TESSy - The European
Surveillance System
HIV Drug Resistance Reporting Protocol
and Analysis Plan 2019
HIV drug resistance surveillance data for 2018 and historical
data
February 2019
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HIVDR Reporting Protocol 2019
Contents
Contents
Introduction ............................................................................................................... 4
How to use this document ..................................................................................................... 4
Finding further information .................................................................................................... 4
Copyright ............................................................................................................................. 4
Reporting to TESSy .................................................................................................... 5
Checking the data collection schedule .................................................................................... 5
Preparing data ...................................................................................................................... 5
Denominator data ............................................................................................................ 5
Historical HIVDR data ....................................................................................................... 6
Checking metadata ............................................................................................................... 6
Checking your data source profile .......................................................................................... 6
Submitting your data ............................................................................................................ 7
Finalising your submission ..................................................................................................... 7
TESSy HelpDesk ................................................................................................................... 7
Changes to current metadata ...................................................................................... 8
Annex 1 HIVDRAGGR metadata ................................................................................... 9
Available record types ...................................................................................................... 9
Current record type version .............................................................................................. 9
Description of dataset: HIVDRAGGR, aggregated record type .................................................. 9
Annex 2 Case definition and analysis plan ................................................................... 13
Introduction ....................................................................................................................... 13
HIVDR case definition .................................................................................................... 13
Draft analysis plan (for information only) ............................................................................. 15
Description of surveillance data ...................................................................................... 15
Data cleaning ................................................................................................................ 15
Calculation of specific indicators ...................................................................................... 15
Principles of analysis ...................................................................................................... 15
Geographical grouping of countries ................................................................................. 15
Absolute numbers .......................................................................................................... 15
Reporting delays ............................................................................................................ 16
Outputs ......................................................................................................................... 16
© ECDC February 2019 All rights reserved.
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HIVDR Reporting Protocol 2019
Introduction
Introduction
This reporting protocol is for the 2019 data call for transmitted HIV drug resistance (HIVDR) diagnoses
made in 2018. Acquired drug resistance is out of scope for this surveillance data collection and reporting
protocol. The objective of HIVDR data collection are:
1. Monitoring the prevalence of and trends in HIV drug resistance in newly diagnosed HIV patients,
when they start antiretroviral treatment (ART) for the first time, to inform national treatment
policies in the EU/EEA Member States;
2. Identification of at-risk populations for transmission of drug-resistant HIV;
3. Identification of high-risk geographical areas;
4. Reporting emerging trends in resistance to learned societies and professional associations to help
guide their treatment protocol updates.
This reporting protocol covers the 31 European Union/European Economic Area (EU/EEA) countries.
The reporting of HIVDR is voluntary. Reporting protocols are data collection guidelines for data
managers in reporting countries.
The TESSy website contains additional generic technical information for each data collection in the
general technical annex and surveillance protocol. Additional information on the HIV and AIDS data
collection is available in
TESSy HIVAIDS reporting protocol.
How to use this document
This reporting protocol has three main sections:
Reporting to TESSy – contains guidelines on how to prepare data for submission to TESSy,
deadlines for data submission, subject-specific information (e.g. new changes to metadata),
and links to further information.
Annex 1 HIVDR metadata – contains the metadata set for the subject(s) covered by this
reporting protocol.
Annex 2 HIVDR-specific material – contains subject-specific material relevant for distribution
with the reporting protocol:
o Case definitions.
o Analysis plan.
Finding further information
Paragraphs denoted by the information icon tell where you can find further information.
Updated links to all the schedules, documentation and training materials mentioned in this reporting
protocol are included in the technical annex on the TESSy website, including:
Metadata sets and history.
Tutorials for data transformation using respectively Excel and Access.
TESSy user documentation.
CSV and XML transport protocols.
Copyright
© European Centre for Disease Prevention and Control, 2019. Reproduction is authorised, provided
the source is acknowledged.
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HIVDR Reporting Protocol 2019
Reporting to TESSy
Reporting to TESSy
This section provides both an overview of the TESSy reporting process and tips on where you can find
useful information.
The overall process is:
1.
Familiarise yourself with the data collection deadlines.
2.
Prepare (export and transform) your data.
3.
Check that your data comply with the metadata.
4.
Check that your data source profile is up-to-date.
5.
Submit your file(s) to TESSy.
6.
Finalise and approve your submission.
Checking the data col ection schedule
An updated link to the current data collections schedule is provided in the technical annex.
The 2018 HIV/AIDS surveillance data collection opens in March 2019 and closes on
15 September
2019. Please inform us as soon as possible if you are unable to meet the 15 September
deadline, and on a case-by-case basis, we will determine whether countries reporting later can be
included in the 2018 data report planned to be published in Q1 in 2020.
Table 1. Indicative timeframe for 2018 HIVDR data collection.
Description of process
Date
Data cal for submission of HIVDR data
Open from March 2019
Data submission for HIVDR closes
15 September 2019
Validation of data tables
Within two-three weeks of country data upload
Data analysis and report drafting
October 2019
Validation of draft report by countries
October-November 2019
Publication of the surveil ance report
Q1/2020
Preparing data
After you have exported the data from your national database, you need to ensure that the data are in
a format that TESSy can accept. This applies both to the type of file submitted to TESSy (only CSV and
XML files can be submitted) and to the format of the data in certain fields.
Tutorials covering how you can transform your data to the correct TESSy format using Excel or
Access are available on the TESSy documents website. Information on the file formats is available in
the CSV Transport Protocol and XML Transport Protocol.
Annex 1 HIVDR metadata describes the HIV/AIDS variables for reporting to TESSy, including a
detaile
d description of HIVDR variables in the TESSy metadata set. The data will be submitted in aggregate format.
Denominator data
The total number of patients tested for HIVDR needs to be collected as denominator for calculation of
the overall transmitted drug resistance (TDR) prevalence.
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HIVDR Reporting Protocol 2019
Reporting to TESSy
Historical HIVDR data
It is recommended that historical data are updated every time data are submitted to TESSy. If historical
data for HIVDR exist, you may upload such data since year 2000.
Checking metadata
The TESSy metadata define the fields and data formats that are valid as input to TESSy for a given
subject. The metadata set is the set of standard variables that is applied for reporting to TESSy across
all diseases under EU surveillance and hence defines all details of each variable and its coding. New
versions reflect changes in one or more disease areas.
As surveillance requirements change, the data changes needed to support the new requirements are
identified and agreed upon by nominated surveillance contact points in countries and are then
implemented as changes to the TESSy metadata.
In order to ensure that your data can be saved correctly in TESSy, you therefore need to check that
your data are correctly formatted according to the most recent metadata set.
It is especially important to focus on:
Field formats
Many fields require that data are formatted in a specific way. For example, dates must be in the
YYYY-MM-DD format; dates in the DD/MM/YYYY format will be rejected.
Coded values
Some fields only permit the use of specific values (coded values). For example, MSM, HETERO,
IDU and OTH
are the
coded values for Transmission and any other value in a Transmission field
will be rejected.
The metadata file contains all the definitions and rules you need to comply with to format your data
correctly for every subject (usually a disease). The file can be downloaded as an Excel file from the
TESSy documents website.
By filtering the fields in the file by subject, you can see the fields required for your subject and the rules
applying to these fields.
The technical annex provides an overview of how you work with the metadata file, and the TESSy
user documentation provides in-depth details on metadata.
Checking your data source profile
Before submitting your file(s), please review the profile for your data source(s) in TESSy (go to
Data
sources), and update the information for record type HIVDRAGGR.
Complete and up-to-date data source information for each subject is important for improving
interpretation of data - each surveillance system has different features that need to be taken into
account when comparing data at international level.
If your data source information is out-of-date and you do not have access rights to update it, please
request your National Focal Point for Surveillance or National Coordinator to do so.
In-depth information on the data source variables is available in the TESSy user documentation.
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HIVDR Reporting Protocol 2019
Reporting to TESSy
Submitting your data
Data are submitted through the TESSy web interface (go to
Upload).
The
Technical Annex provides an overview of how you submit files to TESSy, and the TESSy user
documentation provides in-depth descriptions of all the upload methods.
Finalising your submission
The compliance of your data with the validation rules in the metadata is checked automatically during
the data upload.
The result of your upload – i.e. rejected or validated – is displayed immediately after the conclusion of
the check in the
Validation details webpage. Please review the result carefully:
If your file has been rejected, there will be a message explaining each instance of non-
compliance with the metadata that you need to correct.
If your file has been validated, there might be warnings and remarks relating to possible data
quality issues or to potential overwriting of existing records that you should consider.
When your file has been validated and you are satisfied that all corrections have been made, please
ensure prompt approval – unapproved uploads can block the approval of other uploads.
HIVDR verification reports are available online to check if data in TESSy are the same data the user has
submitted. The data are presented either by date used for statistics or date of diagnosis. Information
on the “data source” is displayed as well for countries to keep information on their national surveillance
systems updated.
The TESSy user documentation provides information on reviewing validation results and adjusting
reporting periods to avoid overwriting existing records.
TESSy HelpDesk
Email:
xxxxx@xxxx.xxxxxx.xx
Telephone number:
+46-(0)8-5860 1601
Availability: 9:00 – 16:00 Stockholm time, Monday to Friday (except ECDC
Holidays)
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HIVDR Reporting Protocol 2019
Changes to current metadata
Changes to current metadata
HIVDRAGGR is a new record type and no changes have yet been applied.
Information on changes to the metadata for other subjects is available on the TESSy documentation
website.
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HIVDR Reporting Protocol 2019
Annex 1 HIVDRAGGR metadata
Annex 1 HIVDRAGGR metadata
This section describes:
The HIVDRAGGR metadata set
Dataset structure: HIVDR aggregated record type
Available record types
Different record types are available for European level reporting of HIV/AIDS surveillance data. HIVDR
data are reported
in aggregate in the HIVDRAGGR record type.
The dataset structure for HIVDR is provided in this section. For all the other record types related to
HIV epidemiological reporting, please refer t
o HIV/AIDS reporting protocol.
Current record type version
Table 2 shows the record type available for reporting 2018 HIVDR surveillance data to TESSy.
Table 2. HIVDRAGGR record version type for 2018 data.
Subject
Record type
Aggregated
record type version
HIVDR
HIVDRAGGR
HIVDRAGGR 1
Description of dataset: HIVDRAGGR, aggregated record type
The variables used for aggregate reporting include drug class, transmission, country of origin, reporting
country and the number of cases. All variables are mandatory, unless otherwise specified.
1. RecordType
The record type defines the structure and the format of the data reported. It is defined by ECDC and
specifies what data values TESSy expects to receive. The record type is related to the ‘subject’. Only
valid combinations of record type, subject and data source will be accepted. For aggregated HIVDR
data, the record type is
HIVDRAGGR.
2. RecordTypeVersion (not mandatory)
The version of the record type defines the current structure of the data reported. If the original dataset
for any particular disease changes, the version number increases. All record types started at version 1
with the launch of TESSy. This variable can be omitted if a valid metadata set is provided.
Coding for HIVDRAGGR value =
1.
3. Subject
The subject describes the disease or related health topic under surveillance:
HIVDR.
4. DataSource
The data source specifies the surveillance system from which the data on this particular disease
originate. The list of available surveillance systems per country is an integral part of TESSy and will be
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HIVDR Reporting Protocol 2019
Annex 1 HIVDRAGGR metadata
generated and revised/updated in collaboration with the nominated contact points for surveillance in
each MS.
5. ReportingCountry
The country reporting the record.
Coding: Country = ISO 3166-1 alpha-2 (two-letter code).
6. DateUsedForStatistics
This is the date used by the national surveillance institute or organisation in the national and other
official statistics to indicate the period for which HIVDRAGGR data are reported. The date is expressed
as a year and should have the following format:
Coding: YYYY
7. ResistanceDrugClass
This variable specifies the drugs under HIVDR surveillance. Only low, intermediate and high-level
resistance as defined by the Stanford HIVdb susceptibility algorithm should be reported. ‘Potentially
low’ resistance will be considered as not clinically relevant and therefore be excluded.
When reporting HIVDR by drug class, the following categorisation should be used:
Nucleoside reverse transcriptase inhibitor (NRTI) class refers to any NRTI. Examples include
abacavir (ABC), emtricitabine (FTC), lamivudine (3TC), tenofovir disoproxil fumarate (TDF),
zidovudine (ZDV);
Non-nucleoside reverse transcriptase inhibitors (NNRTI) class refers to any NNRTI. Examples
include: efavirenz (EFV), etravirine (ETV), nevirapine (NVP), rilpivirine (RIL);
Protease inhibitor (PI) class refers to any PI such as atazanavir (ATV), darunavir (DRV),
fosamprenavir (FPV), lopinavir/ritonavir (LPV/r), ritonavir (RTV), saquinavir (SQV), tipranavir (TPV);
Integrase inhibitor (INI)1 class refers to any INI such as dolutegravir (DTG), raltegravir (RAL).
It is possible to code resistance to one or multiple classes of drugs. When reporting resistance against
a combination of different drug classes, the resistance level can vary between the drug classes, e.g.
being low for one and intermediate or high for another.
Each case should be categorised only once. If a case is reported as resistant to a combination of drug
classes, the same case should not be reported again under the individual drug classes.
Coding:
NRTI
NNRTI
PI
INI
NRTI + NNRTI
PI + NRTI
PI + NNRTI
PI + NRTI + NNRTI
1 Also referred to as integrase strand transfer inhibitors (INSTI)
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Annex 1 HIVDRAGGR metadata
8. NumberDetected
Total number of patients with laboratory-detected HIVDR against any of the existing NRTI, NNRTI, INI
and PI or their combination (see ResistanceDrugClass).
Coding:
Number = Min:0; Max:999999999
9. NumberTested
This variable specifies the number of newly diagnosed HIV patients tested during the reporting period
for susceptibility upon ART initiation by route of transmission. It is required as denominator for
calculation of the overall TDR prevalence.
Coding:
Number = Min:0; Max:999999999
UNK
Unknown
10. Transmission
Describes the most probable route of HIV transmission. ‘Heterosexual contact’ is used for cases for
which heterosexual transmission is highly probable and which do not fit into another category. Cases
not fully documented should be coded as UNK.
Coding:
HETERO
heterosexual contact
IDU
ever injected drugs
MSM
MSM/homo or bisexual male
OTH
Other route of transmission (haemophiliac patient, mother-to-child
transmission, nosocomial or transfusion recipient)
UNK
Unknown or undetermined
11. Origin
Origin of the patient.
Coding:
REPCOUNTRY Case is born in/from the reporting country
ABROAD
Case is from abroad (not from the reporting country)
UNK
Unknown
Table 3. Variables and coded values for HIVDRAGGR record type.
Variables for HIVDRAGGR
Coded values
1. RecordType
HIVDRAGGR
2. RecordTypeVersion
1
3. Subject
HIVDR
4. DataSource
Country-specific code
5. ReportingCountry
2-letter code
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HIVDR Reporting Protocol 2019
Annex 1 HIVDRAGGR metadata
6. DateUsedForStatistics
YYYY
7. ResistanceDrugClass
NRTI; NNRTI; PI; INI; NRTI+NNRTI; PI+NRTI;
PI+NNRTI; PI+NRTI+NNRTI
8. NumberDetected
Number of patients fulfil ing the HIVDR case
definition
9. NumberTested
Number of patients tested
10. Transmission
MSM, HETERO, IDU, OTH, UNK
11. Origin
REPCOUNTRY, ABROAD, UNK
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HIVDR Reporting Protocol 2019
Annex 2 Case definition and analysis plan
Annex 2 Case definition and analysis plan
Introduction
Robust surveillance data are critical to monitor and inform the public health response to the European
HIV epidemic in an accurate and timely fashion. HIV surveillance within Europe has been coordinated
jointly by the European Centre for Disease Prevention and Control (ECDC) and the WHO Regional Office
for Europe since 2008.
ECDC is implementing a surveillance system for HIV drug resistance (HIVDR) in European
Union/European Economic Area (EU/EEA) countries. Increasing the number of people receiving
antiretroviral treatment (ART) among those living with HIV is critical to reduce HIV incidence and AIDS-
related morbidity and mortality in the region. Preventing and managing the emergence of HIVDR is a
key component of a comprehensive and effective HIV response and should be integrated into broader
efforts to ensure sustainability and greatest impact. It is essential that actions to monitor, prevent and
respond to HIVDR are implemented at the clinical, programme and policy levels to address the many
drivers of HIVDR. To this end, WHO published a Global action plan on HIV drug resistance in July 20172.
HIVDR surveillance data are submitted to The European Surveillance System (TESSy); this platform
enables countries to upload and also performs an automated validation to improve data quality.
This document is a practical reference guide for countries reporting HIVDR data to ECDC. It specifies
the
dataset for HIVDR reporting at the European level, and provides detailed definitions and guidelines
for coding each variable. It also provides an
analysis plan to show how the data will be used.
HIVDR is a new record type and will be tested for feasibility of reporting in 2019 with voluntary
countries. The record type will be reviewed and discussed at the European HIV Surveillance Network
meeting in 2020. Revisions based on network feedback will be implemented and further countries
invited for reporting in 2020 to achieve larger representation of the countries of countries who collect
HIVDR data.
The HIVDR record type will first be tested in an aggregate format. A pilot study on implementation of
a HIVDR data collection was performed in 2017-2018 (pending publication, provided upon request).
Each country should examine the contents of the dataset in detail. All fields are mandatory and must
be completed, even if the information is ‘unknown’.
HIVDR case definition
HIVDR case definition:
Any
newly diagnosed treatment-naïve HIV patient3 tested prior to initiating HIV treatment for
susceptibility to any of the 22 available antiretroviral drugs in the four main drug classes.
In context of this data collection, pre-exposure prophylaxis (PrEP) is not considered treatment and
cases on PrEP are included.
Low-level, intermediate and high-level resistance will all be coded as “resistant”.
Required laboratory analysis:
Sequencing of HIV protease and reverse transcriptase and/or integrase genes.
2 World Health Organization. Global action plan on HIV drug resistance 2017–2021. Geneva: WHO; 2017. Available from:
http://apps.who.int/iris/bitstream/10665/255883/1/9789241512848-eng.pdf. 3 Commission Implementing Decision (EU) 2018/945: https://eur-lex.europa.eu/legal-
content/EN/TXT/PDF/?uri=CELEX:32018D0945&from=EN
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Annex 2 Case definition and analysis plan
HIVDR interpretation algorithm:
HIVDR is defined as any mutation or combination of mutations that produces low, intermediate or high-
level resistance to any relevant NRTI, NNRTI, PI or INI. Potential low-level resistance is not included
(see below).
Since 2000, the Stanford University has maintained a free, publicly available drug resistance mutation
(DRM) interpretation system that can be accessed via an HTML or an automated web service, the
Stanford HIV Drug Resistance Database (HIVdb)4. HIVdb is an expert system that accepts user-
submitted HIV-1 sequences in FASTA data format and returns inferred levels of resistance to 22 ARV
drugs including 8 PI, 7 NRTI, 4 NNRTI, and 3 INI. In the HIVdb system, each drug resistance mutation
is assigned a drug penalty score and a comment; the total score for a drug is derived by adding the
scores of each DRM associated with resistance to that drug. Using the total drug score, the programme
reports one of the following 5 levels of inferred drug resistance: susceptible, potential low-level
resistance, low-level resistance, intermediate resistance, and high-level resistance. The scores are the
sum of each mutation penalty score for a drug. Scores of less than 10 indicate susceptibility; scores
between 10 and 14 indicate potential low-level resistance; scores between 15 and 29 indicate low-level
resistance; scores between 30 and 59 indicate intermediate resistance. Scores of 60 or above indicate
high-level resistance. For TESSy HIVDR reporting, cases with scores of 15 and higher were defined as
HIVDR.
These results are aggregated per drug class, transmission route and origin.
4 https://hivdb.stanford.edu/page/release-notes/
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Annex 2 Case definition and analysis plan
Draft analysis plan (for information only)
Description of surveillance data
Data are presented in aggregated format, indicating number of cases per main drug class and overall
resistance by main route of transmission and country of origin.
The overall HIVDR prevalence is defined as the percentage of drug-naïve newly diagnosed patients
infected with an HIV virus carrying any mutation indicative of pre-treatment drug resistance. The
denominator is the total number of persons tested for each risk group (“NumberTested”).
Data cleaning
Data submitter is contacted in case of lack of clarity or detected inconsistencies;
Assessment of data completeness; minimum 30% data completeness is required for any
variable to be included in any further analysis.
Calculation of specific indicators
HIVDR prevalence
Prevalence estimates will be calculated: (1) overall; (2) in each transmission group (MSM, HETERO,
IDU, OTH); (3) per drug class; and (4) by reporting country and origin.
Other indicators include:
Number of newly diagnosed HIV cases (and proportion of tested cases) with any HIVDR
mutations.
Newly diagnosed HIV infections tested for HIVDR, compared to the numbers of new HIV
diagnoses reported to TESSy in 2018, by country.
Number of HIVDR cases, by country, EU/EEA, 2018
Number of HIVDR cases, by drug class resistance, EU/EEA, 2018
Number of HIVDR cases, by country and drug class resistance, EU/EEA, 2018
Number of HIVDR cases, by drug class resistance and transmission mode, EU/EEA, 2018
Number of HIVDR cases, by country of origin, EU/EEA, 2018
Principles of analysis
Geographical grouping of countries
Data are presented for the European Union (EU) and European Economic area (EEA) countries: the
EU consists of 28 Member States and the EEA consists of Norway, Liechtenstein, and Iceland. Data
for country of origin are grouped by “reporting country” and “abroad” (excluding unknown).
Absolute numbers
Data are presented in absolute numbers and proportions of cases resistant to a selected drug class,
where appropriate. In addition, data are presented by year, reporting country, route of transmission
and origin. Due to variations in coverage, completeness and representativeness of the data, direct
comparisons of absolute numbers must be done with caution.
The tables in the report use absolute numbers. Denominators are based on data collected from
‘NumberTested’ variable.
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Annex 2 Case definition and analysis plan
Reporting delays
Data are provisional due to reporting delays, and because previously reported data are subject to
regular updates (e.g. detection and deletion of duplicate cases, inclusion of new information about
cases already reported).
Outputs
Data presentation
The report will include tables, figures, maps, annexes.
Example of tables:
Table 1. Number and proportion of newly diagnosed HIV cases with transmitted drug resistance and
number of new HIV diagnoses reported by country, EU/EEA, 2018.
Reporting country
HIVDR cases (% out of HIVDR
New HIV diagnoses in HIV
tested cases)
surveillance system
Austria
n (%)
n
Belgium
…
Total
n (%)
n
Table 2. Number and proportion of newly diagnosed HIV cases with transmitted drug resistance by
transmission route, EU/EEA, 2018.
Characteristics
Number
(%)
Total number of reported HIVDR diagnoses
Main route of transmission
Men who have sex with men
Heterosexual contact
Injecting drug use
Other
Unknown
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Annex 2 Case definition and analysis plan
Table 3. Number and proportion of newly diagnosed HIV cases with transmitted drug resistance by
drug class and transmission route, EU/EEA, 2018.
Transmission route
Nr of MSM
Nr of
Nr of IDU
Nr of UNK
Nr of OTH
Total
(%)
HETERO
(%)
(%)
(%)
(%)
NRTI
n (%)
NNRTI
PI
INI
NRTI+NNRTI
PI+NRTI
PI+NNRTI
PI+NRTI+NNRTI
Table 4. Number and proportion of newly diagnosed HIV cases with transmitted drug resistance by
reporting country and origin, EU/EEA, 2018.
Reporting country
Number of local cases
Number of cases
Number of cases
(%)
from abroad (%)
with unknown origin
(%)
Austria
n (%)
n (%)
n (%)
Belgium
…
Total
n (%)
n (%)
n (%)
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Annex 2 Case definition and analysis plan
Examples of figures:
Figure 1. Prevalence of HIVDR by drug class, EU/EEA, 2018.
NRTI
NNRTI
PI
INI
NRTI+NNRTI
PI+NRTI
PI+NNRTI
PI+NRTI+NNRTI
Figure 2. Prevalence of HIV drug resistance by drug class and transmission route, EU/EEA, 2018.
60%
50%
%)( 40%
e
nc 30%
e
alve 20%
r
P
10%
0%
MSM
HETERO
IDU
OTH
Output
These results will be reflected in surveillance reports or journal articles.
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