Characteristics, Effective Reproduction Number (Rt), and Spatial

Modelling of Covid-19 Spread at Magetan District, East Java,

Indonesia

Yudhi Wibowo

, Nendyah Roestijawati

Atik C. Hidajah

Agoes Y. Purnomo

and Tutiek Herlina

Department of Public Health and Community Medicine, Faculty of Medicine, Universitas Jenderal Soedirman,

Purwokerto, Indonesia

Department of Epidemiology, Faculty of Public Health, Airlangga University, Surabaya, Indonesia

District Health Office, Magetan, Indonesia

Poltekes of Health Ministry, Surabaya, Indonesia

Keywords: Characteristics, Effective Reproduction Number (Rt), Spatial Modelling, Covid-19.

Abstract: Covid-19 has been rapidly spreading to various regions in Indonesia including to Magetan District

which has the 3rd highest cases (0.91%) in East Java Province. This study was aimed to determine the

characteristics, effective reproduction number (Rt) and spatial modelling of Covid-19 spread in the Magetan

District. This was a cross-sectional study which included 43 patients with confirmed Covid-19. Univariate

analysis was used to describe the characteristics of Covid-19. Epiestim was used to calculate Rt while the

spread of Covid-19 cases was spatially modelled using Crimestat. On June 28, 2020, Magetan had 96

suspected cases, 104 confirmed cases with 75 cases were recovered and 4 people died. Most of the confirmed

cases were at the age group of 40-49 years (22.6%), male (54%), and symptomatic (91.5%). Fever was the

most commonly found symptom (81.7%). The Rt for the period March 10, 2020-June 28, 2020 was 1.27

(0.85-1.82; 95% CrI). Spatial analysis showed that the distribution of confirmed cases was widespread in 15

sub-districts. The Covid-19 outbreak was still out of control and still ongoing in Magetan. Therefore, a strong

implementation of health protocol is recommended.

1 INTRODUCTION

Corona virus disease-19 (Covid-19) is an infectious

disease caused by Severe Acute Respiratory

Syndrome-Corona Virus-2 (SARS-CoV-2) formerly

known as 2019-nCov. This disease was firstly

identified from 41 cases of pneumonia with unknown

cause in Wuhan, Hubei Province, China on December

30, 2019. It was reported that the disease related to

the contact with the seafood market (Isaac I. Bogoch,

Alexander Watts, Andrea Thomas-Bachli, Carmen

Huber, 2020; Lu, Stratton and Tang, 2020; WHO,

2020a, 2020c).

https://orcid.org/0000-0001-7523-2170

https://orcid.org/0000-0003-4232-062X

https://orcid.org/0000-0002-9797-1887

https://orcid.org/0000-0002-8860-8787

https://orcid.org/0000-0002-4238-9574

On March 11, 2020, World Health Organisation

(WHO) declared a global Covid-19 pandemic due the

rapid increase in the number of cases (13 times) and

affected countries (three times) within two weeks

(Cucinotta and Vanelli, 2020; Sohrabi et al., 2020).

As of May 5, 2020, the Covid-19 pandemic has

spread to 215 countries and territories. Globally there

were 3,525,116 confirmed Covid-19 cases and

243,540 deaths (WHO, 2020b).

While in Indonesia as of May 6, 2020, there were

12,071 confirmed Covid-19 and 872 deaths. East Java

Province is the second epicenter of Covid-19 cases in

Indonesia after DKI Jakarta (Kemenkes R, 2020).

Magetan District had 69 positive people with 4 people

Wibowo, Y., Roestijawati, N., Hidajah, A., Pur nomo, A. and Herlina, T.

Characteristics, Effective Reproduction Number (Rt), and Spatial Modelling of Covid-19 Spread at Magetan District, East Java, Indonesia.

DOI: 10.5220/0010487100210027

In Proceedings of the 1st Jenderal Soedirman International Medical Conference in conjunction with the 5th Annual Scientiﬁc Meeting (Temilnas) Consortium of Biomedical Science Indonesia

(JIMC 2020), pages 21-27

ISBN: 978-989-758-499-2

 2021 by SCITEPRESS – Science and Technology Publications, Lda. All rights reser ved

died which make this district had the third highest

confirmed cases in East Java Province. Furthermore,

Magetan District has relatively high population

mobility due to tourism attractions which increase the

risk of Covid-19 spread in this area.

At present, most countries, including Indonesia,

are preparing for a new normal life, as well as the

Magetan District. WHO has issued public health

criteria to adjust public and social health measures in

the context of Covid-19. According to WHO, the

covid-19 outbreak can be considered as “in

controlled” if the Rt <1 for at least 2 weeks.(World

Health Organisation, 2020) This study aims to

determine the characteristics, effective reproduction

number and spatial modeling of Covid-19 spread in

Magetan District, East Java Province, Indonesia.

2 MATERIALS AND METHODS

2.1 Research Design and Population

This study was an observational study using a cross-

sectional design. This study used secondary data from

the Magetan District Health Office. Suspect and

confirmed cases of Covid-19 between the period of

period March 10 to June 28, 2020 were included in

this study. Suspect and confirmed cases were define

according to WHO definition (WHO. World Health

Organization, 2020).

The sample size was calculated using the

assumptions of (i) level of significant = 0.05, (ii) the

power of the study = 80%, (iii) the case proportion p

= q = 0.5, which yielded a minimum sample size of

43 people. The total sample size included in this study

was 71 confirmed cases and 392 suspected cases. The

data were collected by the Magetan District Health

Office through a survey which include demographic

characteristics, geographical location, date of onset,

symptoms and signs, as well as travel history from /

to outside city.

This study has undergone ethics review and

received ethics approval from Health Research Ethics

Committee, Faculty of Medicine, Jenderal Soedirman

University (Reference number 137/KEPK/VI/2020).

2.2 Data Analysis

The basic characteristics of the confirmed cases were

described according to age group, sex, travel history

to / from out of town, symptoms and signs.

The effective reproduction number (Rt) is an

important parameter to find out whether outbreak

control is effective or additional interventions are

needed (Nishiura and Chowell, 2009). Rt values

represent the number of new secondary cases that are

infected from one infective case at time t. If Rt> 1, the

possibility of disease will become epidemic, if Rt = 1,

the disease becomes endemic and if Rt <1, the

possibility of disease will disappear from circulation

(Camacho et al., 2015). In this study, Rt was

calculated using EpiEstim software based on Excel

developed by Cori et al in 2013(Cori et al., 2013), and

corrected by Thomson et al in 2019 (Thompson et al.,

2019). The mean serial interval (SI) and standard

deviation (SD) from of Tindale et al were used in this

study with the average SI = 4.56 and SD = 0.95

(Tindale et al., 2020).

The standard deviational ellipse (SDE) was used

to analyze trends and patterns of dispersion of

confirmed Covid-19 cases. Standard deviation ellipse

is a summary of central tendency and dispersion in

two dimensions, as well as a directional trend. Two

points were used as the basis for the distribution of

point locations on SDE which were central tendency

and dispersion. Central tendency uses the center of

the mean while dispersion refers to the spread of the

center mean bounded by the ellipse. Standard

deviational ellipse models can be used to gain a better

understanding of the geographical aspects of the

phenomenon and identify the cause of an event, based

on specific geographic patterns (Lai, So and Chan,

2008). The spatial analysis was conducted using

Crimestat software.

3 RESULTS

Magetan District is one of the districts in East Java,

Indonesia. Magetan District consists of 18 sub-

districts and 235 villages with land area of 688.8 km2

and total population of 628,924. During the period

from March 10 to June 28, 2020, there were 104

confirmed cases, and 4 cases died due to covid-19.

The characteristics of 104 confirmed cases when

first treated are presented in Table 1. The confirmed

cases were predominantly at the age group of 15-24

years (30.8%) and male (69.2%). Only 20.2% of

confirmed cases were symptomatic with main

symptoms were cough (12.5%) and fatigue (6.7%).

The proportion of confirmed cases with comorbidities

were 17.3% with pneumonia (8.7%) and hypertension

(5.8%) were the most frequent comorbidities. The

number of deaths among confirmed cases was four

people which resulted in mortality rate of 4.8%. Most

of deaths were occurred at the age of 35-64 years and

3 out of 4 cases had comorbid diseases.

JIMC 2020 - 1’s t Jenderal Soedirman International Medical Conference (JIMC) in conjunction with the Annual Scientiﬁc Meeting

(Temilnas) Consortium of Biomedical Science Indonesia (KIBI )

Table 1: The characteristics of confirmed Covid-19 cases.

Characteristics Recovere

Die

Total

n%n%n %

Gende

Male 4 100 68 68 72 69.2

Female 0 0 32 32 32 30.8

Age Group

0-<5 00222 1.9

5-14 00222 1.9

15-24 0 0 32 32 32 30.8

25-34 0 0 17 17 17 16.3

35-44 2 50 11 11 13 12.5

45-54 1 25 20 20 21 20.2

55-64 1 25 11 11 12 11.5

65-74 00444 3.8

75-84 00111 1

Citizenship

Indonesian 4 100 78 78 82 78.8

Forei

0 0 22 22 22 21.2

toms

Yes 4 100 17 17 21 20.2

No 0 0 83 83 83 79.8

Type of symptoms

Feve

250224 3.8

Histor

of feve

375336 5.8

Cou

h 2 50 11 11 13 12.5

Flue 00333 2.9

Sore throat 00222 1.9

Dyspnoea 3 75 2 2 5 4.8

Shiverin

00111 1

Headache 00111 1

Fati

ue 250557 6.7

Myalgia 00222 1.9

Nauseous vomit 1 25 2 2 3 2.9

Abdominal

ain 125223 2.9

Comorbidities

Yes 3 75 15 15 18 17.3

No 1 25 85 85 86 82.7

Type of comorbidities

Diabetes Mellitus 00333 2.9

ertension 1 25 5 5 6 5.8

Cance

00111 1

Liver diseases 00111 1

COPD 00222 1.9

Tuberculosis 00111 1

Pneumonia 2 50 7 7 9 8.7

The trends of effective reproduction number (Rt)

for the period March 10 to June 28, 2020, is shown in

figure 1. From the calculation, the average Rt during

this period was 1.27 (95% CrI: 0.85-1.82). The trends

of Rt are further detailed in the table 3. In the last 14

days of the the observation period from 15-28 June

2020, the Rt for several days are below 1. However,

the upper bond of the Rt is still above 1 in all of the

observation days.

The results of the spatial modelling of the spread

of covid-19 for the period March-July 2020 in

Magetan district are presented in Table 3 and Figure

2. According to Table 3, it is found that the counter

clockwise shifted from 43.81

○

to 60.10

○

, SD x from

0.02 km to 0.05 km and SD y from 0.08 km to 0.11

km. Based on Figure 2, the trend of the spread is

predicted to be towards the southwest and the

northeast and counter clockwise.

Characteristics, Effective Reproduction Number (Rt), and Spatial Modelling of Covid-19 Spread at Magetan District, East Java, Indonesia

Figure 1: Trends of Effective Reproductive Number (Rt) of Covid-19 in Magetan District, Period March 10 to June 28, 2020.

4 DISCUSSION

Our research aims to determine the characteristics,

effective reproduction number (Rt), and spatial

modeling of Covid-19 spread in Magetan district. The

confirmed cases in Magetan District were

predominantly occurred in the age group of 15-24.

Covid-19 affects individuals in all age groups

(Centers for Disease Control and Prevention, 2020).

The high number of confirmed cases in this age of

group related to outbreak which were happened in the

Islamic boarding school located in Magetan District.

At the beginning of the outbreak, no action has yet

been taken to close the learning activity in school and

resulted to rapid transmission of Covid-19 among the

students. One of the Islamic boarding schools had

students from Malaysia which explain a significant

proportion of the confirmed cases were foreign

citizens. The existence of foreign students with travel

history inside and outside of the city increase the risk

of Covid-19 transmission. Previous study shows that

travelling and people mobility increase the risk of

Covid-19 transmission (Bi et al., 2020).

The confirmed Covid-19 cases in this study were

mostly men which are consistent to the findings in

many studies. Men have higher susceptibility to

Covid-19 likely due to exposure of major risk factor

such as smoking. Furthermore, compare to women,

men have less protection the X chromosome and sex

hormones which play an important role in innate

immunity and adaptation (Jaillon, Berthenet and

Garlanda, 2019; Cai, 2020; Chen et al., 2020).

Table 2: Trends of effective reproductive numbers (Rt) of

covid-19 for the last 14 days.

Onset

Q 5% Median Q 95%

15/06/2020 0.19 0.44 0.87

16/06/2020 0.37 0.76 1.35

17/06/2020 0.60 1.15 1.98

18/06/2020 0.99 1.77 2.88

19/06/2020 1.22 2.12 3.36

20/06/2020 0.98 1.74 2.83

21/06/2020 1.04 1.74 2.72

22/06/2020 0.95 1.56 2.40

23/06/2020 0.92 1.49 2.25

24/06/2020 1.11 1.71 2.50

25/06/2020 1.11 1.69 2.43

26/06/2020 1.01 1.53 2.21

27/06/2020 0.90 1.37 1.98

28/06/2020 0.85 1.27 1.82

In this study, the mortality rate of Covid-19

confirmed cases is 4.7% which is relatively high

compare to global mortality rate. The death cases

were occurred in the age group of 35-64 years and

most of them had comorbidities. Older individual and

individuals with comorbidities such as chronic

disease have been known to have the higher fatality

risk of Covid-19. However, when individuals are 80

years old or older, the risk of fatality are more and

less the same disregard to the presence of

comorbidities (Chen et al., 2020; Onder, Rezza and

Brusaferro, 2020). According to the Centers for

Disease Control and Prevention (CDC), the risk of

fatality is significantly higher for the age group of ≥65

years and for all age groups with comorbidities such

JIMC 2020 - 1’s t Jenderal Soedirman International Medical Conference (JIMC) in conjunction with the Annual Scientiﬁc Meeting

(Temilnas) Consortium of Biomedical Science Indonesia (KIBI )

as chronic lung disease, moderate-severe asthma,

heart disease, and immunocompromised patient

(cancer treatment, smoking, organ transplantation) or

bone marrow, immune deficiency, uncontrolled HIV

/ AIDS, prolonged use of corticosteroids, and other

treatments that weaken the immune system), severe

obesity, diabetes mellitus, chronic kidney disease,

and liver disease, increase the risk of suffering from

severe covid-19.(Centers for Disease Control and

Prevention, 2020)

Table 3: Results of Spatial Modeling of Spread of Covid-19 in Magetan District, Period March-July, 2020.

March April May June July

Sample size 9 46 56 60 122

Clockwise an

le of Y-axis rotation

(

)

43.81 33.90 44.95 43.11 60.10

Ratio of the lon

to the short axis after rotation 4.46 1.87 1.99 1.50 2.17

Standard deviation alon

the new X axes

(

)

0.02 0.03 0.03 0.04 0.05

Standard deviation along the new Y axes (km) 0.08 0.05 0.06 0.06 0.11

X-axes length 0.04 0.06 0.06 0.09 0.10

Y-axes len

th 0.16 0.11 0.12 0.13 0.22

Area of the elli

se defined b

these axes

(

)

0.00 0.00 0.01 0.01 0.02

Standard deviation alon

the X axes

(

)

0.04 0.06 0.06 0.09 0.10

Standard deviation along the Y axes (km) 0.16 0.11 0.12 0.13 0.22

X-axes length for a 2× SDE 0.07 0.11 0.13 0.17 0.20

Y-axes length for a 2× SDE 0.32 0.21 0.25 0.26 0.43

Area of the 2× elli

se defined b

these axes

(

)

0.02 0.02 0.02 0.03 0.07

Figure 2: Results of SDEs Map of Covid-19 in Magetan District, Period March-July, 2020.

The effective reproduction number (Rt) in the last

14 observation days (June 15, 2020 to June 28, 2020)

was still above one. This indicates that the Covid-19

outbreak in Magetan Districs are still not under

controlled (World Health Organisation, 2020).

Spatial modeling of spread covid-19 found that

the prediction of the spread of covid-19 to the

southwest and northeast in a counter clockwise

direction. This can be seen from the results of the

analysis of the standard deviation ellipse (SDE). SDE

and mean center visually form spatial and temporal

movement of disease explicitly. The spatiotemporal

analysis of this disease estimates future disease

patterns based on previous disease trends. This has

Characteristics, Effective Reproduction Number (Rt), and Spatial Modelling of Covid-19 Spread at Magetan District, East Java, Indonesia

implications for policy development and resource

planning according to the groups most at risk (Lai, So

and Chan, 2008). Therefore, efforts to increase

discipline on health protocols such as wearing face

masks properly, maintaining distance from others at

least 1-2 meters, and handwashing regularly. In

addition of that, contact tracing, testing and treatment

need to be continued and improved, as well as

protection for the vulnerable groups.

5 CONCLUSIONS

The covid-19 outbreak in Magetan Districs is still not

under controlled. Therefore, it is still necessary to

strictly implement health protocols and other

prevention efforts. Tracing contacts, testing and

treatment need to be strengthened as well as effort to

protect the vulnerable groups.

ACKNOWLEDGEMENTS

The authors thank hhe Institute for Research and

Community Service, Faculty of Medicine, Jenderal

Sudirman University, and Magetan District Health

Office for their cooperation and assistance.

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