2000 HIV Human Functional Genomics Partnership Program

Study population:

A cohort with a total of 2000 HIV patients will be built, consisting of a discovery cohort (n=1200) and confirmation cohort (n=800). The investigators estimate a 2-year inclusion and 2-year follow-up period and will strive for the inclusion of several clinical phenotypes such as long-term non-progressors (~2-3%), immunologic non-responders (~3%), and rapid progressors (~4-5%) and classical risk group patients such as men who have sex with men (MSM), females, and subjects from Sub-Sahara Africa. Patients will be recruited from the following Dutch HIV Treatment Centres: Radboudumc (Nijmegen), Erasmus MC (Rotterdam), Onze Lieve Vrouwe Gasthuis (Amsterdam), Elisabeth Twee-Steden Ziekenhuis (Tilburg).

A sample size calculation cannot be provided due to the variable frequencies of the various traits in genome-microbiome interaction (SNP frequency, variable prevalence of specific microbial genera and species, etc.), and their effect on cytokine production. Because of the explorative nature of this study, the size calculation will be variable depending on the type of polymorphism analyzed. The frequencies of the various microorganism classes in the colonizing microbiome is not known in our study population, and therefore power calculations are impossible to be performed.

Earlier studies in the Human Functional Genomics Project have assessed microbiome traits in 250-500 individuals. An earlier HFGP study included a uniform cohort of 200 HIV-infected individuals (all MSM). The present study will also include HIV-infected patients with a more extreme phenotype, females and subjects originating from Sub-Sahara Africa. Because of this, the investigators decided to increase the number of individuals tested to 2000, consisting of a discovery cohort of 1200 subjects, and a confirmation cohort of 800 participants.

Study visits and procedures:

At inclusion

1. The investigators will collect metadata from all the participants using questionnaires on lifestyle, health and clinical symptoms, including neuropsychiatric symptoms. Relevant data will also be collected from the patients records in the medical centers and the HIV Monitoring Foundation.

2. Co-pathology will be assesed:

- Cardiovascular risk scores (D:A:D risk score and Framingham CVD score) will be collected as well as ECG and intima-media thickness (IMT) measurements.

- Non-Alcoholic Fatty Liver Disease (NAFLD) assessment through liver ultrasound and FibroScan.

3. Blood will be drawn (90 ml):

- DNA will be isolated for genetic analysis.

- The function of the immune system will be analyzed at several levels using circulating white blood cells from venous blood.

- Metabolism will be analyzed by metabolome analysis.

- Virological analysis, characterizing the HIV reservoir, HIV resistance and viral sequences in circulating DNA and RNA.

4. Microbiome analysis will be performed on stool and saliva samples.

5. Urine sample will be collected for creatinine measurements and microbiome.

After 2 years (20-26 months) follow-up

1. The investigators will collect metadata from all the participants using questionnaires on lifestyle, health and clinical symptoms, including neuropsychiatric symptoms. Relevant data will also be collected from the patients records in the medical centers and the HIV Monitoring Foundation.

2. Co-pathology will be assesed:

- Cardiovascular risk scores (D:A:D risk score and Framingham CVD score) will be collected as well as ECG.

- Non-Alcoholic Fatty Liver Disease (NAFLD) assessment through liver ultrasound and FibroScan.

3. Blood samples (10ml) will be collected for biomarker and infection/inflammation parameter analysis.

Patient informed consent procedure:

Patients will always be approached first by a treating physician or specialized nurse. They will be provided with information and will be asked if a physician-researcher may contact the patient in one week. If there is oral consent for this, the researcher contacts the patient in one week to ask if they are interested in participating in the study. the physician-researcher will answer any questions the patient may have and plan the first visit. The informed consent procedure will be conducted during the patient's first visit to the physician-researcher.

Patient registry procedures:

All patient data will be recorded only in coded form in a secure database with audit and edit trail (CASTOR EDC). During the informed consent procedure, the patient is given a study code. The identifying patient data and study code is kept in a password-protected key file, only accessible to the local research team. No patient-identifying data will leave the local medical center.

In the questionnaires and eCRFs in CASTOR, the investigators will enter as many data checks as possible (e.g. specified ranges for laboratory results, and questions popping up dependent on certain answers).

Biomaterials:

All biomaterial (blood, stool, urine, saliva) will be transported to and processed in the laboratory of Experimental Internal Medicine of the Radboudumc in Nijmegen. Here, all the biometarial will also be stored collectively. All materials will be handled and stored only under the patient's study code.

Monitoring:

Monitoring will be performed by an independent monitor according to the lastest guidelines of the The Netherlands Federation of University Medical Centres (NFU, April 2019). An initiation and close-out visit will be planned in plenary form with all the centers in Radboudumc. There will be one extra visit per center. This will be an on-site visit in Radboudumc, and a teleconference monitoring visit in the other centers. During these visits informed consents will be checked, as well as inclusion and exclusion criteria and source data verification in a small subset of total participants.

Data collection for patient registry:

Baseline data collected from electronic patient files or the HIV Monitoring Foundation during inclusion visit:

Medical history

1. Inclusion date

2. Length and weight

3. Last known blood pressure (and date measured)

4. Seroconversion date (if known)

5. Date first HIV-postive test

6. Date start cART

7. HIV transmission risk behavior:

- MSM

- Heterosexual

- Injecting drug use

- Contaminated blood products

- Unknown

8. First CD4 count

9. CD4 nadir

10. CD4/CD8 ratio pre-cART

11. HIV stadium at start cART according to CDC criteria

12. Pre-cART HIV RNA zenith (Note the mean if multiple HIV-RNA known pre-CART)

13. Opportunistic conditions before start cART (if known)

- None

- MTB If yes, specify when and treatment

- Fungal infections If yes, specify what kind, when and treatment

- Parasitic infections, If yes, specify what kind, when and treatment

- Bacterial infections If yes, specify what kind, when and treatment

14. Malignancies before start cART (if known)

- None

- If yes, specify what kind, when and treatment

15. Other known medical problems before start cART, which require long-term treatment (such as asthma, IBD, gout, etc).

- None

- If yes, specify what kind, when and treatment

16. Response cART:

- Period between start cART and viral load < 500 (months)

- Viral loads:

- Undetectable after 24 weeks: yes/no

- Number/frequency of residual viremia (positive test with signal <50 copies): last year and last 5 years

- Number of viral blips (50-200): last year and last 5 years

- Number of viremia: 200-1000: last year and last 5 years

- Number of failing cART (>1000): last year and last 5 years

- Resistance associated mutations pre-cART and following failure

- CD4 reconstitution

- CD4/CD8 ratio and normalization >1 yes/no after cART initiation

17. IRIS, yes/no

According to Up-to-date criteria, most or all of the following features should be present in order to make the diagnosis:

- The presence of AIDS with a low pretreatment CD4 count (often less than 100 cells/microL). One important exception to this general rule is tuberculosis. IRIS secondary to preexisting M. tuberculosis infection may occur in individuals with CD4 counts >200 cells/microL.

- A positive virologic and immunological response to antiretroviral therapy (ART).

- The absence of evidence of drug-resistant infection, bacterial superinfection, drug allergy or other adverse drug reactions, patient noncompliance, or reduced drug levels due to drug-drug interactions or malabsorption after appropriate evaluation for the clinical presentation.

- The presence of clinical manifestations consistent with an inflammatory condition

- A temporal association between ART initiation and the onset of clinical features of illness

18. Opportunistic conditions after start cART (if known)

- None

- MTB If yes, specify when and treatment

- Fungal infections If yes, specify what kind, when and treatment

- Parasitic infections, If yes, specify what kind, when and treatment

- Bacterial infections If yes, specify what kind, when and treatment 19. Malignancies after start cART (if known)

- None

- If yes, specify what kind, when and treatment 20. Vascular diseases after start cART:

- None

- Stroke/ TIA

- Angina pectoris

- Myocardial infarction

- Claudicatio intermittens

- Venous thrombo-embolism

- Other … 21. STDs

- None

- HAV: yes/no, if yes: treatment and how often

- HBV:

- Infected: active infection (PCR+) or non-active infection

- Vaccination: No/Yes

- Once with anti-HBs> 100

- Two times vaccination leading to

- anti-HBs> 100

- anti-HBs< 100

- No infection

- HCV: yes/no, if yes: treatment and how often

- Lues: yes/ no: if yes: treatment and how often

- Chlamydia/Go: yes/ no: if yes: treatment and how often

- HPV 22. cART regimes

- Reasons for switching available from 'Stichting HIV Monitoring' 23. Prescribed co-medication

- Full current medication list

Physical examination

- Signs of Kaposi sarcoma

- Lymphadenopathy

- For determination of medication levels: when was the last date and time HIV-medication was taken?

- Other abnormalities: …

Cardiovascular risk profile:

- D:A:D (R) and Framingham scores

- ECG

Laboratory results of date closest to inclusion date (standard care at least once a year according to Dutch guidelines):

- Full blood count

- Liver enzymes (ALAT, AF, bilirubin)

- Creatinine

- HIV-RNA

- CD4 and CD8 counts

- Glucose

- Lipid profile

- TPHA/VDRL

- HCV serology (for all at risk, such as MSM and i.v. drug users)

o If positive, HCV PCR

- HPV diagnostics in females (PAP, PCR)

- Urine diagnostics (if available): α1-microglobulin, protein, albumin, phosphate, creatinine.

Data to be collected after 2 years from electronic patient files or HIV Monitoring Foundation (20-26 months)

Medical history last 2 years:

1. Date of 2 year follow-up visit

2. Last known weight

3. Last known blood pressure (and date measured)

4. Response cART last 2 years

- Number of residual viremia (positive test with signal <50 copies*): last 2 years. *lowest level of detection

- Number of viral blips (20-200): last 2 years

- Number of viremia (200-1000): last 2 years

- Number of failing cART (>1000): last 2 years

- CD4 count

- CD4/CD8 ratio (if known)

5. Opportunistic conditions last 2 years

- None

- MTB If yes, specify when and treatment

- Fungal infections If yes, specify what kind, when and treatment

- Parasitic infections, If yes, specify what kind, when and treatment

- Bacterial infections If yes, specify what kind, when and treatment

6. Malignancies in the last 2 years

- None

- If yes, specify what kind, when and treatment

7. Signs/symptoms of cardiovascular diseases in the last 2 years:

- None

- Stroke/ TIA

- Angina pectoris

- Myocardial infarction

- Claudicatio intermittens

- Venous thrombo-embolism

- Other …

8. New SOAs in the last 2 years

- HAV: yes/no, if yes: treatment and how often

- HBV:

- Infected: active infection (PCR+), non-active infection,

- Vaccination: No/Yes

- Once with anti-HBs> 100

- Two times vaccination leading to

- anti-HBs> 100

- anti-HBs< 100

• No infection

- HCV: yes/no, if yes: treatment and how often

- Lues: yes/ no: if yes: treatment and how often

- Chlamydia/Go: yes/ no: if yes: treatment and how often

9. cART regimes in the last 2 years

o Reasons for switching available from 'Stichting HIV Monitoring'

10. Prescribed co-medication o Full current medication list

Physical examination

- Signs of Kaposi sarcoma

- Lymphadenopathy

- For determination of medication levels: when was the last date and time HIV-medication was taken?

- Other abnormalities: …

Cardiovascular risk profile:

- D:A:D (R) and Framingham scores

- ECG

Laboratory results of date closest to follow-up visit date (standard care at least once a year according to Dutch guidelines):

- Full blood count

- Liver enzymes (ALAT, AF, bilirubin)

- Creatinine

- HIV-RNA

- CD4 and CD8 counts

- Glucose

- Lipid profile

- TPHA/VDRL

- HCV serology (for all at risk, such as MSM and i.v. drug users)

o If positive, HCV PCR

- HPV diagnostics in females (PAP, PCR)

- Urine diagnostics (if available): α1-microglobulin, protein, albumin, phosphate, creatinine