Measles outbreak report

Introduction to this template

This is a template which can be used to create an automated outbreak situation report for
measles.
• It is organised by time, place and person. For a more detailed explanation of this
template, please visit https://r4epis.netlify.com/outbreaks
• Feedback and suggestions are welcome at the GitHub issues page
• Text within <! > will not show in your final document. These comments are used to
explain the template. You can delete them if you want.

Installing and loading required packages

Person
From the start of the outbreak up until 2019-W25 there were a total of 300 cases. There
were 77 (25.7%) females and 100 (33.3%) males.
The most affected age group was 45+ years.

Demographics
Cases by age group and definition
There were 123 (41.0%) cases missing information on sex and 0 (0.0%) missing age group.
Cases by age group and sex

Male Female Missin

Age cases cases g cases
group (n) % (n) % (n) % Total
0-2 2 2 3 3.9 2 1.6 7
3-14 13 13 4 5.2 15 12.2 32
15-29 12 12 5 6.5 14 11.4 31
30-44 11 11 15 19.5 13 10.6 39
45+ 62 62 50 64.9 79 64.2 191
Total 100 100 77 100.0 123 100.0 300

Cases by population proportion (age group and sex)

 Male Female Missin
Age cases cases g cases
group (n) % (n) % (n) % Total
0-2 2 0.7 3 1.0 2 0.7 7
3-14 13 4.3 4 1.3 15 5.0 32
15-29 12 4.0 5 1.7 14 4.7 31
30-44 11 3.7 15 5.0 13 4.3 39
45+ 62 20.7 50 16.7 79 26.3 191
Total 100 33.3 77 25.7 123 41.0 300

Age pyramid

0 (0.0%) reported previous vaccination. 76 (25.3%) were unvaccinated and 0 (0.0%) were
unsure.
Cases by vaccination status

Vaccination status Cases (n) %

Yes - vaccination 84 28.0
card/ink
Yes - verbal 74 24.7
Vaccination status Cases (n) %

No 76 25.3
Unsure 66 22.0
Total 300 100.0

Cases by illness severity at visit/admission

Illness severity Cases (n) %

Simple 160 53.3
Complicated 140 46.7
Total 300 100.0

Of the patients, 150 (50.0%) were seen as outpatients and 150 (50.0%) were inpatients.
Among inpatients, the median number of days admitted was 20, with a range between 1
and 105 days.
Cases by symptoms
## Note: Using an external vector in selections is ambiguous.
## i Use `all_of(SYMPTOMS)` instead of `SYMPTOMS` to silence this message.
## i See <https://tidyselect.r-lib.org/reference/faq-external-vector.html>.
## This message is displayed once per session.

variable n %
Fever 148 49.3
Cough 156 52.0
Nasal discharge 151 50.3
Croup 147 49.0
Maculopapular rash 163 54.3
Xerophthalmia 135 45.0
Candidiasis 157 52.3
Severe oral lesions 147 49.0
Acute otitis media 162 54.0
Seizure episodes 160 53.3
Encephalitis 147 49.0
Late complications 144 48.0

Case fatality ratio

Of 150 (50.0%) inpatients, there have been 51 (17.0%) deaths, of which 56 (18.7%) were
dead on arrival.
Among inpatients who died, the time to death is shown below.

Time (hours) Deaths (n) %

0-4 hours 14 27.5
>4-24 hours 18 35.3
>24-48 hours 12 23.5
>48 hours 7 13.7
Total 51 100.0

The case fatality ratio among inpatients with known outcomes is below.

Deaths Cases CFR (%) 95%CI

51 150 34 (26.90–41.90)

The case fatality ratio by sex among inpatients with known outcomes is below.

Sex Deaths Cases CFR (%) 95%CI

Male 11 46 23.9 (13.91–
37.94)
Female 14 44 31.8 (20.00–
46.56)
- 26 60 43.3 (31.57–
55.90)
Total 51 150 34.0 (26.90–
41.90)

CFR by age group among inpatients with known outcomes

## Error in `stop_vctrs()`:
## ! Can't convert `replace$ci` <double> to match type of `data$ci`
<character>.

Attack rate
The attack rate per 10,000 population is below (based on available population data
available for the catchment area/region of interest).
Below gives the attack rate per 10,000 population (N = 4,999.5)

Cases (n) AR (per 10,000) 95%CI

300 600.1 (537.54–669.33)

Here, we can see that the attack rate for a population of 4,999.5 was 600.06 (CI 537.54–
669.33).
To give attack rate by age group, with appropriate population denominators, use the
following code.

AR (per
Age group Cases (n) Population 10,000) 95%CI
0-2 7 340.0 205.9 (100.08–
418.81)
3-14 32 1,811.0 176.7 (125.44–
248.38)
15-29 31 1,380.0 224.6 (158.70–
317.09)
30-44 39 808.0 482.7 (355.07–
653.02)
45+ 191 660.5 2,891.7 (2558.97–
3248.91)

Mortality attributable to measles

Mortality rate attributable to measles per 10,000 population

Mortality (per
Deaths Population 10,000) 95%CI
99 4999.5 198 (162.93–240.49)

Crude mortality rate attributable to measles per 10,000 population per day

Mortality (per
Deaths Person-days 10,000/day) 95%CI
99 2619738 0.4 (0.31–0.46)

Mortality rate attributable to measles per 10,000 patients per day

Mortality (per
Deaths Population 10,000/day) 95%CI
99 8928 110.9 (91.17–134.81)

Time
There were 0 (0.0%) cases missing dates of onset.
## Warning: It is deprecated to specify `guide = FALSE` to remove a guide.
Please
## use `guide = "none"` instead.
The peak of the outbreak was in 2018-W16
## Warning: It is deprecated to specify `guide = FALSE` to remove a guide.
Please
## use `guide = "none"` instead.
Cases by week of onset among inpatients by sex
Attack rate per 10,000 population by week

AR (per
Epiweek Cases (n) Population 10,000) 95%CI
2018-W03 1 4999.5 2 (0.35–11.32)
2018-W04 3 4999.5 6 (2.04–17.63)
2018-W05 5 4999.5 10 (4.27–23.39)
2018-W06 3 4999.5 6 (2.04–17.63)
2018-W07 8 4999.5 16 (8.11–31.55)
2018-W08 15 4999.5 30 (18.19–
49.45)
2018-W09 15 4999.5 30 (18.19–
49.45)
2018-W10 15 4999.5 30 (18.19–
49.45)
2018-W11 14 4999.5 28 (16.69–
46.95)
2018-W12 24 4999.5 48 (32.28–
71.33)
 AR (per
Epiweek Cases (n) Population 10,000) 95%CI
2018-W13 28 4999.5 56 (38.78–
80.83)
2018-W14 22 4999.5 44 (29.08–
66.54)
2018-W15 26 4999.5 52 (35.52–
76.09)
2018-W16 40 4999.5 80 (58.81–
108.76)
2018-W17 26 4999.5 52 (35.52–
76.09)
2018-W18 27 4999.5 54 (37.14–
78.46)
2018-W19 13 4999.5 26 (15.20–
44.44)
2018-W20 15 4999.5 30 (18.19–
49.45)

Cumulative attack rate per 10,000 population per week

AR (per
Epiweek Cases (n) Population 10,000) 95%CI
2018-W03 1 4999.5 2.0 (0.35–11.32)
2018-W04 4 4999.5 8.0 (3.11–20.56)
2018-W05 9 4999.5 18.0 (9.47–34.18)
2018-W06 12 4999.5 24.0 (13.74–
41.91)
2018-W07 20 4999.5 40.0 (25.91–
61.71)
2018-W08 35 4999.5 70.0 (50.38–
97.20)
2018-W09 50 4999.5 100.0 (75.95–
131.60)
2018-W10 65 4999.5 130.0 (102.14–
165.36)
2018-W11 79 4999.5 158.0 (126.98–
196.49)
2018-W12 103 4999.5 206.0 (170.17–
249.23)
2018-W13 131 4999.5 262.0 (221.25–
 AR (per
Epiweek Cases (n) Population 10,000) 95%CI
310.07)
2018-W14 153 4999.5 306.0 (261.77–
357.50)
2018-W15 179 4999.5 358.0 (309.99–
413.21)
2018-W16 219 4999.5 438.0 (384.73–
498.36)
2018-W17 245 4999.5 490.0 (433.59–
553.43)
2018-W18 272 4999.5 544.1 (484.53–
610.42)
2018-W19 285 4999.5 570.1 (509.12–
637.79)
2018-W20 300 4999.5 600.1 (537.54–
669.33)

Case fatality ratio as a proportion among inpatients by week

Epiweek Deaths Cases CFR (%) 95%CI

2018-W03 1 1 100.0 (20.65–
100.00)
2018-W04 2 2 100.0 (34.24–
100.00)
2018-W05 1 3 33.3 (6.15–79.23)
2018-W06 0 2 0.0 (0.00–65.76)
2018-W07 4 6 66.7 (30.00–
90.32)
2018-W08 2 5 40.0 (11.76–
76.93)
2018-W09 1 5 20.0 (3.62–62.45)
2018-W10 2 8 25.0 (7.15–59.07)
2018-W11 2 4 50.0 (15.00–
85.00)
2018-W12 7 10 70.0 (39.68–
89.22)
2018-W13 1 16 6.2 (1.11–28.33)
2018-W14 3 11 27.3 (9.75–56.56)
2018-W15 2 13 15.4 (4.33–42.23)
 Epiweek Deaths Cases CFR (%) 95%CI
2018-W16 8 22 36.4 (19.73–
57.05)
2018-W17 6 12 50.0 (25.38–
74.62)
2018-W18 4 14 28.6 (11.72–
54.65)
2018-W19 2 7 28.6 (8.22–64.11)
2018-W20 3 9 33.3 (12.06–
64.58)
Inpatient admissions by case definition and week

Probable Suspected
value (n) % (n) % Total
2018-W03 0 0.0 1 0.9 1
 Probable Suspected
value (n) % (n) % Total
2018-W04 0 0.0 2 1.7 2
2018-W05 1 2.9 2 1.7 3
2018-W06 0 0.0 2 1.7 2
2018-W07 1 2.9 5 4.3 6
2018-W08 1 2.9 4 3.4 5
2018-W09 1 2.9 4 3.4 5
2018-W10 2 5.9 6 5.2 8
2018-W11 0 0.0 4 3.4 4
2018-W12 0 0.0 10 8.6 10
2018-W13 5 14.7 11 9.5 16
2018-W14 3 8.8 8 6.9 11
2018-W15 3 8.8 10 8.6 13
2018-W16 4 11.8 18 15.5 22
2018-W17 5 14.7 7 6.0 12
2018-W18 4 11.8 10 8.6 14
2018-W19 2 5.9 5 4.3 7
2018-W20 2 5.9 7 6.0 9
Total 34 100.0 116 100.0 150

Inpatient discharges by reason for exit and week

Tran
Disch sferr
Wee Died arge Left ed
k (n) % d (n) % (n) % (n) % Total
2018 1 2.0 0 0 0 0.0 0 0.0 1
-W03
2018 2 3.9 0 0 0 0.0 0 0.0 2
-W04
2018 1 2.0 0 0 1 3.8 1 1.9 3
-W05
2018 0 0.0 0 0 0 0.0 2 3.8 2
-W06
2018 4 7.8 0 0 1 3.8 1 1.9 6
-W07
2018 2 3.9 0 0 2 7.7 1 1.9 5
-W08
 Tran
Disch sferr
Wee Died arge Left ed
k (n) % d (n) % (n) % (n) % Total
2018 1 2.0 1 5 1 3.8 2 3.8 5
-W09
2018 2 3.9 2 10 0 0.0 4 7.5 8
-W10
2018 2 3.9 1 5 0 0.0 1 1.9 4
-W11
2018 7 13.7 0 0 2 7.7 1 1.9 10
-W12
2018 1 2.0 4 20 2 7.7 9 17.0 16
-W13
2018 3 5.9 2 10 2 7.7 4 7.5 11
-W14
2018 2 3.9 1 5 3 11.5 7 13.2 13
-W15
2018 8 15.7 3 15 5 19.2 6 11.3 22
-W16
2018 6 11.8 1 5 3 11.5 2 3.8 12
-W17
2018 4 7.8 2 10 2 7.7 6 11.3 14
-W18
2018 2 3.9 1 5 1 3.8 3 5.7 7
-W19
2018 3 5.9 2 10 1 3.8 3 5.7 9
-W20
Total 51 100. 20 100 26 100. 53 100. 150
0 0 0

Place

Descriptive
Cases by region and facility type

Outpatient Inpatient
Region (n) % (n) % Total
Village A 35 23.3 34 22.7 69
Village B 44 29.3 42 28.0 86
Village C 32 21.3 33 22.0 65
 Outpatient Inpatient
Region (n) % (n) % Total
Village D 39 26.0 41 27.3 80
Total 150 100.0 150 100.0 300

Inpatient discharges by reason for exit and region

Tran
Disch sferr
Regi Died arge Left ed
on (n) % d (n) % (n) % (n) % Total
Villa 12 23.5 3 15 5 19.2 14 26.4 34
ge A
Villa 12 23.5 4 20 7 26.9 19 35.8 42
ge B
Villa 13 25.5 5 25 6 23.1 9 17.0 33
ge C
Villa 14 27.5 8 40 8 30.8 11 20.8 41
ge D
Total 51 100. 20 100 26 100. 53 100. 150
0 0 0

Attack rage per 10,000 population by region

AR (per
Region Cases (n) Population 10,000) 95%CI
Village A 69 1,105 624.4 (496.37–
782.81)
Village B 86 870 988.5 (807.47–
1204.81)
Village C 65 1,775 366.2 (288.35–
464.06)
Village D 80 1,225 653.1 (527.85–
805.45)
Mortality rate per 10,000 population by region

Mortality
Region Deaths Population (per 10,000) 95%CI
Village A 22 1105 199.1 (131.84–
299.61)
Village B 26 870 298.9 (204.75–
434.29)
Village C 22 1775 123.9 (81.99–
186.96)
Village D 29 1225 236.7 (165.33–
337.92)
Maps