RESEARCH QUESTIONS:

1. Primary research question:

What factors are important in generating HIV transmission among men who have sex with men?

18 _{Brown AE., Tomkins SE., Logan LE et al. Monitoring the effectiveness of HIV and STI}

prevention initiatives in England, Wales and Northern Ireland: where are we now? Sex Transm Infect 2006;82:4-10

19

Elford J and Hart G. If HIV prevention works, why are rates of high-risk sexual behaviour increasing among MSM? AIDS Educ Prev 2003;15:294-308

20

Brighton and Sussex PCT level data. SOPHID, Centre for Infections, Health Protection Agency: 2006.

http://www.hpa.org.uk/infections/topics_az/hiv_and_sti/hiv/sophid/sophid_main.htm

21 _{Dodds JP, Mercey DE, Parry JV and Johnson AM. Increasing risk behaviour and high levels of}

undiagnosed HIV infection in a community sample of homosexual men. Sex Transm Infect 2004;80(3):236-40

transmission?

3. How does ART impact on transmission?

4. To what degree is co-infection with an STI associated with transmission?

5. To what extent do individuals infected with resistant viruses (transmitted drug resistance) cluster with other individuals with resistant viruses?

1. Study design

● The study will involve a population based approach that combines epidemiology with phylogenetics22. We intend to create a database of HIV genetic sequences from HIV-infected men who have sex with men (MSM) attending Brighton HIV/GUM clinic between 2000-2005.

● We will use laboratory algorithms23 to categorise patients into those who have been recently infected and those that have a chronic infection.

● We will then analyse the evolutionary relationships that exist between HIV DNA/RNA sequences by construction of a phylogenetic tree.

● Through statistical analyses we will assess the impact of various clinical factors on transmission.

2. Inclusion criteria:

MSM diagnosed with HIV-1 infection who are under the care of it HIV clinic and seen at least once between 2000 and 2005. MSM must have been aged at least 16 at diagnosis.

3. Exclusion criteria:

MSM in group 3 who refuse consent (see section 4.4.) will be excluded. 4. Subjects:

To facilitate phylogenetic analysis, HIV-1 polymerase (Pol) sequence data will be obtained for all our study subjects (total = 1306). Study subjects will be divided into the following three groups, based on availability of their sequence data:

i. Individuals, from whom we already have Pol sequence data available. (n~850)

Since 2000, the British HIV Association (BHIVA) has recommended routine antiretroviral resistance testing on all new diagnoses of HIV infection24. Therefore

Pol sequence data is already available for all of this group.

22

Grenfell BT, Pybus OG, Gog JR, Wood JL, Daly JM, Mumford JA and Holmes EC. Unifying the epidemiological and evolutionary dynamics of pathogens. Science. 2004:303(5656):327-32

23 _{Murphy G, Charlett A, Jordan LF, Osner N, Gill ON and Parry JV. HIV incidence appears}

constant in men who have sex with men despite widespread use of effective antiretroviral therapy. AIDS 2004;18:265-72

24

Pozniak A, Gazzard B, Anderson J, Babiker A, Churchill D, Collins S et al. British HIV Association (BHIVA) guidelines for the treatment of HIV-infected adults with antiretroviral therapy. HIV Med 2003; 4 Suppl 1:1-41.

Approximately 50 patients have stored blood samples taken around the time of diagnosis that have not yet been tested for antiretroviral resistance. For these patients, the samples will be sent to the Health Protection Agency for sequencing for routine resistance testing according to BHIVA guidelines24.

iii. Individuals who have never had a blood test taken for genotypic testing. (n~400)

These patients do not have stored blood samples taken around the time of diagnosis. They were generally diagnosed before BHIVA guidelines24 were put into effect.

For these patients, informed consent will be obtained to take a new blood sample (10ml) for sequence based resistance testing. This group can be further divided into

two sub-groups:

● For patients that have a detectable viral load (VL>1000) blood will be taken from which plasma RNA will be sequenced.

● For patients with an undetectable viral load (VL < 1000), blood will be taken from which proviral DNA will be sequenced.

5. Procedures and tests: For groups 1, 2 and 3:

During each year of the study period (2000-2005) the following information will be collected from the HIV clinical database:

i. ART (Y/N)

ii. If (i) was Y, then classification of their viral load into one of the following categories (VL < 1000, VL>1000, VL > 50000)

iii. Any evidence of STI (one or more of the following: gonorrhoea, chlamydia trachomatis, non-specific urethritis, primary syphilis, primary genital herpes simplex and Trichomoniasis)

iv. Stage of HIV infection:

a. acute infection within 6 months:

Defined if any of the following are present:

i. Positive HIV Antibody + previous negative HIV test within 6 months

ii. Negative HIV antibody in association with positive RT-PCR or p24 Ag

b. semi-acute infection

i. Positive HIV Antibody + previous negative HIV test within 6-12 months + STARHS not suggestive of recent infection.

c. established infection

i. Positive HIV Antibody + (previous negative HIV test >12 months or no previous HIV test) + STARHS not suggestive of recent infection

For group 3 only:

Written, informed consent will be obtained from study subjects in Group 3, by the patients regular clinic doctor.

● The following will be collected or performed: ○ An extra 10 mls of blood

For groups 2 and 3 only:

● Blood will be spun and stored at the Virology Department at Brighton and Sussex University Hospitals (BSUH)

● Blood samples will be sent to the Health Protection Agency for genotypic testing