) 50% (women) 22-37% (women) 50% (men) 42% (men) 11% (assuming infected while pregnant)

Trichomoniasis is caused by the protozoan Trichomonas vaginalis and is a common cause of vaginitis.  Symptoms include pain, burning, or itching in the urethra, penis, or vagina.  For women there can be an itchy, yellow-green, frothy, foul-smelling vaginal discharge.  However, nearly half of all women[64] and men[65]  are asymptomatic.

Trichomoniasis (and other bacterial vaginosis) during pregnancy is associated with preterm delivery of a low-birth-weight infant, with an odds ratio of 1.4, according to a cohort study of 13,914 women.[69]  8% of infants are born with low birth weight,[70] so the probability given the mother has trichomoniasis is 11%.

Trichonomiasis also increases the risk of HIV infection by a factor of 1.52[71].

Incidence and Risks

 Prevalence 3.1% Male-to-female per-partner transmission rate 66-100% Female-to-male per-partner transmission rate 40-80%

The prevalence of trichomoniasis infection is estimated to be 3.1% among women ages 14-49.[66]  2.8% of 454 men attending an STD clinic tested positive for trichonomas vaginalis.[67]

66-100% of the female partners of infected men had trichomoniasis; 40-80% of the male partners of infected women had trichomoniasis.[72]

Diagnosis

Trichomoniasis is usually diagnosed with microscopic examination of a sample of vaginal fluid.  This has only a 60-70% sensitivity, and so often results in false negatives.[73]

Treatment

Trichomoniasis is treated with metronidazole, an antibiotic typically used for protozoa.  For 95-97% of cases, a single dose resolves the infection.[68]

Gonorrhea

 Symptom Prevalence in Chlamydia patients Common Pain during urination or sex, genital discharge, (in women) abdominal pain roughly 50% Moderate Sore throat Pelvic inflammatory disease (increases risk of infertility and cancer in women) Sore throat: 10% PID: roughly 9% Rare Gonococcal arthritis (causes joint pain, rash, and fevers) 0.5-3%

Symptoms

About half of women have no symptoms; the other half have vaginal discharge, lower abdominal pain, or pain during intercourse. Most men with gonorrhea have infection of the urethra, which causes burning during urination and/or discharge.

Gonorrhea in the throat causes a sore throat about 10% of the time.

Gonorrhea, if left untreated, can cause pelvic inflammatory disease in women. The risk of developing pelvic inflammatory disease from gonorrhea is somewhat unclear.  A meta-analysis found that gonococcal cases of PID outnumbered non-gonococcal PID in three-fourths of the studies, but the gonococcal-to-non-gonococcal ratio varied from 1:1.5 to 8:1.  (In other words: the distribution of STDs depends dramatically on the location of the clinic doing the epidemiological study.)  In the Women’s Health Study, women with a history of gonorrhea had an 80% increase in the risk of pelvic inflammatory disease relative to women without such a history.[24]  (Overall population prevalence of PID in US women 18-44 is roughly 5%.)

Untreated gonorrhea can spread to the joints, causing gonococcal arthritis.  This occurs in roughly 0.3-5% of cases of gonorrheal infection.  It causes joint pain, skin lesions, and fever and chills. Standard treatment is intravenous or intramuscular ceftriaxone (an antibiotic).[25]

Incidence and Risks

 Overall prevalence 0.5% (among 15-25-year-olds), 0.1% (in general US population.) Female-to-male per-partner transmission risk 22%

Prevalence is about 0.5% among 15-25-year-olds (the highest-risk population), in both men and women.  The overall US prevalence is 0.1%.[27]

Female-to-male transmission (in a 1978 study of sailors on shore leave in East Asia) was 19% for white men and 53% for black men.[5]  Another study of transmission rates among sailors found that the female-to-male transmission rate was 22%.[26]

Condoms prevent gonorrhea. Consistent condom users have lower rates of chlamydia and gonorrhea than nonusers.[6][7]

Gonorrhea can be transmitted by oral, anal, or vaginal intercourse. In a study of men who have sex with men, seen at a gay men’s community health center, prevalence rates were 6.9%, 6.0%, and 9.2% for anal, urethral, and pharyngeal chlamydia respectively.[4]  Men who have sex with men have higher than average rates of gonorrhea in general: 16.4%.[28]

Treatment

Gonorrhea is treatable with antibiotics.  Standard treatment is intramuscular ceftriaxone and oral azithromycin.  This has a 99% cure rate.[29]

HSV

Symptoms

 Symptom Prevalence in HSV patients Common Fever, headache, malaise Local pain and itching Pain urinating Tender lymph nodes Aseptic meningitis 67% 98% 63% 80% 36% women, 13% men (HSV-2) Moderate Bell’s palsy roughly 2% (HSV-1) Rare Encephalitis roughly 0.001%

Herpes simplex virus 1 and 2 (HSV1 and HSV2) cause cold sores and genital herpes, respectively.  They cause watery blisters in the skin and mucous membranes of the mouth, lips, or genitals.  The virus is normally dormant and lives in the cell bodies of sensory nerves throughout a person’s lifetime. When the herpes virus reactivates (note that outbreaks may be asymptomatic), it is shed from skin and becomes contagious.

The first episode often presents with systemic symptoms (fever, malaise, swollen lymph nodes) as well as outbreaks of painful vesicular lesions.  Usually HSV-1 causes mouth lesions and HSV-2 causes genital lesions, but HSV-1 can also cause genital lesions.

One prospective study of 3438 initially HSV-negative women followed for 20 months found that most infections (74% of HSV-1 and 63% of HSV-2) were asymptomatic, that more cases of symptomatic genital herpes were caused HSV-1 than by HSV-2, and that there were no clinical differences between HSV-1-caused and HSV-2-caused genital herpes.[42]

HSV can have complications. Symptoms of aseptic meningitis (stiff neck, headache, and photophobia) were found in 36% of women and 13% of men with primary genital HSV-2 infections.[43]

HSV-1 infection is considered the likely cause of Bell’s palsy, a sudden onset facial paralysis.  HSV-1 DNA was found in 11 of 14 patients with Bell’s palsy.[45]  Lifetime risk of Bell’s palsy is about 1.5%.[46]

HSV-1 encephalitis (an infection of the membrane around the brain, causing fever, headache, seizures, and frequently death) is responsible for about 10-20% of the 20,000 yearly US cases of fatal sporadic encephalitis.[44]

There is early-stage research suggesting that HSV1 is implicated in the pathogenesis of neurological diseases such as Alzheimer’s, multiple sclerosis, and intractable focal epilepsy. The APOE4 allele is a stronger risk factor for Alzheimer’s among patients harboring HSV1 in their brains.  (Patients with HSV1 are not more likely to have Alzheimer’s across the board than patients without it.)[47]

Incidence and Risks

 HSV-1 Seroprevalence 65% HSV-2 Seroprevalence, Women 26% HSV-2 Seroprevalence, Men 18% Per-Partner HSV-2 Transmission Rate 19% Per-Encounter HSV-2 Transmission Rate, Women 0.06%-0.089% Per-Encounter HSV-2 Transmission Rate, Men 0.015%-0.053% Per-Encounter HSV-1 Transmission Rate, Women 0.014% Per-Encounter HSV-1 Transmission Rate, Heterosexual Men 0.024% Per-Encounter HSV-1 Transmission Rate, MSM 0.085

Seroprevalence refers to the presence of antibodies to the virus (which may be asymptomatic.)

16.2% of Americans age 14-49 are infected with HSV2. Seroprevalence increases with age, from 2.9%/0.8% for 14-19-year-old females and males respectively, to 32.3%/19.3% for 40-49-year old females and males respectively. [49]  Seroprevalence rises with number of sex partners, from 3.9% among people with one lifetime sex partner, to 26.7% among people with >10 lifetime sex partners.[49]

The current prevalence of genital herpes caused by HSV-2 in the U.S. is roughly one in four or five adults, with approximately 50 million people infected with genital herpes and an estimated 0.5 million new genital herpes infections occurring each year.[48]

65% of Americans are seropositive for HSV-1; it is commonly acquired in childhood, from contact with family members.[50]

The per-sex-act risk of acquiring HSV-2 for heterosexual women was found to be 0.089%, and the per-sex-act risk for heterosexual men was found to be 0.015%, in a study of 528 monogamous heterosexual couples.[51]  Another study, of 1843 subjects found that the per-sex-act rate of acquiring HSV-2 was 0.06% for women and 0.053% for men.  The per-sex-act rate of acquiring HSV-1 was 0.014% for women, 0.024% for heterosexual men, and 0.085% for men who have sex with men.

In a prospective study of couples where one partner had HSV-2 and the other did not, 19% of the negative partners acquired HSV-2 by the end of the study. The overall risk of acquiring HSV-2 is 10% a year.[52]

Condom use reduces the risk of acquiring HSV-2 among female subjects. When condoms were used more than 25% of the time, women’s risk of acquiring HSV-2 fell over the duration of the study with a hazard ratio of 0.085.  Men’s risk was unaffected.[51]  Because genital herpes is transmitted via a sore, condoms are only protective if they cover the area where the sore is.

Testing

HSV-2 and HSV-1 serologic blood tests can detect the presence of an immune response to the herpes simplex virus.  The CDC recommends testing for people who have symptoms of genital herpes, but not as screening for the general population.[53]  These tests have sensitivities and specificities of 97-100%.[54]

Treatment

Herpes simplex, both HSV-1 and HSV-2, is treated with antiviral drugs, including acyclovir, valacyclovir, famcyclovir, and pencyclovir. No treatment can eliminate herpes simplex virus from the body, but antivirals reduce the frequency of outbreaks and the probability of transmission.  In one double-blind study, during a 120-day treatment period, 94% of placebo patients had a recurrence of herpes, while only 35% of acyclovir-treated patients did.  Recurrences in acyclovir-treated patients were shorter in duration and associated with a lower frequency of viral shedding.[55]

HIV

Symptoms

 Symptom Prevalence in HIV Patients Common Acute infection (fever, swollen lymph nodes, rash, throat inflammation) Eventual progression to AIDS Chronic diarrhea Pneumocystis pneumonia HIV wasting syndrome Kaposi’s sarcoma Lymphoma 40-90% 95% 90% 40% 20% 10-20% 10-20% [83]

Human immunodeficiency virus infection leads to low levels of T cells (specifically, CD4+ helper T-cells).  The initial symptom of HIV infection is an influenza-like illness with rash, followed by a prolonged period (3-20 years) without symptoms. After this, the weakened immune system becomes much more susceptible to opportunistic infections and tumors. The late stages of infection are known as AIDS, and are characterized by certain “AIDS-defining conditions” — infections such as Pneumocystis pneumonia, cancers such as Kaposi’s sarcoma, and severe weight loss.

Tuberculosis and pneumonia are common causes of death in AIDS patients. Esophagitis is a common symptom, often caused by viruses (HSV or cytomegalovirus) or Candida fungus.  Toxoplasmosis, leukoencephalopathy, and AIDS dementia complex are common neurological complications of AIDS.[83]

There is a very wide variety of opportunistic infections and tumors which occur in AIDS patients, and which we do not list here.

The average life expectancy for an American 20-year-old on anti-retroviral therapy is 43 years — that is, half will die by the age of 63.  The average life expectancy for an untreated AIDS patient is 9-11 years.[82]

Incidence and risks

 Prevalence 0.37% Incidence 15 per 100,000 per-partner risk, receptive anal intercourse 40.4% per-partner risk, insertive anal intercourse 21.7% per-partner risk, heterosexual couples 28.9% per-act risk, receptive anal intercourse 1.4% per-act risk, insertive anal intercourse 0.11 circumcised, 0.62% uncircumcised per-act risk, receptive vaginal intercourse 0.08% per-act risk, insertive vaginal intercourse 0.04% per-act risk, receptive fellatio 0.04%

In 2011, an estimated 1,201,100 people over the age of 13 were living with HIV.[84]  This is a prevalence of 0.37% in the US population.

In 2010, there were an estimated 47,500 new HIV infections; this is an incidence of 15 per 100,000.[85]

Unprotected receptive anal intercourse has a per-partner transmission risk of 40.4% and a per-act transmission risk of 1.4%, for both heterosexuals and homosexuals.  Per-partner transmission risk of unprotected insertive anal intercourse is 21.7%.[88]  The per-act transmission risk of unprotected insertive anal intercourse is 0.11% for circumcised men and 0.62% for uncircumcised men.[91]

The per-act transmission risk of unprotected receptive vaginal intercourse is 0.08%, and the per-act transmission risk of unprotected insertive vaginal intercourse is 0.04%. [90]

In a study of heterosexual couples with one HIV-positive and one HIV-negative partner, 28.9% of the uninfected partners acquired HIV within 40 months.[92]

The per-act risk of receptive fellatio is 0-0.04%.[93]

According to a Cochrane review of 14 studies, consistent condom users have an 80% reduced incidence of HIV than non-users.[89]

Diagnosis

HIV is diagnosed with antibody tests of blood serum, which are extremely accurate, with a sensitivity of 99.7% and specificity of 98.5%.[94]  AIDS is diagnosed by low T-cell count or an “AIDS-defining clinical condition”, one out of a list of opportunistic infections and tumors which usually occur only in immunocompromised people.

Treatment

Anti-retroviral drugs are the standard treatment for AIDS.

They also serve as pre-exposure prophylaxis for HIV (they make an infected person less infectious, by a factor of 10-20 [97]) and post-exposure prophylaxis (immediately administering anti-retrovirals after exposure reduces the chance of HIV infection five-fold [96].)

Anti-retroviral therapy is usually given as a cocktail of several drugs.  Anti-retroviral therapy is 95% effective at keeping HIV RNA count below 50 copies/mL.[95]

Syphilis

Symptoms

 Symptom Incidence in Syphilis Patients Common Chancre Rash and systemic symptoms Gumma Cardiac symptoms Almost all Almost all 15% (if untreated) 10% (if untreated) Moderate Neurosyphilis 6.5% (if untreated) Rare many n/a

Syphilis is caused by the spirochete bacterium Treponema pallidum.

Syphilis can have many symptomatic manifestations, but it usually progresses in stages.

Primary syphilis: A painless sore (chancre) on the anus, mouth, penis, or vagina, about 21 days after infection

Secondary syphilis: diffuse, non-itchy rash, frequently including the palms and soles of the feet, consisting of small red or copper-colored macules (non-raised spots); fever, malaise, headache; usually 4-10 weeks after infection

Latent syphilis: no symptoms

Tertiary syphilis: gummas (non-cancerous necrotic growths, either on the skin or inside the body), cardiac and neurological problems.  Years after initial infection.  Without treatment, 15-40% of infected people develop tertiary disease.  People with tertiary syphilis are not infectious.[54]

Tertiary syphilis is extremely varied. Cardiac symptoms (affecting 10% of untreated syphilis patients)  usually involve the aortic arch and can lead to chest pain or aneurysm.

Gummas (affecting 15% of untreated syphilis patients) are rarely physically debilitating but can be disfiguring, and can cause collapse of the palate or nasal septum, or pressure damage to internal organs.

Neurosyphilis (affecting 6.5% of untreated syphilis patients) involves infection of the cerebrospinal fluid.  It can cause a very wide variety of neurological symptoms.  In one study of 161 patients diagnosed with neurosyphilis, 51% presented with symptoms of delirium, dementia, and other neuropsychiatric conditions; 15% had stroke; 9% had spinal cord disease; and 9% had seizures.[57]

Incidence and Risks

 Total population incidence 0.018% Incidence among men who have sex with men 0.54% Penile-anal per-act transmission rate 1.4% Penile-oral per-act transmission rate 1% Per-partner transmission rate 60%

In 2013 there were 56,471 cases of syphilis, for an incidence rate of 0.018%.

Syphilis is much more common in men who have sex with men than any other group; 60% of syphilis cases are from men who have sex with men, who make up just 2% of the US population. The male-female ratio for syphilis was 5.2 in 2003.[58]

There were 21,819 cases of “late and late latent” syphilis in 2013, which includes tertiary syphilis; this is an incidence rate of 0.007%.

Syphilis is transmitted through contact with a chancre; it can happen through vaginal, anal, or oral sex.  The per-partner transmission probability is about 60%.[59]

There is a 60-70% reduction in risk of syphilis among condom users as opposed to non-condom users among non-sex-workers, but several studies of sex workers found no association between condom use and syphilis incidence.[60]  Because syphilis is transmitted via a sore, condoms are only effective at prevention if they cover the area of the sore.

Diagnosis

Syphilis is diagnosed with a blood test. There are nontreponemal tests which recognize nonspecific antibodies, and often have false positives (due, for instance, to another infection.)  These have sensitivities of  78-86% for detecting primary syphilis, 100% for detecting secondary syphilis, and 95-98% for detecting tertiary syphilis. Specificity ranges from 85-99%.  Treponemal tests test for antibodies specific to the bacterium that causes syphilis.  They have a sensitivity of 84% for detecting primary syphilis infection and almost 100% sensitivity for detecting syphilis infection in other stages. Their specificity is 96%.[61][62]

Neurosyphilis is diagnosed by taking samples of cerebrospinal fluid and looking at serologic tests, CSF cell count, and disease symptoms.

Treatment

Intramuscular penicillin injection is the standard treatment for early syphilis. The cure rate is 95%.[63]  Neurosyphilis is treated with large intravenous doses of penicillin.

Hepatitis B

Symptoms

 Symptom Risk Common Acute viral hepatitis 30-50% Moderate Chronic hepatitis <5% Rare hepatocellular carcinoma 0.1%-0.2%

Hepatitis B is caused by the hepatitis B virus (HBV), and is transmitted by infected blood and other bodily fluids. It is preventable by vaccination.

Acute viral hepatitis causes malaise, fever, nausea, vomiting, and dark urine, ultimately progressing to jaundice in 75% of reported cases. This illness usually lasts for a few weeks and then improves.  30-50% of patients with acute hepatitis B will have symptoms.

Chronic hepatitis is inflammation of the liver; in the long term, it can lead to cirrhosis, and increases the incidence of hepatocellular carcinoma. Only <5% of cases of hepatitis B lead to chronic hepatitis.[77]  The relative risk of hepatocellular carcinoma in chronic hepatitis is 18.8 for men and 33.2 for women; with an overall incidence of 6 per 100,000 in the US,[74] this is a risk of 0.2% for women and 0.1% for men.

Incidence and Risks

 Incidence 0.9 per 100,000 Prevalence 4.7% Per-partner transmission risk 25%-59%

There were 2895 cases of acute hepatitis B in the US, for a national incidence rate of 0.9 per 100,000.  42% of cases reported injection drug use; 5% reported sexual contact with a person with confirmed or suspected hepatitis infection.[77]  During the period 1999-2006, the NHANES survey found a prevalence of hepatitis B surface antigen of 4.7%. [78]

Serum, semen, and saliva can transmit HBV. The seroprevalence of HBV infection among heterosexual spouses of people with chronic HBV infection ranges from 25% to 59%. Heterosexual transmission accounts for about 39% of new infections among adults, and transmission among MSM accounts for about 24%.[80] One mathematical model of HBV transmission dynamics used an estimate of 33% transmission risk per year per partnership for heterosexual partnerships, and 42% for homosexual partnerships.[81]

Regular condom users have about a 75% reduced prevalence of hepatitis B.[86]

Diagnosis

Hepatitis is diagnosed with serum assays that detect antibodies or viral antigens.

Treatment

A hepatitis B vaccine is standard for infants in the US, and has 95% effectiveness in preventing HBV until age 40, when it drops to about 90%, and again to around 75% in people over 60.[82]

Acute hepatitis B infections are usually self-limiting; chronic infections are treated with antivirals or the immune modulator interferon-alpha.

Note on Transgender Issues

The vast majority of studies on STD epidemiology do not address transgender people. “Female” and “male” susceptibility rates here implicitly refer to cisgender women and men.

Extrapolating the available information for trans people inevitably requires judgment calls. Per-act transmission rates are based on the type of intercourse (oral, vaginal, anal, receptive or penetrative) and should be extrapolated to trans people accordingly.  Per-partner studies of heterosexual couples do not specify type of intercourse but can probably be assumed to involve chiefly vaginal intercourse.

STD rates among trans people are poorly studied, but HIV rates among trans women appear to be very high.  11.8% of transgender women reported having HIV.[30]

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# Housekeeping Notes

I’ve decided to start blogging actively again.

I’ve been frustrated with the decline of blogging and the move to Tumblr/Twitter/Facebook.

My natural form is the essay. I believe (with caveats) that discussion and speculation are valuable.  Blogging is a way to have an intellectually stimulating exchange — a blog post is long enough to expand and justify an idea, but shorter and less formal than a paper or a book. In a lively blogging community, it’s understood that people’s ideas are interesting but could easily turn out to be wrong.

I find myself wanting to bifurcate — to either write extremely circumspect things that I’m 100% certain are true, or make low-quality off-the-cuff comments in a social-media context where people won’t hold me to a high standard. And I think that impulse is bad. I believe it’s better to think in public, and learn in public, and sometimes be wrong in public.

I’m leaving academia to be a data scientist, and I’m leaving behind the notion that one has to present a flawless and impersonal facade in order to live a successful life.  I genuinely think that’s unhealthy and outdated.  I want to strive to be right, not to appear right.

I’m also going to post my literature reviews on medical topics here. I am not a doctor; making sense out of the medical literature is my side project and passion.  If I make any errors, please don’t hesitate to correct me.