Data for: "Kankasha in Kassala: a prospective observational cohort study of the clinical characteristics, epidemiology, genetic origin, and chronic impact of the 2018 epidemic of Chikungunya virus infection in Kassala, Sudan" – Data Codebook

Persistent identifier

10.17037/DATA.00002018

Description

In 2018/19, Eastern Sudan experienced the largest epidemic of CHIKV in Africa to date, affecting an estimated 487,600 people. Known locally as Kankasha, this study examines the clinical characteristics, risk factors, and phylogenetics of the CHIKV A prospective cohort of 102 adults and 40 children were enrolled at Kassala Teaching Hospital in October 2018. Clinical information, socio-demographic data, and sera samples were analysed to confirm diagnosis, characterise illness, and identify viral strain. CHIKV infection was confirmed by real-time reverse transcription-PCR in 84.5% (120/142) of participants. Nine had concurrent CHIKV/Dengue virus (DENV) infection; 28.8% had a positive Rapid Diagnostic Test for Plasmodium falciparum. Five percent had haemorrhagic symptoms including two children with life-threatening haemorrhage. One CHIKV-positive participant died with acute renal injury. Age was not associated with severity of illness though CHIKV-infected participants were younger (p=0.003). Two to four months post-illness, 63% of adults available for follow-up (30) were still experiencing arthralgia in one or more joints, and 11% remained moderately disabled using Rapid3 assessment. Phylogenetic analysis showed all CHIKV cases identified belonged to a single clade within the Indian Ocean Lineage (IOL) of the East/Central/South African (ECSA) genotype. History of contact with an infected person was the only factor associated with infection (p=0.01), suggesting vector transmission in households is important.

Data Codebook

The quantitative dataset contains information on 142 patients (102 adults and 40 children) enrolled at Kassala Teaching Hospital in October 2018.

Researchers wishing to analyse the data should submit a list of variables that they wish to access. The list will be reviewed and additional processing performed where necessary to protect participant identity.

Variable Name	Variable Label	Answer Label	Answer Code	Variable Type
pin	Patient ID (unlinked)	Open ended		Numeric
iv_date	Date of original interview			Date
sex	Sex of patient			String
		Female	f
		Male	m
ageyr	Patient age in years	Open ended		Numeric
adm_date	Admission date	Date		Date
delay	Delay onset to presentation			Numeric
preg	Is participant pregnant?			String
		Yes	y
		No	n
		Unknown	x
		Not applicable	u
deliv	Has the patient delivered in past 12 weeks?			String
		Yes	y
		No	n
		Unknown	x
		Not applicable	u
trav_loc1	Exposure: Location of travel	Open text		String
house	Exposure: Type of housing			String
		Brick/concrete	Brick/concrete
		Mud	Mud
		Tent	Tent
		Grass hut	Straw
		Other	Other
toilet	Exposure: Household access to toilet			String
		No access	no access
		Family's own	family's own
		Shared toilet	shared toilet
		Unknown	unknown
water	Exposure: Household access to water			String
		Own well	own well
		Well outside compound	well outside compound
		Piped water	piped
		Unknown	unknown
hh_animal	Animals kept in household			String
		Yes	y
		No	n
adm_temp	Symptom at presentation: Temperature	Open ended		Numeric
heartrate	Symptom at presentation: heart rate	Open ended		Numeric
resprate	Symptom at presentation: Respiratory rate	Open ended		Numeric
bp_sys	Blood pressure systolic at presentation	Open ended		Numeric
bp_diast	Blood pressure diastolic at presentation	Open ended		Numeric
othsym1	Symptom at presentation: other Symptoms	Open ended		String
haem1	Biochem results: Haemoglobin (g/dL)	Open ended		Numeric
wbc1	Biochem result: WBC count	Open ended		Numeric
plate1	Biochem result: Platelets	Open ended		Numeric
hct1	Biochem results: Haematocrit	Open ended		Numeric
no1	Biochem result: Nitrogen oxide	Open ended		Numeric
lo1	Biochem result : LO	Open ended		Numeric
urea1	Biochem result: Blood urea nitrogen (mg/d)	Open ended		Numeric
creat1	Biochem result: Creatinine (mg/dl)	Open ended		Numeric
bili1	Biochem result: Bilirubin (mg/dL)	Open ended		Numeric
ast1	Biochem results: AST/SGOT (U/L)	Open ended		Numeric
alt1	Biochem result: ALT/SGPT (U/L)	Open ended		Numeric
outcome	outcome for all followed-up participants			String
		Discharged	Discharged
		Died in facility	Died in facility
den_ct	Linear CT for DV			Numeric
fupiv_date	Date of follow-up interview			Date
fup_sample	Sample given at follow-up			Numeric
		No	0
		Yes	1
fup_admdays	Follow-up: Number of days admitted - adult			Numeric
fup_diab	Follow-up medical history: Diabetes			String
		No	n
		Yes	y
fup_hypert	Follow-up medical history: Hypertension			String
		No	n
		Yes	y
fup_overweight	Follow-up medical history: Overweight			String
		No	n
		Yes	y
fup_cvd	Follow-up medical history: Cardiovascular condition (cvd)			String
		No	n
		Yes	y
fup_respcondit	Follow-up medical history: Respiratory condition			String
		No	n
		Yes	y
fup_rheumat	Follow-up medical history: Rheumatological condition			String
		No	n
		Yes	y
fup_osteoarth	Follow-up medical history: Osteoarthritis (severe knee/ankle/pain)			String
		No	n
		Yes	y
fup_othmed	Follow-up medical history: other medical conditions	Open text		String
fup_arthral	Symptom at Follow-up : Arthralgia			Numeric
		No	0
		Yes	1
fup_fever	Symptom at Follow-up: Fever			Numeric
		No	0
		Yes	1
fup_myal	Symptom at Follow-up : Myalgia			Numeric
		No	0
		Yes	1
fup_head	Symptom at Follow-up : Headache			Numeric
		No	0
		Yes	1
fup_rash	Symptom at Follow-up: Skin rash			Numeric
		No	0
		Yes	1
fup_respsymp	Symptom at Follow-up: Respiratory symptoms			String
		No	n
		Yes	y
fup_gastro	Symptom at Follow-up : Gastro-intestinal symptoms			Numeric
		No	0
		Yes	1
fup_haem	Symptom at Follow-up : Haemorrhagic symptoms			Numeric
		No	0
		Yes	1
fup_dizzy	Symptom at Follow-up: Dizziness			Numeric
		No	0
		Yes	1
fup_confus	Symptom at Follow-up : Confusion and/or concentration disorder			Numeric
		No	0
		Yes	1
fup_sleep	Symptom at Follow-up: Sleeping problems			Numeric
		No	0
		Yes	1
fup_othprob	Symptom at Follow-up: other problems	Open text		String
fup_shoulder	Follow-up: If joint pain present now, which joints affected - Shoulder			Numeric
		No	0
		Yes	1
fup_elbow	Follow-up: If joint pain present now, which joints affected - Elbow			Numeric
		No	0
		Yes	1
fup_hip	Follow-up: If joint pain present now, which joints affected - Hip			Numeric
		No	0
		Yes	1
fup_knee	Follow-up: If joint pain present now, which joints affected - Knee			Numeric
		No	0
		Yes	1
fup_ankle	Follow-up: If joint pain present now, which joints affected - Ankle			String
		No	n
		Yes	y
fup_wrist	Follow-up: If joint pain present now, which joints affected - Wrist			Numeric
		No	0
		Yes	1
fup_feet	Follow-up: If joint pain present now, which joints affected - Feet			Numeric
		No	0
		Yes	1
fup_finger	Follow-up: If joint pain present now, which joints affected - Fingers			Numeric
		No	0
		Yes	1
fup_toes	Follow-up: If joint pain present now, which joints affected - Toes			Numeric
		No	0
		Yes	1
fup_spine	Follow-up: If joint pain present now, which joints affected - Spine			Numeric
		No	0
		Yes	1
fup_severity	Follow-up: perception of pain bet...			Numeric
		No	0
		Yes	1
fup_para	Follow-up: taking Paracetamol			Numeric
		No	0
		Yes	1
fup_nsaid	Follow-up: taking NSAID			Numeric
		No	0
		Yes	1
fup_corticost	Follow-up: taking Corticosteroid			Numeric
		No	0
		Yes	1
fup_absent	Follow-up: Were you absent from work or duties during your illness			String
		Less than one week	<1 week
		1 to 2 weeks	1-2 weeks
		2 to 4 weeks	2-4 weeks
		Over 4 weeks	>4 weeks
fup_dress	Follow-up: Rap3 : difficulty dressing			Numeric
fup_outbed	Follow-up: Rap3 : difficulty getting out of bed			Numeric
fup_liftcup	Follow-up: Rap3 : difficulty lift...			Numeric
fup_walkout	Follow-up: Rap3 : difficulty walking...			Numeric
fup_washdry	Follow-up: Rap3 : difficulty washing...			Numeric
fup_bend	Follow-up: Rap3 difficulty bending			Numeric
fup_faucet	Follow-up: Rap3 : difficulty turn...			Numeric
fup_inout	Follow-up: Rap3 : difficulty gett...			Numeric
fup_walk2m	Follow-up: Rap3 : difficulty walk...			Numeric
fup_recreat	Follow-up: Rap3 : difficulty doin...			Numeric
fup_gdsleep	Follow-up: Rap3 : difficulty gett...			Numeric
fup_anxiet	Symptom at Follow-up : anxiety			Numeric
fup_depress	Symptom at Follow-up: depression			Numeric
fup_pain	Follow-up: Rap3 linear pain score			Numeric
fup_howwell	Follow-up variable : Rap3 wellbeing score			Numeric
fup_rap3	Follow-up: Rap3 linear score			Numeric
fup_r3categ	Follow-up: Rap3 categories			String
		ls	ls
		ms	ms
		nr	nr
adm_fup	Administration follow-up			Numeric
agegrp	Grouped age based on ageyr			String
		Under 2	<2
		2 to 4	2-4
		5 to 14	5-14
		15 to 29	15-29
		30 to 49	30-49
		50 or over	50+
occ	Re-grouped occupation			String
		<5 year old	<5 year old
		Child/Pupil/student	schoolchild/student
		Health worker	Health worker
		Housewife	Housewife
		Outdoor worker	Outdoor worker
		Prof/Business	Prof/Business
		retired/unemployed	retired/unemployed
hhsize	Linear household size (number of adults and children)			Numeric
hhgrp	Grouped household size (number of adults and children)			String
		0 to 2	0-2
		3 to 5	3-5
		6 to 9	6-9
		10 or over	10+
gathern	Exposure: In past month, has patient participated in large gathering			String
		No	n
		Yes	y
funeraln	Exposure: Exposure: In past month, has patient participated in funeral			String
		No	n
		Yes	y
cult_tradn	Exposure: Exposure: In past month, has patient participatedin cultural traditions			String
		No	n
		Yes	y
corpsen	Exposure: Exposure: In past month, has patient had close contact with a corpse or taken part in preparing the body			String
		No	n
		Yes	y
exp_illn	Exposure: In past month, has patient cared for someone with an acute illness (not chronic illness)			String
		No	n
		Yes	y
exp_bloodn	Exposure: Been exposed to someone else’s blood or body fluids			String
		No	n
		Yes	y
baseern	Exposure: In past month, has patient visited traditional medical practice			String
		No	n
		Yes	y
cown	Exposure: Had contact with cows			String
		No	n
		Yes	y
sheep_goatn	Exposure: Had contact with sheep/goat			String
		No	n
		Yes	y
cameln	Exposure: Had contact with camels			String
		No	n
		Yes	y
horsen	Exposure: Had contact with horses/donkeys			String
		No	n
		Yes	y
birdn	Exposure: Had contact with birds/fowl			String
		No	n
		Yes	y
ratsn	Exposure: Had contact with rats			String
		No	n
		Yes	y
dogn	Exposure: Had contact with dog			String
		No	n
		Yes	y
catn	Exposure: Had contact with cats			String
		No	n
		Yes	y
monkeyn	Exposure: had contact with monkeys			String
		No	n
		Yes	y
exp_wildn	Exposure: Had contact with wild meat			String
		No	n
		Yes	y
tickn	Exposure: Bitten by ticks			String
		No	n
		Yes	y
mosquiton	Exposure: Bitten by mosquito			String
		No	n
		Yes	y
traveln	Exposure: Travelled away from home in the past month			String
		No	n
		Yes	y
chkpcr	Result of CHKV pcr: pos/neg			String
		Positive	pos
		Negative	neg
dvpcr	Result of DV PCR : pos/neg			String
		Positive	pos
		Negative	neg
chkctgp	Grouped CT count CHKV			String
		11 to 19	11-19
		20 to 29	20-29
		30 to 38	30-38
combi	CHKV/DV coinfected			String
		Positive	pos
		Negative	neg
malresn	Result of malaria test			String
		Positive	p
		Negative	n
hist_fevern	Symptom at presentation: History of fever			String
		No	n
		Yes	y
dehydrn	Symptom at presentation: Clinical dehydration			String
		No	n
		Yes	y
albuminn	Biochem result: Albumin			Numeric
anybleedn	Symptom at presentation: any bleeding			String
		No	n
		Yes	y
bl_gumn	Symptom at presentation: bleeding from gums			String
		No	n
		Yes	y
bl_mouthn	Symptom at presentation: bleeding from mouth (palate)			String
		No	n
		Yes	y
bl_nosen	Symptom at presentation: bleeding from nose			String
		No	n
		Yes	y
bl_eyen	Symptom at presentation: bleeding from eyes			String
		No	n
		Yes	y
bl_earn	Symptom at presentation: bleeding from ears			String
		No	n
		Yes	y
bl_petecn	Symptom at presentation: Bleeding from Petechiae/Purpura			String
		No	n
		Yes	y
bl_muscl_haemn	Symptom at presentation: Muscle Haematoma			String
		No	n
		Yes	y
bl_coughn	Symptom at presentation: Bloody sputum/cough			String
		No	n
		Yes	y
redbl_vomn	Symptom at presentation: Fresh red blood in vomit			String
		No	n
		Yes	y
brbl_vomn	Symptom at presentation: Brown blood in vomit (coffee grounds)			String
		No	n
		Yes	y
stool_redn	Symptom at presentation: Fresh red blood in stool			String
		No	n
		Yes	y
malaenan	Symptom at presentation: Melaena (black) blood in stool			String
		No	n
		Yes	y
bl_venen	Symptom at presentation: bleeding from Venepuncture sites			String
		No	n
		Yes	y
bl_urinen	Symptom at presentation: blood in urine			String
		No	n
		Yes	y
bl_vagn	Symptom at presentation: bleeding from Vagina (non-menstrual)			String
		No	n
		Yes	y
headachen	Symptom at presentation: headache			String
		No	n
		Yes	y
fatiguen	Symptom at presentation: Fatigue/tiredness/lethargy			String
		No	n
		Yes	y
musclen	Symptom at presentation: Muscle aches/pain (myalgia)			String
		No	n
		Yes	y
jointn	Symptom at presentation: Joint pain (arthralgia)			String
		No	n
		Yes	y
vomitn	Symptom at presentation: Bomiting			String
		No	n
		Yes	y
diarrn	Symptom at presentation: Diarrhoea			String
		No	n
		Yes	y
swallown	Symptom at presentation: Difficulty swallowing			String
		No	n
		Yes	y
sh_breathn	Symptom at presentation: Shortness of breath			String
		No	n
		Yes	y
lossappn	Symptom at presentation: Loss of appetite			String
		No	n
		Yes	y
abdpainn	Symptom at presentation: Abdominal pain			String
		No	n
		Yes	y
hiccn	Symptom at presentation: Hiccups			String
		No	n
		Yes	y
conjuncn	Symptom at presentation: Conjunctivitis (red eyes)			String
		No	n
		Yes	y
rashn	Symptom at presentation: Skin rash			String
		No	n
		Yes	y
dizzyn	Symptom at presentation: Dizziness			String
		No	n
		Yes	y
confusn	Symptom at presentation: Confusion			String
		No	n
		Yes	y
seizuren	Symptom at presentation: Seizures			String
		No	n
		Yes	y
lymphn	Symptom at presentation: Enlarged lymph nodes(lymphadopathy)			String
		No	n
		Yes	y
coughn	Symptom at presentation: Cough			String
		No	n
		Yes	y
throatn	Symptom at presentation: Sore throat			String
		No	n
		Yes	y
jaundn	Symptom at presentation: Jaundice			String
		No	n
		Yes	y
backpainn	Symptom at presentation : Back pain			String
		No	n
		Yes	y
chest_painn	Symptom at presentation: Chest pain			String
		No	n
		Yes	y
min_bruisen	Symptom at presentation: Minor bruising			String
		No	n
		Yes	y
maj_bruisen	Symptom at presentation: Major bruising			String
		No	n
		Yes	y
weak	Symptom at presentation: Lack of strength			String
		No	n
		Yes	y
fup60d	type of 60 day follow-up response			String
		contact-ad	contact-admission
		contact-ch	contact-ch
		No contact	no contact
		Refused	refusal
		Patient died	dead
hospcare	Follow-up: admitted or discharged			String
		Admitted	admitted
		Discharged on same day	discharged same day
dayhosp	Number of of days admitted: adult and child	Open ended		Numeric
ad_ch	Adult/child breakdown whole sample			String
		Adult	adult
		Child	child
cigg2	CHKV IgG2			Numeric
digm2	DEnV IgGM2	Open ended		Numeric
digg2	DENV IgG2	Open ended		Numeric
c_ct	chik_ct	Open ended		Numeric
c_igm1	chik_igm1	Open ended		Numeric
cigg1	CHKV IgG1	Open ended		Numeric
dv_ct	denv_ct	Open ended		Numeric
dv_igm1	denv_igm1	Open ended		Numeric
dv_igg1	denv_igg1	Open ended		Numeric