Resurgence of Dengue Virus Serotype 4 in Malaysia: A Comprehensive Clinicodemographic and Genomic Analysis
Abstract
:1. Introduction
2. Materials and Methods
2.1. Study Subjects
2.2. Analysis of Clinical and Demographic Features
2.3. Viral RNA Extraction and Full Genome Sequencing
2.4. Genomic Data Analysis
2.5. Modelling of DENV-4 Wild Type (WT) and the Mutant of Interest
2.6. Structure Stability and Hydrogen Bond Analyses
3. Results
3.1. Trend of DENV-4 Circulation in Malaysia
3.2. Demographic and Clinical Features of Patients Infected with DENV-4
3.3. Genomic Characteristics of DENV-4
3.4. DENV-4 NS1 Wild Type (WT) and Mutant Models
3.5. Mutation Effect
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Year | Number of Dengue Positive Cases Confirmed by Real-Time rt-PCR | DENV-1 n (%) | DENV-2 n (%) | DENV-3 n (%) | DENV-4 n (%) | Mixed Serotype n (%) |
---|---|---|---|---|---|---|
2017 | 206 | 34 (16.5) | 56 (27.2) | 102 (49.5) | 12 (5.8) | 2 (1.0) |
2018 | 138 | 15 (10.9) | 57 (41.3) | 61 (44.2) | 2 (1.4) | 3 (2.2) |
2019 | 116 | 22 (19.0) | 53 (45.7) | 40 (34.4) | 1 (0.9) | 0 (0.0) |
2020 | 310 | 60 (19.4) | 115 (37.1) | 107 (34.5) | 18 (5.8) | 10 (3.2) |
2021 | 14 | 0 (0.0) | 2 (14.2) | 3 (21.4) | 9 (64.3) | 0 (0.0) |
2022 | 37 | 1(2.7) | 3 (8.1) | 0 (0.0) | 33 (89.2) | 0 (0.0) |
Variable | Overall (n = 75) | |
---|---|---|
% | ||
Age: | ||
Min–Max | 2–80 | |
Mean (SD): | 36.1 (19.2) | |
≤18 years | 13 | 17.3 |
>18 years | 62 | 82.7 |
Gender: | ||
Male | 42 | 56.0 |
Female | 33 | 44.0 |
State: | ||
Johor | 14 | 18.7 |
Kedah | 17 | 22.7 |
Kuala Lumpur | 3 | 4.0 |
Melaka | 2 | 2.7 |
Perak | 5 | 6.7 |
Selangor | 34 | 45.3 |
Region: | ||
South (Johor, Melaka) | 16 | 21.3 |
Central (Kuala Lumpur, Selangor) | 37 | 49.3 |
North (Perak, Kedah) | 22 | 29.3 |
Variable | Overall | |
---|---|---|
n | % | |
Day of fever: | ||
Min–Max | 1–12 | |
Mean (SD) | 4.3 (2.1) | |
Antibody status: | ||
Primary infection | 24 | 32.0 |
Secondary infection | 24 | 32.0 |
NA | 27 | 35.0 |
Diagnosis: | ||
Dengue without warning signs | 24 | 32.0 |
Dengue with warning signs | 30 | 40.0 |
Severe dengue | 19 | 25.3 |
Fatal | 2 | 2.7 |
Clinical Presentation | All (n = 75) |
---|---|
Warning signs: | |
Persistent vomiting | 35 (46.7) |
Persistent diarrhoea | 23 (30.7) |
Lethargy | 16 (21.3) |
Abdominal pain | 10 (13.3) |
Gum bleeding | 5 (6.7) |
Occult bleeding | 7 (9.3) |
Epigastric pain | 4 (5.3) |
Other bleeding | 2 (2.7) |
Hemoconcentration | 10 (13.3) |
Non-warning signs: | |
Myalgia | 14 (18.7) |
Arthralgia | 12 (16.0) |
Cough | 8 (10.7) |
Chills/Rigor | 7 (9.3) |
Headache | 6 (8.0) |
Rash | 2 (2.7) |
Retro-orbital pain | 2 (2.7) |
Severe dengue: | |
Plasma leakage | 5 (6.7) |
Compensated shock | 6 (8.0) |
Decompensated shock | 5 (6.7) |
Complications: | |
Acute kidney injury | 2 (2.7) |
Transaminitis | 12 (16.0) |
Encephalitis | 3 (4.0) |
Hepatitis | 1 (1.3) |
Multiorgan failure | 1 (1.3) |
Myocarditis | 3 (4.0) |
Respiratory distress | 1 (1.3) |
Sample ID | Country | Case Presentation | Collection Year | NS1 Mutations | Clade | ||
---|---|---|---|---|---|---|---|
His50Tyr | Pro144Ser | ||||||
1 | *OP600497 | Malaysia | DF without WS | 2020 | ● | ● | 1 |
2 | *OP600506 | Malaysia | DF with WS | 2020 | 2 | ||
3 | *OP600478 | Malaysia | DF with WS | 2020 | 2 | ||
4 | *OP600495 | Malaysia | DF with WS | 2020 | ● | 1 | |
5 | *OP600507 | Malaysia | DF with WS | 2020 | 2 | ||
6 | *OP600496 | Malaysia | Severe Dengue | 2021 | 2 | ||
7 | *OP600508 | Malaysia | Severe Dengue | 2021 | ● | ● | 1 |
8 | *OP600498 | Malaysia | Severe Dengue | 2021 | ● | ● | 1 |
9 | *OP600499 | Malaysia | DF with WS | 2022 | ● | ● | 1 |
10 | *OP600509 | Malaysia | Severe Dengue | 2022 | ● | 2 | |
11 | *OP600510 | Malaysia | DF with WS | 2022 | ● | ● | 1 |
12 | *OP600511 | Malaysia | DF without WS | 2022 | ● | ● | 1 |
13 | *OP600512 | Malaysia | DF with WS | 2022 | ● | 1 | |
14 | *OP604360 | Malaysia | DF with WS | 2022 | ● | ● | 1 |
15 | MH888334.1 | Malaysia | NA | 2013 | |||
16 | MH051734.1 | Malaysia | NA | 2014 | |||
17 | JX024757.1 | Singapore | NA | 2010 | |||
18 | MW301595.1 | Malaysia | NA | 2013 | |||
19 | KC762695.1 | Indonesia | NA | 2007 | |||
20 | MH823210.1 | Indonesia | NA | 2014 | |||
21 | MH382789.1 | Papua NG | NA | 2016 | |||
22 | KJ579245.1 | Brazil | NA | 2012 | |||
23 | KY474335.1 | Ecuador | NA | 2014 |
Program | WT/ Mutation | Procheck (Ramachandran Plot Statistic (%)) | ProSA | Errat (%) | |||
---|---|---|---|---|---|---|---|
Most Favoured | Additionally Allowed | Generously Allowed | Disallowed | Z-Score | Overall Quality Factor Score | ||
SWISS-MODEL | WT | 85.6 | 13.1 | 0.5 | 0.8 | −6.67 | 91.2442 |
p.His50Tyr | 87.1 | 11.7 | 0.7 | 0.5 | −6.7 | 88.2083 | |
p.Pro144Ser | 87.1 | 11.7 | 0.7 | 0.5 | −6.71 | 88.2083 | |
AlphaFold2 | WT | 90.4 | 9.3 | 0 | 0.3 | −6.95 | 87.1681 |
p.His50Tyr | 90.4 | 9.3 | 0 | 0.3 | −7 | 86.9822 | |
p.Pro144Ser | 90.4 | 9.2 | 0 | 0.3 | −7.04 | 87.1681 |
Program | Mutation | FoldX (kcal/mol) |
---|---|---|
SWISS-MODEL | p.His50Tyr | −0.279206 |
p.Pro144Ser | 2.9665 | |
AlphaFold2 | p.His50Tyr | −0.233207 |
p.Pro144Ser | 3.5151 |
WT/ Mutation | Donor (Amino Acid/Residue/Chain/Atom) | Acceptor (Amino Acid/Residue/Chain/Atom) | Hydrogen (Amino Acid/Residue/Chain/Atom) | Distance (Å) |
---|---|---|---|---|
WT_His50 | HIS 50.A (N) | ILE 46.A (O) | HIS 50.A (H) | 2.937 |
GLY 53.A (N) | HIS 50.A (O) | GLY 53.A (H) | 2.823 | |
HIS 50.A (N) | LEU 47.A (O) | HIS 50.A (H) | 3.14 | |
HIS 50.A (NE) | SER131.A (OG) | HIS 50.A (H) | 3.19 | |
Mut_Tyr50 | TYR 50.A (N) | ILE 46.A (O) | TYR 50.A (H) | 2.844 |
TYR 50.A (OH) | ILE 123.A (O) | TYR 50.A (HH) | 2.952 | |
GLY 53.A (N) | TYR 50.A (O) | GLY 53.A (H) | 2.823 | |
TYR 50.A (N) | LEU 47.A (O) | TYR 50.A (H) | 3.21 | |
WT_Pro144 | ARG 147.A (N) | PRO 144.A (O) | ARG 147.A (H) | 2.831 |
Mut_Ser144 | ARG 147.A (N) | SER 144.A (O) | ARG 147.A (H) | 2.88 |
ARG 147.A (N) | SER 144.A (OG) | ARG 147.A (H) | 3.418 |
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Suppiah, J.; Ali, E.Z.; Mohd Khalid, M.K.N.; Mohd Ghazali, S.; Tee, K.K.; Zulkifli, M.M.S.; Ramli, N.; Adiee, A.H.; Ramly, M.N.; Robert, F.; et al. Resurgence of Dengue Virus Serotype 4 in Malaysia: A Comprehensive Clinicodemographic and Genomic Analysis. Trop. Med. Infect. Dis. 2023, 8, 409. https://doi.org/10.3390/tropicalmed8080409
Suppiah J, Ali EZ, Mohd Khalid MKN, Mohd Ghazali S, Tee KK, Zulkifli MMS, Ramli N, Adiee AH, Ramly MN, Robert F, et al. Resurgence of Dengue Virus Serotype 4 in Malaysia: A Comprehensive Clinicodemographic and Genomic Analysis. Tropical Medicine and Infectious Disease. 2023; 8(8):409. https://doi.org/10.3390/tropicalmed8080409
Chicago/Turabian StyleSuppiah, Jeyanthi, Ernie Zuraida Ali, Mohd Khairul Nizam Mohd Khalid, Sumarni Mohd Ghazali, Kok Keng Tee, Murni Maya Sari Zulkifli, Nuraisyah Ramli, Amir Hussin Adiee, Muhamad Nurrani Ramly, Fionie Robert, and et al. 2023. "Resurgence of Dengue Virus Serotype 4 in Malaysia: A Comprehensive Clinicodemographic and Genomic Analysis" Tropical Medicine and Infectious Disease 8, no. 8: 409. https://doi.org/10.3390/tropicalmed8080409