Table 3 Annotation categories

Patient code

patient code

Sex

gender

Risk factor

HIV risk factor

Tissue bank

tissue bank distributing samples

Patient year of death

patient year of death

Sampling timepoint

Sampling geo-region

patient geo-region at time of sampling

Sampling country

patient country at time of sampling

Sampling city

patient city at time of sampling

Patient age

patient age at sampling

Health status

patient health status at sampling

Subtype

predominant subtype at time of sampling

Drug naïve (ART)

has patient had ART

Antiretroviral treatment (ART)

patient ART history

Viral load plasma (copies/mL)

plasma viral load

Viral load brain (copies/million cells)

brain viral load

Viral load lymphoid (copies/million cells)

lymphoid viral load

CD4 count (cells/uL)

CD4 count

Neurocognitive diagnosis

neurocognitive diagnosis

Neuropathological diagnosis

neuropathological diagnosis

Giant cells

were giant cells present in the brain

Sequence

Genbank accession

Genbank accession number

GI

Genbank GI number

PubMed ID

Pubmed ID for original publicaiton

Sequence length

sequence length

Clone name

publication assigned clone name

Cloning strategy

methods of genome amplification and cloning

Sample tissue class

global tissue class (Brain, Blood & Lymphoid, etc...)

Sample tissue name

tissue source

Sample tissue FMA code

tissue FMA code

Nucleic acid type

was proviral DNA or viral RNA sequenced

Start and end coordinates

sequence start and end referenced to HXB2

Sequence

viral sequence