Co-Circulation of Chikungunya and Multiple DENV Serotypes and Genotypes, Western Indonesia 2015–2016
Abstract
:1. Introduction
2. Materials and Methods
2.1. Study Setting and Patient Recruitment
2.2. NS1 EIA and DENV-Serotyping
2.3. DENV E Genes Amplification and DENV E Gene Sequencing
2.4. CHIKV Whole Genome Sequencing
2.5. Phylogenetic Analysis
3. Results
3.1. Patient Characteristics
3.2. Serotype Distributions of DENV in Aceh and Jambi
3.3. Distribution of DENV Genotypes and Lineages in Aceh and Jambi
3.3.1. DENV-1
3.3.2. DENV-2
3.3.3. DENV-3
3.4. Currently Circulating CHIKV in Aceh and Jambi
4. Discussion
4.1. Distinct DENV Lineages Circulate in Aceh and Jambi
4.2. Continuous Co-Circulation of CHIKV and DENV in Jambi
5. Conclusions
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Characteristics | Aceh (n = 29) n (%) | Jambi (n = 27) n (%) | Total n (%) |
---|---|---|---|
Gender | |||
Male | 13 (44.8) | 15 (55.6) | 28 (50.0) |
Female | 16 (55.2) | 12 (44.4) | 28 (50.0) |
Age (year) | |||
0–10 | 3 (10.3) | 9 (33.3) | 12 (21.4) |
11–20 | 12 (41.4) | 3 (11.1) | 15 (26.8) |
21–30 | 12 (41.4) | 7 (25.9) | 19 (33.9) |
31–40 | 2 (6.9) | 5 (18.5) | 7 (12.5) |
41–50 | 0 (0.0) | 2 (7.4) | 2 (3.6) |
>50 | 0 (0.0) | 1 (3.7) | 1 (1.8) |
Clinical symptoms (n = 43) | n= 16 | n= 26 | |
Fever | 16 (100.0) | 27 (100.0) | 43 (100.0) |
Nausea or vomiting | 15 (93.8) | 27 (100.0) | 42 (97.7) |
Aches and pains | 15 (93.8) | 12 (44.4) | 27 (62.8) |
Retro-orbital pain | 10 (62.5) | 4 (14.8) | 14 (32.6) |
Headache | 13 (81.3) | 25 (92.6) | 38 (88.4) |
Warming signs (n = 43) | |||
Abdominal pain or tenderness | 8 (50.5) | 1 (3.7) | 9 (20.9) |
Persistent vomiting | 0 (0.0) | 0 (0.0) | 0 (0.0) |
Clinical fluid accumulation | 0 (0.0) | 0 (0.0) | 0 (0.0) |
Mucosal bleeding | 4 (25.5) | 0 (0.0) | 4 (9.3) |
Lethargy | 0 (0.0) | 0 (0.0) | 0 (0.0) |
Liver enlargement | 2 (12.5) | 0 (0.0) | 2 (4.7) |
Severe dengue signs (n = 43) | |||
Respiratory distress | 0 (0.0) | 0 (0.0) | 0 (0.0) |
Severe bleeding | 0 (0.0) | 0 (0.0) | 0 (0.0) |
Impaired consciousness | 0 (0.0) | 0 (0.0) | 0 (0.0) |
Origin | Sex | Age (Year) | Collection Date (D/M/Y) | Isolate ID | Serotype | Genotype | Lineage | E-Gene Sequence |
---|---|---|---|---|---|---|---|---|
Aceh | Female | 53 | 27/03/2015 | D1/IDN_Aceh_006/2015 | DENV-1 | I | L2 | Complete |
Aceh | Female | 21 | 14/09/2015 | D1/IDN_Aceh_007/2015 | DENV-1 | I | L2 | Complete |
Aceh | Male | 19 | 12/12/2015 | D1/IDN_Aceh_014/2015 | DENV-1 | I | L1 | Partial (227 bp) |
Aceh | Female | 11 | 21/09/2015 | D1/IDN_Aceh_021/2015 | DENV-1 | I | L4 | Complete |
Aceh | Female | 18 | 29/09/2015 | D1/IDN_Aceh_040/2015 | DENV-1 | I | L3 | Partial (227 bp) |
Aceh | Male | 17 | 14/09/2015 | D2/IDN_Aceh_017/2015 | DENV-2 | Cosmopolitan | L2 | Complete |
Aceh | Female | 27 | 19/08/2015 | D2/IDN_Aceh_036/2015 | DENV-2 | Cosmopolitan | L2 | Complete |
Aceh | Female | 20 | 16/06/2015 | D2/IDN_Aceh_046/2015 | DENV-2 | Cosmopolitan | L2 | Complete |
Jambi | Female | 6 | 07/11/2016 | D1/IDN_Jambi_022/2016 | DENV-1 | I | L5 | Complete |
Jambi | Male | 33 | 08/08/2016 | D1/IDN_Jambi_031/2016 | DENV-1 | I | L5 | Complete |
Jambi | Male | 6 | 30/06/2016 | D2/IDN_Jambi_021/2016 | DENV-2 | Cosmopolitan | L2 | Complete |
Jambi | Male | 7 | 22/07/2016 | D2/IDN_Jambi_024/2016 | DENV-2 | Cosmopolitan | L2 | Complete |
Jambi | Female | 35 | 22/12/2016 | D2/IDN_Jambi_025/2016 | DENV-2 | Cosmopolitan | L1 | Complete |
Jambi | Female | 43 | 08/08/2016 | D2/IDN_Jambi_029/2016 | DENV-2 | Cosmopolitan | L2 | Complete |
Jambi | Male | 24 | 11/08/2016 | D2/IDN_Jambi_032/2016 | DENV-2 | Cosmopolitan | L1 | Complete |
Jambi | Male | 38 | 24/08/2016 | D2/IDN_Jambi_038/2016 | DENV-2 | Cosmopolitan | L2 | Complete |
Jambi | Male | 23 | 16/09/2016 | D2/IDN_Jambi_043/2016 | DENV-2 | Cosmopolitan | L2 | Complete |
Jambi | Female | 30 | 21/11/2016 | D2/IDN_Jambi_102/2016 | DENV-2 | Cosmopolitan | L2 | Complete |
Jambi | Male | 17 | 25/09/2016 | D3/IDN_Jambi_048/2016 | DENV-3 | I | L1 | Complete |
Jambi | Female | 9 | 25/09/2016 | D3/IDN_Jambi_049/2016 | DENV-3 | I | L1 | Partial (663 bp) |
Jambi | Female | 3 | 07/10/2016 | D3/IDN_Jambi_056/2016 | DENV-3 | I | L1 | Complete |
Jambi | Male | 21 | 05/12/2016 | D3/IDN_Jambi_134/2016 | DENV-3 | I | L1 | Complete |
Sex | Age (Year) | Collection Date (D/M/Y) | ID | RT-PCR CHIKV | Genotype | Sequence |
---|---|---|---|---|---|---|
Male | 53 | 21/11/2016 | CHIKV/IDN_Jambi_101/2016 | Positive | Asian | Full genome |
Female | 10 | 24/11/2016 | CHIKV/IDN_Jambi_112/2016 | Positive | Asian | Full genome |
Female | 29 | 02/12/2016 | CHIKV/IDN_Jambi_129/2016 | Positive | Asian | Partial genome |
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Harapan, H.; Michie, A.; Ernst, T.; Panta, K.; Mudatsir, M.; Yohan, B.; Haryanto, S.; McCarthy, S.; Sasmono, R.T.; Imrie, A. Co-Circulation of Chikungunya and Multiple DENV Serotypes and Genotypes, Western Indonesia 2015–2016. Viruses 2022, 14, 99. https://doi.org/10.3390/v14010099
Harapan H, Michie A, Ernst T, Panta K, Mudatsir M, Yohan B, Haryanto S, McCarthy S, Sasmono RT, Imrie A. Co-Circulation of Chikungunya and Multiple DENV Serotypes and Genotypes, Western Indonesia 2015–2016. Viruses. 2022; 14(1):99. https://doi.org/10.3390/v14010099
Chicago/Turabian StyleHarapan, Harapan, Alice Michie, Timo Ernst, Kritu Panta, Mudatsir Mudatsir, Benediktus Yohan, Sotianingsih Haryanto, Suzi McCarthy, R. Tedjo Sasmono, and Allison Imrie. 2022. "Co-Circulation of Chikungunya and Multiple DENV Serotypes and Genotypes, Western Indonesia 2015–2016" Viruses 14, no. 1: 99. https://doi.org/10.3390/v14010099
APA StyleHarapan, H., Michie, A., Ernst, T., Panta, K., Mudatsir, M., Yohan, B., Haryanto, S., McCarthy, S., Sasmono, R. T., & Imrie, A. (2022). Co-Circulation of Chikungunya and Multiple DENV Serotypes and Genotypes, Western Indonesia 2015–2016. Viruses, 14(1), 99. https://doi.org/10.3390/v14010099