Dataset: CEPHIA HIV Recency Assay Data

About this Dataset

CEPHIA HIV Recency Assay Data

Global Assay Results and Participant Characteristics

About this dataset

The Consortium for the Evaluation and Performance of HIV Incidence Assays (CEPHIA) is continually striving to deepen understanding of HIV epidemiology around the world. By collecting and testing samples from collaborations across the globe they are able to monitor the accuracy and precision of HIV recency assays. This dataset contains assay results plus corresponding participant characteristics, enabling researchers to gain knowledge about both incidence rates as well as long-term dynamics in different cohorts throughout numerous countries.

This data set provides key information such as assay type, specimen type, testing laboratory, participant demographic factors (e.g., sex and country), HIV status at visit time, cohort entry HIV status, elite controller status over time and antiretroviral use history (both current ART treatment & past first treatment episode). Plus viral load test results with related information such as closest measure to visit date offset , sensitivity level , EDDI interval size and number of days since EDDI for enhanced analysis capabilities. All together these variables make this a powerful tool allowing you to probe a myriad of questions ranging from understanding how incidence changes over time by population or country & reducing infection levels in especially vulnerable communities through to exploring potential interactions between other factors such as wealth or gender based disparities in those affected by this virus

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How to use the dataset

This dataset provides a comprehensive look at CEPHIA collaborations across the world to evaluate the accuracy of HIV recency assays. It contains information on assay results and participant characteristics such as HIV status, HIV subtype, country of origin and demographics. The data can be used to gain insight into global trends in HIV incidence and dynamics.

To get started with this dataset, explore the different columns available to you such as assay, cephia_panel, testing_laboratory, etc. These will give an indication of what kind of assay was used, where it was conducted and what samples were tested. Then look at the other columns which provide more detailed information about each participant such as their HIV subtype, HIV status at visit and visit date.

Once you have familiarized yourself with the column titles, start by selecting only those that are relevant for your analysis - there is no need to include all columns if they don't add value your analysis. This will reduce clutter and make analysing your data much easier.

Finally if you have any questions or would like further explanation on any aspect of this dataset please refer to CEPHIA's website or contact them directly for help!

Research Ideas

Using the HIV subtype and HIV treatment information, researchers can develop and evaluate models that predict treatment effectiveness for different types of HIV.

Examining the viral load closest to a certain visit date, as well as the viral load type used, allows researchers to better understand the dynamics of viral load within cohorts.

Analyzing designated-elite controllers during visits can help characterize and track times where a person is intermittently controlling their infection without medication over time allowing investigators to investigate how this occurs in different patient populations with different responses to medications

Acknowledgements

If you use this dataset in your research, please credit the original authors.
Data Source

License

License: CC0 1.0 Universal (CC0 1.0) - Public Domain Dedication
No Copyright - You can copy, modify, distribute and perform the work, even for commercial purposes, all without asking permission. See Other Information.

Columns

File: cephia_public_use_dataset_20210604.csv

Column name	Description
assay	The type of assay used to test the specimen. (String)
cephia_panel	The CEPHIA panel used for testing the specimen. (String)
testing_laboratory	The laboratory performing the testing procedures. (String)
test_date	The date the specimen was tested. (Date)
assay_result_field	The field containing the results obtained from the assay. (String)
assay_result_value	The value of the results obtained from the assay. (Numeric)
assay_result_method	The method used to obtain the results from the assay. (String)
specimen_type	The type of specimen used for the assay. (String)
hiv_status_at_visit	The HIV status of the participant at the time of the visit. (String)
cohort_entry_hiv_status	The HIV status of the participant at the time of cohort entry. (String)
days_since_cohort_entry	The number of days since the participant entered the cohort. (Numeric)
hiv_subtype	The HIV subtype of the participant. (String)
hiv_subtype_confirmed	Whether the HIV subtype of the participant has been confirmed. (Boolean)
country	The country the participant is from. (String)
sex	The sex of the participant. (String)
age_in_years	The age of the participant in years. (Numeric)
eddi_interval_size	The size of the EDDI interval. (Numeric)
days_since_eddi	The number of days since the EDDI. (Numeric)
days_since_ep_ddi	The number of days since the EP DDI. (Numeric)
days_since_lp_ddi	The number of days since the LP DDI. (Numeric)
designated_as_elite_controller_at_visit	Whether the participant was designated as an elite controller at the time of the visit. (Boolean)
ever_designated_as_elite_controller	Whether the participant has ever been designated as an elite controller. (Boolean)

Acknowledgements

If you use this dataset in your research, please credit the original authors.
If you use this dataset in your research, please credit .

Tables

Cephia Public Use Dataset 20210604

@kaggle.thedevastator_cephia_hiv_recency_assay_data.cephia_public_use_dataset_20210604

2.99 MB
212831 rows
38 columns


CREATE TABLE cephia_public_use_dataset_20210604 (
  "assay" VARCHAR,
  "cephia_panel" VARCHAR,
  "testing_laboratory" VARCHAR,
  "test_date" TIMESTAMP,
  "assay_result_field" VARCHAR,
  "assay_result_value" DOUBLE,
  "assay_result_method" VARCHAR,
  "specific_result_identifier" BIGINT,
  "generic_result_identifier" BIGINT,
  "participant_identifier" BIGINT,
  "visit_identifier" BIGINT,
  "specimen_type" VARCHAR,
  "hiv_status_at_visit" VARCHAR,
  "cohort_entry_hiv_status" VARCHAR,
  "days_since_cohort_entry" BIGINT,
  "hiv_subtype" VARCHAR,
  "hiv_subtype_confirmed" BOOLEAN,
  "country" VARCHAR,
  "sex" VARCHAR,
  "age_in_years" DOUBLE,
  "eddi_interval_size" DOUBLE,
  "days_since_eddi" DOUBLE,
  "days_since_ep_ddi" DOUBLE,
  "days_since_lp_ddi" DOUBLE,
  "designated_as_elite_controller_at_visit" BOOLEAN,
  "ever_designated_as_elite_controller" BOOLEAN,
  "treatment_naive_at_visit" BOOLEAN,
  "on_treatment_at_visit" BOOLEAN,
  "first_treatment_episode" VARCHAR,
  "days_since_first_art" DOUBLE,
  "days_since_current_art" DOUBLE,
  "days_from_eddi_to_first_art" DOUBLE,
  "days_from_eddi_to_current_art" DOUBLE,
  "viral_load_closest_to_visit" DOUBLE,
  "viral_load_date_offset_from_visit_date" DOUBLE,
  "viral_load_type" VARCHAR,
  "viral_load_detectable" VARCHAR,
  "cd4_count_at_visit" DOUBLE
);