Data for: "The epidemiology and clinical features of HIV and Trypanosoma cruzi (Chagas disease) co-infection: A systematic review and individual patient data analysis" – Data Codebook

Persistent identifier

10.17037/DATA.00004916

Description

Supporting files for a systematic review entitled "The epidemiology and clinical features of HIV and Trypanosoma cruzi (Chagas disease) co-infection: A systematic review and individual patient data analysis", published in PLOS Neglected Tropical Diseases”. These include:

Individual-level patient information recorded in the dataset is non-identifiable and has been obtained using public information.

The protocol for the systematic review was registered in advance on PROSPERO and is published online: https://www.crd.york.ac.uk/PROSPERO/view/CRD42020216125. Ethical approval was not required for this systematic review.

Data Codebook

The dataset is comprised of two tables.

Publication basic information

The ‘All_152_papers_basic_info_only’ table contains 9 variables.

Variable Name Variable Label Answer Label Answer Code Variable Type
rayyan The ID for linking to Rayyan     Numeric
Citation The article citation     String
Type_pub Type of publication     Numeric
    journal article 1  
    conference abstract/poster 2  
    online report 3  
    other 4  
Year_pub Year of publication     Numeric
Studydesign Study design     Numeric
    Case report 1  
    Case series 2  
    Cohort 3  
    Case-control 4  
    Cross-sectional 5  
numbercoinfected Number of co-infected     Numeric
countrysetting Country setting     Numeric
    Argentina 1  
    Belize 2  
    Bolivia 3  
    Brazil 4  
    Chile 5  
    Colombia 6  
    Costa Rica 7  
    Ecuador 8  
    El Salvador 9  
    French Guiana 10  
    Guatemala 11  
    Guyana 12  
    Honduras 13  
    Mexico 14  
    Nicaragua 15  
    Panama 16  
    Paraguay 17  
    Peru 18  
    Suriname 19  
    Uruguay 20  
    Venezuela 21  
    US 22  
    UK 23  
    Spain 24  
    Other 25  
countryofbirth Patient's country of birth     Numeric
    Argentina 1  
    Belize 2  
    Bolivia 3  
    Brazil 4  
    Chile 5  
    Colombia 6  
    Costa Rica 7  
    Ecuador 8  
    El Salvador 9  
    French Guiana 10  
    Guatemala 11  
    Guyana 12  
    Honduras 13  
    Mexico 14  
    Nicaragua 15  
    Panama 16  
    Paraguay 17  
    Peru 18  
    Suriname 19  
    Uruguay 20  
    Venezuela 21  
    US 22  
    UK 23  
    Spain 24  
    Other 25  
notes_datachanges Notes on data changes     String

Patient data

The ‘Individual_patient_data’ contains 193 variables. All information has been collated from publicly available journal publications.

Variable Name Variable Label Answer Label Answer Code Variable Type
No_patients Numerical ID for individual patients Open ended   Numeric
Studyid Study ID Open ended   Numeric
rayyan ID number for linking to Rayyan Open ended   Numeric
patientid Within articles, an additional way of distinguishing between patients (if more than one patient extracted per article)     Numeric
duplicate_case Duplicate case No 0  
    Yes, case duplicated 1  
duplicate_details An explanation of the duplication Open ended   String
citation The article citation Open ended   String
newreactivation The definition of reactivation (as presented in the final published article)     Numeric
    No reactivation 0  
    Reactivation 1  
microscopy_any T. cruzi detected by microscopy in any fluid or tissue     Numeric
    No 0  
    Any microscopy positive for T. cruzi 1  
csf_para Parasites detected in CSF     Numeric
    No 0  
    Yes 1  
other_tissue Parasites detected in other tissue Open ended   String
microscopy_tissue Microscopy positive in tissue     Numeric
    No 0  
    Yes 1  
csfmicroscopy Microscopy positive in CSF     Numeric
    No 0  
    Yes 1  
myocarditisintext Myocarditis referred to in article     Numeric
    No 0  
    Yes 1  
type_pub Type of publication     Numeric
    Journal article 1  
    Conference abstract/poster 2  
    Online report 3  
    Other 4  
year_pub Year of publication Open ended   Numeric
stud_design Study design     Numeric
    Case report 1  
    Case series 2  
    Cohort 3  
    Case-control 4  
    Cross-sectional 5  
no_patients Number of patients presented in article Open ended   Numeric
country Country setting     Numeric
    Argentina 1  
    Belize 2  
    Bolivia 3  
    Brazil 4  
    Chile 5  
    Colombia 6  
    Costa Rica 7  
    Ecuador 8  
    El Salvador 9  
    French Guiana 10  
    Guatemala 11  
    Guyana 12  
    Honduras 13  
    Mexico 14  
    Nicaragua 15  
    Panama 16  
    Paraguay 17  
    Peru 18  
    Suriname 19  
    Uruguay 20  
    Venezuela 21  
    US 22  
    UK 23  
    Spain 24  
    Other 25  
other_country Country setting if not specified above     String
age Age of patient Open ended   Numeric
sex Sex of patient     Numeric
    female 0  
    male 1  
birthcountry Country of birth of patient     Numeric
    Argentina 1  
    Belize 2  
    Bolivia 3  
    Brazil 4  
    Chile 5  
    Colombia 6  
    Costa Rica 7  
    Ecuador 8  
    El Salvador 9  
    French Guiana 10  
    Guatemala 11  
    Guyana 12  
    Honduras 13  
    Mexico 14  
    Nicaragua 15  
    Panama 16  
    Paraguay 17  
    Peru 18  
    Suriname 19  
    Uruguay 20  
    Venezuela 21  
    US 22  
    UK 23  
    Spain 24  
    Other 25  
otherbirth Other country of birth if not specifed above     String
hiv_known HIV known at presentation     Numeric
    No 0  
    Yes 1  
onart On ART at presentation     Numeric
    No 0  
    Yes 1  
chagas_known Chagas known at presentation     Numeric
    No 0  
    Yes 1  
chagas_cardiac Cardiac Chagas disease present     Numeric
    No 0  
    Yes 1  
chagas_gut Gastrointestinal Chagas disease present     Numeric
    No 0  
    Yes 1  
priorchagas_treat Prior treatment for Chagas disease reported     Numeric
    No 0  
    Yes 1  
immuno Any other forms of immunosuppresssion known     Numeric
    No 0  
    Yes 1  
pregnant Pregnant     Numeric
    No 0  
    Yes 1  
rf Any risks factors known     Numeric
    No 0  
    Yes 1  
rf_msm Men who have sex with men     Numeric
    No 0  
    Yes 1  
rf_ivdu Intravenous drug use     Numeric
    No 0  
    Yes 1  
rf_farm Exposure to animals/farm     Numeric
    No 0  
    Yes 1  
rf_sexwork Sex worker     Numeric
    No 0  
    Yes 1  
rf_fh Family history of Chagas disease     Numeric
    No 0  
    Yes 1  
rf_transfusion Previous blood transfusions     Numeric
    No 0  
    Yes 1  
rf_verthiv Vertical transmission of HIV     Numeric
    No 0  
    Yes 1  
rfvertchagas Vertical transmission of Chagas     Numeric
    No 0  
    Yes 1  
rforal Oral transmission of Chagas     Numeric
    No 0  
    Yes 1  
acute Acutely unwell     Numeric
    No 0  
    Yes 1  
fever Fever     Numeric
    No 0  
    Yes 1  
headache Headache     Numeric
    No 0  
    Yes 1  
weightloss Weight loss     Numeric
    No 0  
    Yes 1  
seizures Seizures     Numeric
    No 0  
    Yes 1  
nausea Nausea     Numeric
    No 0  
    Yes 1  
vomiting Vomitting     Numeric
    No 0  
    Yes 1  
swallow Difficulty swallowing, dysphagia     Numeric
    No 0  
    Yes 1  
diarrhoea Diarrhoea     Numeric
    No 0  
    Yes 1  
gastro Any gastrointestinal presentation     Numeric
    No 0  
    Yes 1  
focal Focal neurological deficit     Numeric
    No 0  
    Yes 1  
syncope Syncope     Numeric
    No 0  
    Yes 1  
neck Neck stiffness     Numeric
    No 0  
    Yes 1  
visual Visual disturbance     Numeric
    No 0  
    Yes 1  
loc Loss of consciousness     Numeric
    No 0  
    Yes 1  
weak Weakness     Numeric
    No 0  
    Yes 1  
speech Speech disturbance     Numeric
    No 0  
    Yes 1  
cog Cognitive deficit     Numeric
    No 0  
    Yes 1  
tremor Tremor     Numeric
    No 0  
    Yes 1  
cough Cough     Numeric
    No 0  
    Yes 1  
sob Shortness of breath     Numeric
    No 0  
    Yes 1  
palp Palpitations     Numeric
    No 0  
    Yes 1  
cp Chest pain     Numeric
    No 0  
    Yes 1  
cardio Any cardia presentation     Numeric
    No 0  
    Yes 1  
skin Skin lesions     Numeric
    No 0  
    Yes 1  
other Any other presentation     Numeric
    No 0  
    Yes 1  
anyneuro Any neurological presentation     Numeric
    No 0  
    Yes 1  
neuro Neurological presentation     Numeric
    No 0  
    Yes 1  
otherpresent Other form of presentation described Open ended   String
cd4 CD4 count Open ended   Numeric
viral_load HIV viral load Open ended   Numeric
elisa Chagas ELISA     Numeric
    Negative 0  
    Positive 1  
ifat Chagas IFAT     Numeric
    Negative 0  
    Positive 1  
iha Chagas IHA     Numeric
    Negative 0  
    Positive 1  
western Chagas Western blot     Numeric
    Negative 0  
    Positive 1  
pcr T. cruzi PCR     Numeric
    Negative 0  
    Positive 1  
rdt T. cruzi rapid diagnostic test     Numeric
    Negative 0  
    Positive 1  
microscopy T. cruzi microscopy     Numeric
    Negative 0  
    Positive 1  
bloodculture T. cruzi blood culture     Numeric
    Negative 0  
    Positive 1  
xenodiagnosis T. cruzi xenodiagnosis     Numeric
    Negative 0  
    Positive 1  
other_diagnosis Other form of diagnosis described Open ended   String
diagnosis_autopsy Diagnosis at autopsy     Numeric
    No 0  
    Yes 1  
svt Supraventricular tachycardia     Numeric
    No 0  
    Yes 1  
vt Ventricular tachycardia     Numeric
    No 0  
    Yes 1  
rbbb Right bundle branch block     Numeric
    No 0  
    Yes 1  
lbbb Left bundle branch block     Numeric
    No 0  
    Yes 1  
avb AV block     Numeric
    No 0  
    Yes 1  
brady Bradycardia     Numeric
    No 0  
    Yes 1  
ve Ventricular ectopics     Numeric
    No 0  
    Yes 1  
st ST changes     Numeric
    No 0  
    Yes 1  
qt Prolongued QT     Numeric
    No 0  
    Yes 1  
microvoltage Microvoltage     Numeric
    No 0  
    Yes 1  
af Atrial fibrillation     Numeric
    No 0  
    Yes 1  
otherecg Other ECG findings     String
abnormalecg Abnormal ECG     Numeric
    No 0  
    Yes 1  
normalcxr Normal chest xray     Numeric
    No 0  
    Yes 1  
cardiomegaly Cardiomegaly     Numeric
    No 0  
    Yes 1  
pneumonia Pneumonia     Numeric
    No 0  
    Yes 1  
infiltrates Pulmonary inflitrates     Numeric
    No 0  
    Yes 1  
effusion Plueral effusion     Numeric
    No 0  
    Yes 1  
othercxr Other chest xray abnormalities (specify)     String
anyCXR Any chest xray abnormalities     Numeric
    No 0  
    Yes 1  
abnormalcxr Abnormal chest xray     Numeric
    No 0  
    Yes 1  
normalecho Normal echocardiogram     Numeric
    No 0  
    Yes 1  
systolic Systolic dysfunction     Numeric
    No 0  
    Yes 1  
diastolic Diastolic dysfunction     Numeric
    No 0  
    Yes 1  
thrombus Thrombus     Numeric
    No 0  
    Yes 1  
valve Valve disease     Numeric
    No 0  
    Yes 1  
pericard Pericardial disease     Numeric
    No 0  
    Yes 1  
dilated Dilated chambers     Numeric
    No 0  
    Yes 1  
otherecho Other abnormality on echo     Numeric
    No 0  
    Yes 1  
abnormalecho Abnormality on echo     Numeric
    No 0  
    Yes 1  
ctscan CT scan reported     Numeric
    No 0  
    Yes 1  
mriscan MRI scan reported     Numeric
    No 0  
    Yes 1  
noneuro No neuroimaging     Numeric
    No 0  
    Yes 1  
normalneuro Normal neuroimaging     Numeric
    No 0  
    Yes 1  
single Single lesion     Numeric
    No 0  
    Yes 1  
multiple Multiple lesions     Numeric
    No 0  
    Yes 1  
ring Ring enhancing lesion(s)     Numeric
    No 0  
    Yes 1  
white Lesion reported to be in white matter     Numeric
    No 0  
    Yes 1  
grey Lesion reported to be in grey matter     Numeric
    No 0  
    Yes 1  
mass_effect Mass effect     Numeric
    No 0  
    Yes 1  
cerebral_oedema Cerebral oedema     Numeric
    No 0  
    Yes 1  
otherneuro Other neuroimaging abnormality     Numeric
    No 0  
    Yes 1  
abnormalneuro Abnormal neuroimaging     Numeric
    No 0  
    Yes 1  
lp Lumbar puncture     Numeric
    No 0  
    Yes 1  
normallp Normal lumbar puncture/CSF analysis     Numeric
    No 0  
    Yes 1  
tryplp T. cruzi detected in cerebrospinal fluid     Numeric
    No 0  
    Yes 1  
lpviral HIV viral load in cerebrospinal fluid     Numeric
    No 0  
    Yes 1  
csfpcr T. cruzi PCR in cerebrospinal fluid     Numeric
    No 0  
    Yes 1  
csfserology T. cruzi serology in cerebrospinal fluid     Numeric
    No 0  
    Yes 1  
otherlp Other finding from lumbar puncture     String
lpresults Lumbar puncture results     Numeric
    No 0  
    Yes 1  
csf_appearance Appearance of cerebrospinal fluid Open ended   String
cellcount Cell count Open ended   String
lpculture Culture of cerebrospinal fluid Open ended   String
protein Protein (cerebrospinal fluid) Open ended   String
glc Glucose (cerebrospinal fluid) Open ended   String
biopsy Biopsy performed     Numeric
    No 0  
    Yes 1  
skin_biopsy Skin biopsy performed     Numeric
    No 0  
    Yes 1  
liver_biopsy Liver biopsy performed     Numeric
    No 0  
    Yes 1  
brain_biopsy Brain biopsy performed     Numeric
    No 0  
    Yes 1  
pericardial Pericardial biopsy performed     Numeric
    No 0  
    Yes 1  
bal Bronchoalveolar lavage performe     Numeric
    No 0  
    Yes 1  
pleuraltap Plural tap     Numeric
    No 0  
    Yes 1  
endoscopy Endoscopy     Numeric
    No 0  
    Yes 1  
ascitic Ascitic tap     Numeric
    No 0  
    Yes 1  
otherbiopsy Other biopsy      
o_ix Other investigations Open ended   String
aspergillosis Aspergillosis     Numeric
    No 0  
    Yes 1  
mycobacteriosis Mycobacteriosis     Numeric
    No 0  
    Yes 1  
bacteraemia Bacteraemia     Numeric
    No 0  
    Yes 1  
candidiasis Candidiasis     Numeric
    No 0  
    Yes 1  
cmv Cytomegalovirus     Numeric
    No 0  
    Yes 1  
cryptococcosis Cryptococcosis     Numeric
    No 0  
    Yes 1  
cryptosporidiosis cryptosporidiosis     Numeric
    No 0  
    Yes 1  
enteritis enteritis     Numeric
    No 0  
    Yes 1  
hsv Herpes simplex virus     Numeric
    No 0  
    Yes 1  
histo Histoplasmosis     Numeric
    No 0  
    Yes 1  
ks Kaposi's sarcoma     Numeric
    No 0  
    Yes 1  
lYmp Lymphoma     Numeric
    No 0  
    Yes 1  
nocardi Nocardiosis     Numeric
    No 0  
    Yes 1  
pen Peniciliosis     Numeric
    No 0  
    Yes 1  
pml Progressive multifocal leukoencephalopathy     Numeric
    No 0  
    Yes 1  
pcp Pneumocystic pneumonia     Numeric
    No 0  
    Yes 1  
toxo Toxoplasmosis     Numeric
    No 0  
    Yes 1  
tb Tuberculosis     Numeric
    No 0  
    Yes 1  
otheroi Other opportunistic infection     Numeric
    No 0  
    Yes 1  
anyoi Any opportunistic infection     Numeric
    No 0  
    Yes 1  
otherinvest Other investigations     Numeric
    No 0  
    Yes 1  
art_yes Given ART     Numeric
    No 0  
    Yes 1  
art_delay Delay in ART     Numeric
    No 0  
    Yes 1  
         
chag_treat Given Chagas treatment     Numeric
    Benznidazole 1  
    Nifurtimox 2  
    Other 3  
anychagtreat Any Chagas treatment     Numeric
    No 0  
    Yes 1  
secondchag_treat Second Chagas treatment     Numeric
    Benznidazole 1  
    Nifurtimox 2  
    Other 3  
stop Chagas treatment stopped     Numeric
    No 0  
    Yes 1  
adverse Adverse effects reported     Numeric
    No 0  
    Yes 1  
duration_antip_days Duration of antiparasitic therapy in days Open ended   Numeric
toxo_treat Treated for toxoplasmosis     Numeric
    No 0  
    Yes 1  
steroids Given steroids     Numeric
    No 0  
    Yes 1  
surgery Surgical intervention     Numeric
    No 0  
    Yes 1  
type surgery Type of surgery Open ended   String
othermanagement Other management Open ended   String
death_dis_recov Outcome     Numeric
    Death 1  
    Any disability 2  
    Full recovery 3  
death Patient death is recorded     Numeric
    No 0  
    Yes 1  
disability Describe disability Open ended   String
timeoutcome Time to outcome Open ended   Numeric
daystooutcome Days to outcome Open ended   Numeric
autopsy_yn Autopsy performed     Numeric
    No 0  
    Yes 1  
autopsy Autopsy findings Open ended   String
otherinfo Other information Open ended   String