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. 2022 May 12;17(5):e0268241. doi: 10.1371/journal.pone.0268241

Prevalence and epidemiological characteristics of COVID-19 after one year of pandemic in Jakarta and neighbouring areas, Indonesia: A single center study

Wuryantari Setiadi 1, Ismail Ekoprayitno Rozi 1, Dodi Safari 1, Wa Ode Dwi Daningrat 1, Edison Johar 1, Benediktus Yohan 1, Frilasita Aisyah Yudhaputri 1, Karina Dian Lestari 1, Sukma Oktavianthi 1, Khin Saw Aye Myint 1, Safarina G Malik 1, Amin Soebandrio 1,2,*; on behalf of the Wascove team
Editor: Rizaldy Taslim Pinzon3
PMCID: PMC9098020  PMID: 35550635

Abstract

We determined the prevalence and epidemiological characteristics of COVID-19 in Jakarta and neighboring areas, Indonesia from March 2020 to February 2021, based on nasopharyngeal/oropharyngeal (NP/OP) swab specimens that were tested at the Eijkman Institute for Molecular Biology, Jakarta. NP/OP swab specimens were collected from COVID-19 suspects or individuals in contact tracing programs from primary healthcare centers (PHC) and hospitals. The specimens were screened for the SARS-CoV-2 by qRT-PCR. Demography data and clinical symptoms were collected using national standardized laboratory form. Of 64,364 specimens, 10,130 (15.7%) were confirmed positive for SARS-CoV-2, with the peak prevalence of infection in March 2020 (26.3%) follow by in January 2021 (23.9%) and February 2021 (21.8%). We found that the positivity rate of the specimens from Jakarta, West Java, and Banten was 16.3%, 13.3%, and 16.8%, respectively. Positivity rate was higher in specimens from hospitals (16.9%) than PHC (9.4%). Of the positive specimens, 29.6% were from individuals aged >60 years old, followed by individuals aged 41–60 years old (24.2%). Among symptomatic cases of SARS-CoV-2, the most common symptoms were cough, fever, and a combination of both cough & fever. In conclusion, this study illustrates the prevalence and epidemiological characteristics from one COVID-19 diagnostic center in Jakarta and neighbouring areas in Indonesia.

Introduction

SARS-CoV-2 infection was first reported in 2019, and has since spread throughout the world causing more than 208,470,375 COVID-19 cases and 4,377,979 deaths globally, as of August 18, 2021 [1]. Indonesia confirmed the first positive COVID-19 case on March 2, 2020 [2]. Within 40 days, COVID-19 cases were reported by all provinces [3]. As of August, 2021, Indonesia had 3,892,479 confirmed COVID-19 cases, with 120,013 deaths [4].

In the early phase of COVID-19 pandemic, besides the vast territory, Indonesia was also challenged with limited laboratory infrastructure and capacity for COVID-19 diagnosis. Lack of test reagents, consumables, personal protective equipment, and shortage of human resources further exacerbated the situation [5–7]. The recent emergence of more transmissible variants, such as the Alpha and Delta variants, put an additional burden on the government effort to contain COVID-19 [8,9].

Eijkman Institute for Molecular Biology (EIMB) in Jakarta, Indonesia, was appointed by the Indonesian Ministry of Health as one of the regional laboratories to test for SARS-CoV-2 [5]. Since then, over 69,000 specimens have been submitted from primary healthcare centers (PHC) and hospitals mainly from Jakarta and neighboring areas. In this study, we reported the prevalence and epidemiological characteristics of COVID-19 cases from samples tested in EIMB from March 2020 to February 2021.

These findings could contribute to the diagnostic, preventive and curative measures of COVID-19 pandemic in Indonesia.

Materials and method

Study design and data collection

This was a retrospective study using of SARS-CoV-2 surveillance data conducted at EIMB, Jakarta as one of the referral laboratories for SARS-CoV-2 testing in Indonesia. This study was performed in accordance with the human subject protection guidance provided by the Eijkman Institute Research Ethics Committee No. 127. All data were fully anonymized before accessing the database. Nasopharyngeal/oropharyngeal (NP/OP) swabs, sputum, and serum specimens were submitted by PHCs and hospitals in Jakarta Province (n = 25,314) and neighbouring areas in Indonesia including Banten Province (Tangerang [n = 11,901], South Tangerang [n = 4,519], and Serang [n = 6], West Java Province (Bekasi [n = 11,385], Bogor [n = 5,577], Depok [n = 3,865], Purwakarta [n = 162], Karawang [n = 114], Bandung [n = 4]). We also received a number of specimens from other provinces such as North Sulawesi (n = 1,324), South Sulawesi (n = 11), Riau (n = 3), Papua (n = 5), East Nusa Tenggara (n = 82), Lampung (n = 261), East Kalimantan (n = 1), Central Kalimantan (n = 50), Central Java (n = 8), Jambi (n = 18), Yogyakarta (n = 6), and Bali (n = 1).

All NP/OP swab specimens were tested for SARS-CoV-2 by quantitative reverse-transcription-polymerase chain reaction (qRT-PCR) assay based on Charité Institute of Virology Universitätsmedizin Berlin (modified), US-Centers for Disease Control (modified), and Hong Kong University, in accordance with WHO, or with Cobas® 6800 automated nucleic acid test system (Roche USA) [10–12]. Demographic and clinical data were collected using national standard laboratory form that include symptom onset date, specimen collection date, contact history in the past 14 days, clinical manifestations, underlying health conditions, contact tracing, and community screening. Symptoms or clinical manifestation were defined based on self-reported symptoms by subjects except for pneumonia. Chest X-Ray results were used to defined pneumonia [13,14]

Data analysis

Statistical analyses were carried out in Stata Software. Univariate analysis using Pearson’s Chi-Square or Fisher’s exact test was performed to determined factors associated with the COVID-19 positive cases. Association between symptoms with age and gender were performed using Pearson’s Chi-Square. Stratification analysis was performed to compare symptoms between samples acquired from hospitals and PHCs. Multivariate analysis was performed to identify factors associated with the COVID-19 positive cases, and controlled in fitted model using multiple logistic regression.

Results

From March 12, 2020, to February 26, 2021, a total of 64,364 NP/OP swab specimens were tested at the EIMB for SARS-CoV-2 nucleic acid test from health facilities in Jakarta, neighbouring areas and other provinces (Fig 1). The majority of the specimens were from three provinces: Jakarta (n = 25,174; 39.1%), West Java (n = 20,993; 32.6%), and Banten (n = 16,394; 25.5%) (Fig 1). Most of the NP/OP swab specimens were collected from hospital (n = 54,372; 84.5%) and followed by PHC (n = 8,701; 13.5%). NP/OP swabs from Provincial and District Health Offices, Private Clinics and Laboratories were accounted for 2.0% of all specimens (n = 1,258) (Table 1). We identified, 95.5% of specimens were from adults aged >18 years old (n = 61,403), and 61.6% (n = 39,477) were from females.

Fig 1. NP/OP swab specimens were submitted to EIMB form health facilities in different regions of Indonesia from March 2020 –February 2021.

Fig 1

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The majority of the specimens were from three provinces: Jakarta (n = 25,314; 39.2%) followed by West Java especially Bogor, Bekasi, and Depok (n = 21,107; 32.6%), and Banten especially South Tangerang and Tangerang (n = 16,426; 25.4%). (https://www.naturalearthdata.com/).

Table 1. Demographics and characteristics of COVID-19 suspects, or individuals in contact tracing program with eligible specimens collected at EIMB, from March 2020 to February 2021.

Variables Category SARS-CoV-2 crude OR (95% CI) p-Value Adjusted OR (95% CI) p-Value
Positive Negative % Positive
Age
0–5 126 1,021 11.0% ref ref ref ref
6–18 271 1,445 15.8% 1.5 (1.2–1.9) <0.001 2.1 (1.0–4.3) 0.053
19–40 4,676 36,751 11.3% 1.0 (0.9–1.2 0.750 1.6 (0.8–3.1) 0.215
41–60 3,899 12,214 24.2% 2.6 (2.1–3.1) <0.001 3.3 (1.7–6.7) 0.001
>60 1,143 2,720 29.6% 3.4 (2.8–4.1) <0.001 3.7 (1.8–7.5) <0.001
Gender
Female 5,527 33,950 14.0% ref ref ref ref
Male 4,549 20,068 18.5% 1.4 (1.3–1.5) <0.001 1.2 (1.1–1.2) <0.001
Occupation
Healthcare Workers 1,348 17,095 7.3% ref ref ref ref
Non-Healthcare Worker 3,508 16,219 17.8% 2.7 (2.6–2.9) <0.001 2.6 (2.4–2.8) <0.001
Type of Facilities
PHC 814 7,887 9.4% ref ref ref ref
Hospital 9,176 45,196 16.9% 2.0 (1.8–2.1) <0.001 4.1 (3.6–4.7) <0.001
Other * 138 1,120 11.0% 1.2 (1.0–1.4) 0.069 1.5 (1.0–2.1) 0.043
Province
Jakarta 4,111 21,063 16.3% 3.0 (2.0–4.5) <0.001 ref ref
Banten 2,182 14,212 13.3% 2.4 (1.6–3.5) <0.001 2.9 (1.8–4.7) <0.001
West Java 3,518 17,475 16.8% 3.1 (2.1–4.6) <0.001 2.3 (1.4–3.8) 0.001
North Sulawesi 290 1,034 21.9% 4.4 (2.9–6.6) <0.001 2.7 (1.7–4.4) <0.001
  Other # 27 419 6.1% ref ref 1.9 (0.2–16.6) 0.543
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*Provincial & District Health Offices, Clinic Laboratorium.

#Lampung, Bali, DI Yogyakarta, Jambi, Central Java, Central Kalimantan, East Kalimantan, East Nusa Tenggara, Papua, Riau, South Sulawesi and North Sumatera.

Of the 64,364 swab specimens tested, 15.7% (n = 10,130) were positive for SARS-CoV-2. The percentage of COVID-19 positive cases varied from March 2020 to February 2021 (Fig 2). The highest positive rate were observed in the first month of the pandemic (March 2020; 652/2,481; 26.3%) followed by early 2021 (January 2021; 1,543/6,415; 24.1%, and February 2021; 1,039/4,757; 21.8%). The lowest percentage of positive case was observed in May 2020 (134/2,952; 4.5%) followed by the month of June 2020 (522/8,773; 6.0%), and July 2020 (801/7,798; 10,3%) (Fig 2).

Fig 2. SARS-CoV-2 positivity rate during the first year of pandemic in Jakarta, neighbouring areas, and other provinces in Indonesia from March 2020 –February 2021.

Fig 2

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The positive rate for COVID-19 was higher in >60 years of age group (1,143/3,863; 29.6%) followed by 41–60 years of age group (3,899/16,113; 24.2%) (Table 1). The lowest COVID-19 positive rate was observed in children under five (126/1,147; 11.0%) as compared to other age groups (Table 1). the specimens collected from hospitals had higher COVID-19 positivity rate (9,176/54,372; 16.9%) compared to PHC (814/8,701; 9.4%). (Table 1).

Chest X-ray data were available from 845 out of 10130 positive cases, which were reported as: pneumonia 679/845 (80.4%), other abnormalities (including bronchitis, pleural effusion, lung abscess, and increased bronchovascular markings) 46/845 (5.4%), and normal 120/845 (14.2%). Most of SARS-CoV-2 cases were asymptomatic (74.0%). Among symptomatic cases of SARS-CoV-2, we found that the most common reported clinical symptoms (or combination of symptoms) (n = 1,577) were cough (20.9%), a combination of both cough & fever (7.0%), and fever (6.8%) (Fig 3).

Fig 3. Most common symptoms among PCR confirmed SARS-CoV-2 subjects in Indonesia from March 2020 –February 2021.

Fig 3

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Chest X-Ray results were used to defined pneumonia.

Subjects aged above 60 years old had a 3.4-fold higher risk of COVID-19 compare to other age groups (95% confidence interval (CI): 2.8–4.1). This followed by subjects aged 41–60 years old with odds ratio (OR) = 2.6 (95%CI: 2.1–3.1). In a fitted model, these results were consistently increased with ORs of 3.7 (95%CI 1.8–7.5) and 3.3 (95%CI 1.7–6.7), respectively. In this analysis, non-healthcare workers showed a 2.7-fold increase in the risk to COVID-19 than healthcare workers (95% CI: 2.6–2.9). When controlled with other factors in a fitted model, the odds were slightly lower with OR 2.6 (95% CI: 2.4–2.8). Hospital-based specimens have higher positive results of SARS-CoV-2 compare to those from PHC or private clinics or laboratories with OR 2.0 (95%CI: 1.8–2.1). The odds were doubled when other factors were considered with OR 4.1 (95%CI: 3.6–4.7).

Discussion

In this study, we described prevalence and epidemiological characteristic of COVID-19 in Jakarta, and its surrounding areas after the COVID-19 first case was confirmed in Indonesia in March 2020. As one of the appointed laboratories for COVID-19 detection, we tested more than sixty thousand NP/OP swab specimens from COVID-19 suspects or individuals under contact tracing program within the first year of the pandemic. A proportion of 15.7% of those specimens were positive for the COVID-19 positivity rates range from 4.5% (May 2020) to 26.5% (March 2020). As per 22 August 2021, The National Committee for Corona Virus Disease 2019 Handling and Economic Recovery (Komite Penanganan Covid-19 dan Pemulihan Ekonomi Nasional) reported that the five provinces with the highest COVID-19 confirmed cases (as % of the total national cases) are: Jakarta (21.3%), West Java (16.8%), Central Java (11.6%), East Java (9.4%), and East Kalimantan (3.7%) [15]. These provinces contributed to over 60% of the national cases six months after the COVID-19 pandemic [3,15].

In this study, we found that the lowest positive rate of COVID-19 was in May 2020 (4.5%). We suggest this condition was due to strict implementation of the public health social measures including the mask wearing, mobility restriction, and school or business closure [4]. In addition, the observance of Ramadan session which started on 23 April 2020 to 23 May 2020 is also possible to contribute to the decrease of the positivity rate. After Ramadan, however, the COVID-19 positivity rate started to raise again from 6% in June to 17% in December 2020. Although the Government has made efforts to limit holidays and travel to other cities during the holiday season and New Year’s celebrations, the positive rate of COVID-19 increased in the month of January and February 2021 to 23.9% and 21.4%, respectively. As reported previously, COVID-19 cases started to increase one or two weeks following holiday sessions [16].

In this study, we also found that the subjects aged over 40 years old had a higher positive rate of COVID-19 than other age groups, while a lower positive rate of COVID-19 were observed in children under the age of five. This finding is in line with other studies which reported that the older age group is more prone to COVID-19 compare to the younger age group [3,17,18]. In recent report from hospitals in Jakarta, Indonesia, the age-specific mortalities due to COVID-19 infection were 11% for <5 years, 2.5% for 5–19 years, 7.9% for 20–60 years, and 25.5% for >60 years [14,18]. Several probabilities which affect transmission in children include having fewer outdoor activities, no face-to-face school learning, and undertaking less domestic and international travel making this age group less likely to contract the virus [19]. Since March 17, 2020, most of schools and universities in Indonesia have applied the full distance learning [20].

We found that non-healthcare workers have higher risk of COVID-19 compared to healthcare workers with the odds of COVID-19 for non-healthcare workers were almost triple the risk of healthcare workers. Positivity rates are likely affected by the nature of the individuals tested, as shown by the higher positivity rates from hospital-based specimens compared to PHC-sourced specimens. For hospitals, the majority of the samples were collected from COVID-19 suspected individuals. On the other hand, PHC samples were mostly obtained from individuals under contact tracing in collaboration with local health agency. Moreover, the Indonesian government have started to vaccinate the population since mid-January 2021 by prioritizing frontline medical and public workers as well as older age group. More than 50 million people had received first dose, and half of them had received the second dose of COVID-19 vaccine per August 15, 2021 [15]. This warrant further studies to describe the prevalence of COVID-19 after the mass vaccination campaign. There are some limitations to our study: This study was a retrospective assessment on data of specimens submitted for routine hospital COVID-19 contact tracing and there were missing data including symptoms and patient outcome, that could alter the characteristic of COVID-19 data presentation. This study we provided data in the early of pandemic when testing capacity still limited. The data we have collected during the past year could be used to picture the overall prevalence of COVID-19 in Indonesia, and also as a baseline in evaluating the development of this pandemic in Indonesia.

Acknowledgments

We thank multiple health facilities in different regions of Indonesia for submitting respiratory specimens.

We also thank the WASCOVE (Waspada COVID-19 Lembaga Biologi Molekuler Eijkman) team, composed by:

Lead author: Wuryantari Setiadi tari@eijkman.go.id.

Eijkman Institute for Molecular Biology, Jakarta: AA Raka Pratama, Agatha Mia Puspitasari, Ageng Wiyatno, Aghnianditya Kresno Dewantari, Ari Satyagraha, Arkasha Sadewa, Bertha Letizia Utami, Billy Witanto, Chairin Nisa Ma’roef, Chelzie Crenna Darusallam, Chrysantine Paramayuda, Clarissa Asha Febinia, Decy Subekti, Dendi Hadi Permana, Dhita Prabasari Wibowo, Eva Maria Manullang, Evira Cahya Putri, Faiza Az Zahra, Farahana Kresno Dewayanti, Fauzyah Fadlan, Firman Prathama Idris, Gladis R. Hutahaen, Hanifah Fajri Maharani Putri, Hannie Dewi Hadiani Kartapradja, Herawati Sudoyo, Hidayat Trimarsanto, I Made Artika, Indah Delima, Iskandar Alisyahbana Adnan, Jessica Rodearni Saragih, Kartika Saraswati, Korrie Salsabila, Leily Trianty, Lenny Lia Ekawati, Leonard, Leppa Shahrani, Lidwina Priliani, Lydia Visita Pangalo, Marsha S. Santoso, Miftahuddin Majid Khoeri, Muhammad Rezki Razak, Novi Dwi Susilowati, Nunung Nuraini, Rahmadania Marita Joesoef", Rifqi Risandi, Ristya Amalia, Saraswati Soebianto, Sinta Hamidatus Saidah, Tina Kusumaningrum, Ungke Antonjaya, Willy Agustine, Winahyu Handayani, Windy Joanmawanti, Wisiva Tofriska Paraimaswari, Wisnu Tafroji, Yayah Winarti, Yora Permata Dewi, Yulia Widyasanty

Data Availability

All relevant data are within the manuscript.

Funding Statement

This work was supported by The Ministry of Research and Technology/National Research and Innovation Agency, Republic of Indonesia. The PCR reagents to test outbreak specimens were provided by U.S. Centers for Disease Control and Prevention (US CDC), Indonesian National Board for Disaster Management (Badan Nasional Penanggulangan Bencana; BNPB), Embassy of New Zealand in Indonesia, and Indonesian States Intelligence Agency (Badan Intelijen Negara Republik Indonesia; BIN). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

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Decision Letter 0

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14 Feb 2022

PONE-D-21-28166Prevalence and epidemiological characteristics of COVID-19 after one year of pandemic in Jakarta and neighbouring areas, Indonesia: A single center studyPLOS ONE

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Please include your amended statements within your cover letter; we will change the online submission form on your behalf.

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“This work was supported by The Ministry of Research and Technology/National Research and Innovation Agency, Republic of Indonesia. The PCR reagents to test outbreak specimens were provided by U.S. Centers for Disease Control and Prevention (US CDC), Indonesian National Board for Disaster Management (Badan Nasional Penanggulangan Bencana; BNPB), Embassy of New Zealand in Indonesia, and Indonesian States Intelligence Agency (Badan Intelijen Negara Republik Indonesia; BIN).”

Please state what role the funders took in the study.  If the funders had no role, please state: ""The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.""

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Please include this amended Role of Funder statement in your cover letter; we will change the online submission form on your behalf.

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6. Please include your full ethics statement in the ‘Methods’ section of your manuscript file. In your statement, please include the full name of the IRB or ethics committee who approved or waived your study, as well as whether or not you obtained informed written or verbal consent. If consent was waived for your study, please include this information in your statement as well.

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The following resources for replacing copyrighted map figures may be helpful:

USGS National Map Viewer (public domain): http://viewer.nationalmap.gov/viewer/

The Gateway to Astronaut Photography of Earth (public domain): http://eol.jsc.nasa.gov/sseop/clickmap/

Maps at the CIA (public domain): https://www.cia.gov/library/publications/the-world-factbook/index.html and https://www.cia.gov/library/publications/cia-maps-publications/index.html

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Please review your reference list to ensure that it is complete and correct. If you have cited papers that have been retracted, please include the rationale for doing so in the manuscript text, or remove these references and replace them with relevant current references. Any changes to the reference list should be mentioned in the rebuttal letter that accompanies your revised manuscript. If you need to cite a retracted article, indicate the article’s retracted status in the References list and also include a citation and full reference for the retraction notice.

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Comments to the Author

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Reviewer #1: Yes

**********

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Reviewer #1: Yes

**********

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Reviewer #1: Yes

**********

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Please use the space provided to explain your answers to the questions above. You may also include additional comments for the author, including concerns about dual publication, research ethics, or publication ethics. (Please upload your review as an attachment if it exceeds 20,000 characters)

Reviewer #1: Mr. Amin Soebandrio, M, PhD.

please make the correction of no of specimen. Refer the no of specimens in abstract and No. of specimens in line no 102,

please add a comma between fever and cough in line no 127

**********

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Reviewer #1: No

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PLoS One. 2022 May 12;17(5):e0268241. doi: 10.1371/journal.pone.0268241.r002

Author response to Decision Letter 0

20 Mar 2022

Rebuttal Letter

1. There are some suggestion for revision in the text.

RESPONSE: Thank you for your suggestion. We revised it

2. Please follow the instruction from the reviewer.

RESPONSE: We revised it based on the instruction from the reviewer

3. Please add the novelty and limitation in your study in the discussion section.

RESPONSE: Thank you for your suggestion. We add the novelty and limitation in our study in the discussion section as below (Line 191-198):

…..”There are some limitations to our study: This study was a retrospective assessment on data of specimens submitted for routine hospital COVID-19 contact tracing and there were missing data including symptoms and patient outcome, that could alter the characteristic of COVID-19 data presentation. This study we provided data in the early of pandemic when testing capacity still limited. The data we have collected during the past year could be used to picture the overall prevalence of COVID-19 in Indonesia, and also as a baseline in evaluating the development of this pandemic in Indonesia”…..

4. In the ethics statement in the manuscript and in the online submission form, please provide additional information about the patient records used in your retrospective study, including: a) whether all data were fully anonymized before you accessed them. If the ethics committee waived the need for informed consent, or patients provided informed written consent to have data from their medical records used in research, please include this information.

RESPONSE: We add the ethics statement and the patient records used in the manuscript as below (Line 74-76):

…..” This study was performed in accordance with the human subject protection guidance provided by the Eijkman Institute Research Ethics Committee No. 127. All data were fully anonymized before accessing the database.”…..

5. Thank you for stating the following in the Acknowledgments Section of your manuscript:

“This work was supported by The Ministry of Research and Technology/National Research and Innovation Agency, Republic of Indonesia. The PCR reagents to test outbreak specimens were provided by U.S. Centers for Disease Control and Prevention (US CDC), Indonesian National Board for Disaster Management (Badan Nasional Penanggulangan Bencana; BNPB), Embassy of New Zealand in Indonesia, and Indonesian States Intelligence Agency (Badan Intelijen Negara Republik Indonesia; BIN).” We note that you have provided funding information that is not currently declared in your Funding Statement. However, funding information should not appear in the Acknowledgments section or other areas of your manuscript. We will only publish funding information present in the Funding Statement section of the online submission form. Please remove any funding-related text from the manuscript and let us know how you would like to update your Funding Statement. Currently, your Funding Statement reads as follows:

“This work was supported by The Ministry of Research and Technology/National Research and Innovation Agency, Republic of Indonesia. The PCR reagents to test outbreak specimens were provided by U.S. Centers for Disease Control and Prevention (US CDC), Indonesian National Board for Disaster Management (Badan Nasional Penanggulangan Bencana; BNPB), Embassy of New Zealand in Indonesia, and Indonesian States Intelligence Agency (Badan Intelijen Negara Republik Indonesia; BIN).” Please include your amended statements within your cover letter; we will change the online submission form on your behalf.

RESPONSE: Thank you for your suggestion. We add our amended statements within our cover letter.

Financial Disclosure:

This work was supported by The Ministry of Research and Technology/National Research and Innovation Agency, Republic of Indonesia. The PCR reagents to test outbreak specimens were provided by U.S. Centers for Disease Control and Prevention (US CDC), Indonesian National Board for Disaster Management (Badan Nasional Penanggulangan Bencana; BNPB), Embassy of New Zealand in Indonesia, and Indonesian States Intelligence Agency (Badan Intelijen Negara Republik Indonesia; BIN). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript

6. Thank you for stating the following financial disclosure:

“This work was supported by The Ministry of Research and Technology/National Research and Innovation Agency, Republic of Indonesia. The PCR reagents to test outbreak specimens were provided by U.S. Centers for Disease Control and Prevention (US CDC), Indonesian National Board for Disaster Management (Badan Nasional Penanggulangan Bencana; BNPB), Embassy of New Zealand in Indonesia, and Indonesian States Intelligence Agency (Badan Intelijen Negara Republik Indonesia; BIN).”

Please state what role the funders took in the study. If the funders had no role, please state: ""The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript."" If this statement is not correct you must amend it as needed. Please include this amended Role of Funder statement in your cover letter; we will change the online submission form on your behalf.

7. RESPONSE: Thank you for your suggestion. We add our amended statements within our cover letter.

Financial Disclosure:

This work was supported by The Ministry of Research and Technology/National Research and Innovation Agency, Republic of Indonesia. The PCR reagents to test outbreak specimens were provided by U.S. Centers for Disease Control and Prevention (US CDC), Indonesian National Board for Disaster Management (Badan Nasional Penanggulangan Bencana; BNPB), Embassy of New Zealand in Indonesia, and Indonesian States Intelligence Agency (Badan Intelijen Negara Republik Indonesia; BIN). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript

One of the noted authors is a group or consortium [Wascove team]. In addition to naming the author group, please list the individual authors and affiliations within this group in the acknowledgments section of your manuscript. Please also indicate clearly a lead author for this group along with a contact email address.

RESPONSE: Membership of the Wascove team is provided in the Acknowledgments.

“We also thank the WASCOVE (Waspada COVID-19 Lembaga Biologi Molekuler Eijkman) team, composed by:

Lead author: Wuryantari Setiadi tari@eijkman.go.id

Eijkman Institute for Molecular Biology, Jakarta: AA Raka Pratama, Agatha Mia Puspitasari, Ageng Wiyatno, Aghnianditya Kresno Dewantari, Ari Satyagraha, Arkasha Sadewa, Bertha Letizia Utami, Billy Witanto, Chairin Nisa Ma'roef, Chelzie Crenna Darusallam, Chrysantine Paramayuda, Clarissa Asha Febinia, Decy Subekti, Dendi Hadi Permana, Dhita Prabasari Wibowo, Eva Maria Manullang, Evira Cahya Putri, Faiza Az Zahra, Farahana Kresno Dewayanti, Fauzyah Fadlan, Firman Prathama Idris, Gladis R. Hutahaen, Hanifah Fajri Maharani Putri, Hannie Dewi Hadiani Kartapradja, Herawati Sudoyo, Hidayat Trimarsanto, I Made Artika, Indah Delima, Iskandar Alisyahbana Adnan, Jessica Rodearni Saragih, Kartika Saraswati, Korrie Salsabila, Leily Trianty, Lenny Lia Ekawati, Leonard, Leppa Shahrani, Lidwina Priliani, Lydia Visita Pangalo, Marsha S. Santoso, Miftahuddin Majid Khoeri, Muhammad Rezki Razak, Novi Dwi Susilowati, Nunung Nuraini, Rahmadania Marita Joesoef", Rifqi Risandi, Ristya Amalia, Saraswati Soebianto, Sinta Hamidatus Saidah, Tina Kusumaningrum, Ungke Antonjaya, Willy Agustine, Winahyu Handayani, Windy Joanmawanti, Wisiva Tofriska Paraimaswari, Wisnu Tafroji, Yayah Winarti, Yora Permata Dewi, Yulia Widyasanty”

8. Please include your full ethics statement in the ‘Methods’ section of your manuscript file. In your statement, please include the full name of the IRB or ethics committee who approved or waived your study, as well as whether or not you obtained informed written or verbal consent. If consent was waived for your study, please include this information in your statement as well.

RESPONSE: We add the ethics statement and the patient records used in the manuscript as below (Line 74-76):

…..” This study was performed in accordance with the human subject protection guidance provided by the Eijkman Institute Research Ethics Committee No. 127. All data were fully anonymized before accessing the database.”…..

9. We note that [Figure 1 ] in your submission contain [map/satellite] images which may be copyrighted. All PLOS content is published under the Creative Commons Attribution License (CC BY 4.0), which means that the manuscript, images, and Supporting Information files will be freely available online, and any third party is permitted to access, download, copy, distribute, and use these materials in any way, even commercially, with proper attribution. For these reasons, we cannot publish previously copyrighted maps or satellite images created using proprietary data, such as Google software (Google Maps, Street View, and Earth). For more information, see our copyright guidelines: http://journals.plos.org/plosone/s/licenses-and-copyright.

We require you to either (1) present written permission from the copyright holder to publish these figures specifically under the CC BY 4.0 license, or (2) remove the figures from your submission: You may seek permission from the original copyright holder of Figure 1 to publish the content specifically under the CC BY 4.0 license. We recommend that you contact the original copyright holder with the Content Permission Form (http://journals.plos.org/plosone/s/file?id=7c09/content-permission-form.pdf) and the following text: “I request permission for the open-access journal PLOS ONE to publish XXX under the Creative Commons Attribution License (CCAL) CC BY 4.0 (http://creativecommons.org/licenses/by/4.0/). Please be aware that this license allows unrestricted use and distribution, even commercially, by third parties. Please reply and provide explicit written permission to publish XXX under a CC BY license and complete the attached form.” Please upload the completed Content Permission Form or other proof of granted permissions as an ""Other"" file with your submission. In the figure caption of the copyrighted figure, please include the following text: “Reprinted from [ref] under a CC BY license, with permission from [name of publisher], original copyright [original copyright year].”

If you are unable to obtain permission from the original copyright holder to publish these figures under the CC BY 4.0 license or if the copyright holder’s requirements are incompatible with the CC BY 4.0 license, please either i) remove the figure or ii) supply a replacement figure that complies with the CC BY 4.0 license. Please check copyright information on all replacement figures and update the figure caption with source information. If applicable, please specify in the figure caption text when a figure is similar but not identical to the original image and is therefore for illustrative purposes only.The following resources for replacing copyrighted map figures may be helpful:

USGS National Map Viewer (public domain): http://viewer.nationalmap.gov/viewer/

The Gateway to Astronaut Photography of Earth (public domain): http://eol.jsc.nasa.gov/sseop/clickmap/

Maps at the CIA (public domain): https://www.cia.gov/library/publications/the-world-factbook/index.html and https://www.cia.gov/library/publications/cia-maps-publications/index.html

NASA Earth Observatory (public domain): http://earthobservatory.nasa.gov/

Landsat: http://landsat.visibleearth.nasa.gov/

USGS EROS (Earth Resources Observatory and Science (EROS) Center) (public domain): http://eros.usgs.gov/#

Natural Earth (public domain): http://www.naturalearthdata.com/

RESPONSE: We revised the Figure 1 to meet to meet PLOS ONE's guidelines using http://www.naturalearthdata.com/

10. Please review your reference list to ensure that it is complete and correct. If you have cited papers that have been retracted, please include the rationale for doing so in the manuscript text, or remove these references and replace them with relevant current references. Any changes to the reference list should be mentioned in the rebuttal letter that accompanies your revised manuscript. If you need to cite a retracted article, indicate the article’s retracted status in the References list and also include a citation and full reference for the retraction notice.

[Note: HTML markup is below. Please do not edit.]

RESPONSE: We reviewed our reference list. We confirmed that is complete and correct

11. Reviewer #1: Mr. Amin Soebandrio, M, PhD.

please make the correction of no of specimen. Refer the no of specimens in abstract and No. of specimens in line no 102,

RESPONSE: We revised it

12. please add a comma between fever and cough in line no 127

RESPONSE: We revised it

Attachment

Submitted filename: response to reviewers.docx

Click here for additional data file. (19.5KB, docx)

Decision Letter 1

Rizaldy Taslim Pinzon

4 Apr 2022

PONE-D-21-28166R1Prevalence and epidemiological characteristics of COVID-19 after one year of pandemic in Jakarta and neighbouring areas, Indonesia: A single center studyPLOS ONE

Dear Dr.  Amin Soebandrio 

Thank you for submitting your manuscript to PLOS ONE. After careful consideration, we feel that it has merit but does not fully meet PLOS ONE’s publication criteria as it currently stands. Therefore, we invite you to submit a revised version of the manuscript that addresses the points raised during the review process. Some minor revision and clarification: The data in the text mention that : The province that contribute for more than 60% cases are Jakarta (21.3%), West Java (16.8%), Central Java (11.6%), East Java (9.4%), and East Kalimantan (3.7%). The figure 1 do not showed any data from East Kalimantan. Please add not only symptoms, but also radiological finding for pneumonia in the text and figure 3. 

Please submit your revised manuscript by 10 April 2022. If you will need more time than this to complete your revisions, please reply to this message or contact the journal office at plosone@plos.org. When you're ready to submit your revision, log on to https://www.editorialmanager.com/pone/ and select the 'Submissions Needing Revision' folder to locate your manuscript file.

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If you would like to make changes to your financial disclosure, please include your updated statement in your cover letter. Guidelines for resubmitting your figure files are available below the reviewer comments at the end of this letter.

If applicable, we recommend that you deposit your laboratory protocols in protocols.io to enhance the reproducibility of your results. Protocols.io assigns your protocol its own identifier (DOI) so that it can be cited independently in the future. For instructions see: https://journals.plos.org/plosone/s/submission-guidelines#loc-laboratory-protocols. Additionally, PLOS ONE offers an option for publishing peer-reviewed Lab Protocol articles, which describe protocols hosted on protocols.io. Read more information on sharing protocols at https://plos.org/protocols?utm_medium=editorial-emailutm_source=authorlettersutm_campaign=protocols.

We look forward to receiving your revised manuscript.

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Rizaldy Taslim Pinzon

Academic Editor

PLOS ONE

Journal Requirements:

Please review your reference list to ensure that it is complete and correct. If you have cited papers that have been retracted, please include the rationale for doing so in the manuscript text, or remove these references and replace them with relevant current references. Any changes to the reference list should be mentioned in the rebuttal letter that accompanies your revised manuscript. If you need to cite a retracted article, indicate the article’s retracted status in the References list and also include a citation and full reference for the retraction notice.

[Note: HTML markup is below. Please do not edit.]

Reviewers' comments:

[NOTE: If reviewer comments were submitted as an attachment file, they will be attached to this email and accessible via the submission site. Please log into your account, locate the manuscript record, and check for the action link "View Attachments". If this link does not appear, there are no attachment files.]

While revising your submission, please upload your figure files to the Preflight Analysis and Conversion Engine (PACE) digital diagnostic tool, https://pacev2.apexcovantage.com/. PACE helps ensure that figures meet PLOS requirements. To use PACE, you must first register as a user. Registration is free. Then, login and navigate to the UPLOAD tab, where you will find detailed instructions on how to use the tool. If you encounter any issues or have any questions when using PACE, please email PLOS at figures@plos.org. Please note that Supporting Information files do not need this step.

PLoS One. 2022 May 12;17(5):e0268241. doi: 10.1371/journal.pone.0268241.r004

Author response to Decision Letter 1

11 Apr 2022

PONE-D-21-28166R1

Prevalence and epidemiological characteristics of COVID-19 after one year of pandemic in Jakarta and neighbouring areas, Indonesia: A single center studyPLOS ONEDear

1. Some minor revision and clarification: The data in the text mention that: The province that contribute for more than 60% cases are Jakarta (21.3%), West Java (16.8%), Central Java (11.6%), East Java (9.4%), and East Kalimantan (3.7%). The figure 1 do not showed any data from East Kalimantan.

RESPONSE: Thank you for your comments. These data were cited from the National Committee for Corona Virus Diseases 2019 Handling and Economic Recovery reported on August 2021 (In discussion part: Line 155-161). Meanwhile, Figure 1 showed data for current study (Line 107-111). We cited the report from the National Committee to provide comparison (Reference No. 15). We have revised the text and added citation and reference accordingly.

2. Please add not only symptoms, but also radiological finding for pneumonia in the text and figure 3.

RESPONSE: Thank you for your suggestion. We have revised the text to include pneumonia based on chest x-ray results and figure 3 has been updated accordingly. Please see line 130-136 and Figure 3:

……..”Chest X-ray data were available from 845 out of 10130 positive cases, which were reported as: pneumonia 679/845 (80.4%), other abnormalities (including bronchitis, pleural effusion, lung abscess, and increased bronchovascular markings) 46/845 (5.4%), and normal 120/845 (14.2%). Most of SARS-CoV-2 cases were asymptomatic (74.0%). Among symptomatic cases of SARS-CoV-2, we found that the most common reported clinical symptoms (or combination of symptoms) (n=1,577) were cough (20.9%), a combination of both cough fever (7.0%), and fever (6.8%) (Figure 3).”……..

Attachment

Submitted filename: Response to Reviewers.docx

Click here for additional data file. (116KB, docx)

Decision Letter 2

Rizaldy Taslim Pinzon

26 Apr 2022

Prevalence and epidemiological characteristics of COVID-19 after one year of pandemic in Jakarta and neighbouring areas, Indonesia: A single center study

PONE-D-21-28166R2

Dear Dr. Amin Soebandrio

We’re pleased to inform you that your manuscript has been judged scientifically suitable for publication and will be formally accepted for publication once it meets all outstanding technical requirements.

Within one week, you’ll receive an e-mail detailing the required amendments. When these have been addressed, you’ll receive a formal acceptance letter and your manuscript will be scheduled for publication.

An invoice for payment will follow shortly after the formal acceptance. To ensure an efficient process, please log into Editorial Manager at http://www.editorialmanager.com/pone/, click the 'Update My Information' link at the top of the page, and double check that your user information is up-to-date. If you have any billing related questions, please contact our Author Billing department directly at authorbilling@plos.org.

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Kind regards,

Rizaldy Taslim Pinzon

Academic Editor

PLOS ONE

Additional Editor Comments (optional):

Reviewers' comments:

Acceptance letter

Rizaldy Taslim Pinzon

3 May 2022

PONE-D-21-28166R2

Prevalence and epidemiological characteristics of COVID-19 after one year of pandemic in Jakarta and neighbouring areas, Indonesia: A single center study

Dear Dr. Soebandrio:

I'm pleased to inform you that your manuscript has been deemed suitable for publication in PLOS ONE. Congratulations! Your manuscript is now with our production department.

If your institution or institutions have a press office, please let them know about your upcoming paper now to help maximize its impact. If they'll be preparing press materials, please inform our press team within the next 48 hours. Your manuscript will remain under strict press embargo until 2 pm Eastern Time on the date of publication. For more information please contact onepress@plos.org.

If we can help with anything else, please email us at plosone@plos.org.

Thank you for submitting your work to PLOS ONE and supporting open access.

Kind regards,

PLOS ONE Editorial Office Staff

on behalf of

Dr. Rizaldy Taslim Pinzon

Academic Editor

PLOS ONE

Associated Data

    This section collects any data citations, data availability statements, or supplementary materials included in this article.

    Supplementary Materials

    Attachment

    Submitted filename: response to reviewers.docx

    Click here for additional data file. (19.5KB, docx)
    Attachment

    Submitted filename: Response to Reviewers.docx

    Click here for additional data file. (116KB, docx)

    Data Availability Statement

    All relevant data are within the manuscript.

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