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  1. Fulltext Dengue virus type 2 envelope protein displayed as recombinant phage attachment protein reveals potential cell binding sites
    Abd-Jamil J, Cheah CY, AbuBakar S
    Protein Eng. Des. Sel., 2008 Oct;21(10):605-11.
    PMID: 18669522 DOI: 10.1093/protein/gzn041
    A method to map the specific site on dengue virus envelope protein (E) that interacts with cells and a neutralizing antibody is developed using serially truncated dengue virus type 2 (DENV-2) E displayed on M13 phages as recombinant E-g3p fusion proteins. Recombinant phages displaying the truncated E consisting of amino acids 297-423 (EB2) and amino acids 379-423 (EB4) were neutralized by DENV-2 patient sera and the DENV-2 E-specific 3H5-1 monoclonal antibodies suggesting that the phages retained the DENV-2 E antigenic properties. The EB4 followed by EB2 recombinant phages bound the most to human monocytes (THP-1), African green monkey kidney (Vero) cells, mosquito (C6/36) cells, ScFv specific against E and C6/36 cell proteins. Two potential cell attachment sites were mapped to loop I (amino acids 297 to 312) and loop II (amino acids 379-385) of the DENV-2 E using the phage-displayed truncated DENV-2 E fragments and by the analysis of the E structure. Loop II was present only in EB4 recombinant phages. There was no competition for binding to C6/36 cell proteins between EB2 and EB4 phages. Loop I and loop II are similar to the sub-complex specific and type-specific neutralizing monoclonal antibody binding sites, respectively. Hence, it is proposed that binding and entry of DENV involves the interaction of loop I to cell surface glycosaminoglycan-motif and a subsequent highly specific interaction involving loop II with other cell proteins. The phage displayed truncated DENV-2 E is a powerful and useful method for the direct determination of DENV-2 E cell binding sites.
  2. Antibody neutralization and viral virulence in recurring dengue virus type 2 outbreaks
    Wong SS, Abd-Jamil J, Abubakar S
    Viral Immunol, 2007 Sep;20(3):359-68.
    PMID: 17931106
    Outbreaks involving dengue viruses (DENV) of the same genotype occur in a cyclical pattern in Malaysia. Two cycles of outbreaks involving dengue virus type 2 (DENV-2) of the same genotype occurred in the 1990s in the Klang Valley, Malaysia. Sera of patients from the first outbreak and sera of mice inoculated with virus from the same outbreak had poorer neutralization activity against virus of the second outbreak. Conversely, patient sera from the second outbreak showed higher neutralization titer against virus of the early outbreak. At subneutralizing concentrations, sera of mice immunized with second outbreak virus did not significantly enhance infection with viruses from the earlier outbreak. Amino acid substitution from valine to isoleucine at position 129 of the envelope protein (E), as well as threonine to alanine at position 117 and lysine to arginine at position 272 of the NS1 protein, differentiated viruses of the two outbreaks. These findings highlight the potential influence of specific intragenotypic variations in eliciting varied host immune responses against the different DENV subgenotypes. This could be an important contributing factor in the recurring homogenotypic dengue virus outbreaks seen in dengue-endemic regions.
  3. Fulltext Detecting dengue outbreaks in Malaysia using geospatial techniques
    Nellis S, Loong SK, Abd-Jamil J, Fauzi R, AbuBakar S
    Geospat Health, 2021 11 03;16(2).
    PMID: 34730321 DOI: 10.4081/gh.2021.1008
    Dengue is a complex disease with an increasing number of infections worldwide. This study aimed to analyse spatiotemporal dengue outbreaks using geospatial techniques and examine the effects of the weather on dengue outbreaks in the Klang Valley area, Kuala Lumpur, Malaysia. Daily weather variables including rainfall, temperature (maximum and minimum) and wind speed were acquired together with the daily reported dengue cases data from 2001 to 2011 and converted into geospatial format to identify whether there was a specific pattern of the dengue outbreaks. The association between these variables and dengue outbreaks was assessed using Spearman's correlation. The result showed that dengue outbreaks consistently occurred in the study area during a 11-year study period. And that the strongest outbreaks frequently occurred in two high-rise apartment buildings located in Kuala Lumpur City centre. The results also show significant negative correlations between maximum temperature and minimum temperature on dengue outbreaks around the study area as well as in the area of the high-rise apartment buildings in Kuala Lumpur City centre.
  4. Fulltext Isolation of ancestral sylvatic dengue virus type 1, Malaysia
    Teoh BT, Sam SS, Abd-Jamil J, AbuBakar S
    Emerg Infect Dis, 2010 Nov;16(11):1783-5.
    PMID: 21029545 DOI: 10.3201/eid1611.100721
    Ancestral sylvatic dengue virus type 1, which was isolated from a monkey in 1972, was isolated from a patient with dengue fever in Malaysia. The virus is neutralized by serum of patients with endemic DENV-1 infection. Rare isolation of this virus suggests a limited spillover infection from an otherwise restricted sylvatic cycle.
  5. Fulltext The Use of NS1 Rapid Diagnostic Test and qRT-PCR to Complement IgM ELISA for Improved Dengue Diagnosis from Single Specimen
    Teoh BT, Sam SS, Tan KK, Johari J, Abd-Jamil J, Hooi PS, et al.
    Sci Rep, 2016 06 09;6:27663.
    PMID: 27278716 DOI: 10.1038/srep27663
    Timely and accurate dengue diagnosis is important for differential diagnosis and immediate implementation of appropriate disease control measures. In this study, we compared the usefulness and applicability of NS1 RDT (NS1 Ag Strip) and qRT-PCR tests in complementing the IgM ELISA for dengue diagnosis on single serum specimen (n = 375). The NS1 Ag Strip and qRT-PCR showed a fair concordance (κ = 0.207, p = 0.001). While the NS1 Ag Strip showed higher positivity than qRT-PCR for acute (97.8% vs. 84.8%) and post-acute samples (94.8% vs. 71.8%) of primary infection, qRT-PCR showed higher positivity for acute (58.1% vs. 48.4%) and post-acute (50.0% vs.41.4%) samples in secondary infection. IgM ELISA showed higher positivity in samples from secondary dengue (74.2-94.8%) than in those from primary dengue (21.7-64.1%). More primary dengue samples showed positive with combined NS1 Ag Strip/IgM ELISA (99.0% vs. 92.8%) whereas more secondary samples showed positive with combined qRT-PCR/IgM ELISA (99.4% vs. 96.2%). Combined NS1 Ag Strip/IgM ELISA is a suitable combination tests for timely and accurate dengue diagnosis on single serum specimen. If complemented with qRT-PCR, combined NS1 Ag Strip/IgM ELISA would improve detection of secondary dengue samples.
  6. Fulltext Review of Dengue hemorrhagic fever fatal cases seen among adults: a retrospective study
    Sam SS, Omar SF, Teoh BT, Abd-Jamil J, AbuBakar S
    PLoS Negl Trop Dis, 2013;7(5):e2194.
    PMID: 23658849 DOI: 10.1371/journal.pntd.0002194
    Dengue is a mosquito-borne viral disease endemic in many countries in the tropics and sub-tropics. The disease affects mainly children, but in recent years it is becoming more of an adult disease. Malaysia experienced a large dengue outbreak in 2006 to 2007, involving mostly adults, with a high number of deaths.
  7. Fulltext Molecular identification of adenovirus causing respiratory tract infection in pediatric patients at the University of Malaya Medical Center
    Abd-Jamil J, Teoh BT, Hassan EH, Roslan N, Abubakar S
    BMC Pediatr, 2010;10:46.
    PMID: 20594359 DOI: 10.1186/1471-2431-10-46
    There are at least 51 adenovirus serotypes (AdV) known to cause human infections. The prevalence of the different human AdV (HAdV) serotypes varies among different regions. Presently, there are no reports of the prevalent HAdV types found in Malaysia. The present study was undertaken to identify the HAdV types associated primarily with respiratory tract infections (RTI) of young children in Malaysia.
  8. Fulltext Possible Factors Influencing the Seroprevalence of Dengue among Residents of the Forest Fringe Areas of Peninsular Malaysia
    Abd-Jamil J, Ngui R, Nellis S, Fauzi R, Lim ALY, Chinna K, et al.
    J Trop Med, 2020;2020:1019238.
    PMID: 32536945 DOI: 10.1155/2020/1019238
    Dengue is an endemic mosquito-borne viral disease prevalent in many urban areas of the tropic, especially the Southeast Asia. Its presence among the indigenous population of Peninsular Malaysia (Orang Asli), however, has not been well described. The present study was performed to investigate the seroprevalence of dengue among the Orang Asli (OA) residing at the forest fringe areas of Peninsular Malaysia and determine the factors that could affect the transmission of dengue among the OA. Eight OA communities consisting of 491 individuals were recruited. From the study, at least 17% of the recruited study participants were positive for dengue IgG, indicating past exposure to dengue. Analysis on the demographic and socioeconomic variables suggested that high seroprevalence of dengue was significantly associated with those above 13 years old and a low household income of less than MYR500 (USD150). It was also associated with the vast presence of residential areas and the presence of a lake. Remote sensing analysis showed that higher land surface temperatures and lower land elevations also contributed to higher dengue seroprevalence. The present study suggested that both demographic and geographical factors contributed to the increasing risk of contracting dengue among the OA living at the forest fringe areas of Peninsular Malaysia. The OA, hence, remained vulnerable to dengue.
  9. A TaqMan minor groove binder probe-based quantitative reverse transcription polymerase chain reaction for detection and quantification of chikungunya virus
    Lim YZ, Teoh BT, Sam SS, Azizan NS, Khor CS, Nor'e SS, et al.
    Trop Biomed, 2023 Sep 01;40(3):313-319.
    PMID: 37897164 DOI: 10.47665/tb.40.3.007
    Chikungunya virus (CHIKV) is a mosquito-borne alphavirus with widespread distribution across the globe. Since 2016, CHIKV re-emerged in several countries including Indian subcontinent and Southeast Asia. A proper diagnostic tool for early diagnosis of CHIKV infection is crucial to facilitate patient management and control virus transmission at the earliest stage of outbreak. Therefore, a TaqMan minor groove binder (MGB) probe-based quantitative reverse transcription polymerase chain reaction (qRT-PCR) assay was developed to detect and quantify the CHIKV. The primers and probe were designed based on a conserved genomic region of 730 global CHIKV sequences that is located between nsP1 and nsP2 genes. The nucleotide mismatches of primers and probe with 730 global CHIKV sequences and 13 alphaviruses were then analysed in silico. In this study, the last 5 nucleotides at 3' end of primers and 5' end of probe were considered to be the critical regions for priming. In silico analysis revealed that the critical regions of primers and probe were at least 99.6% matched with the 730 global CHIKV sequences. Besides, the primers and probe showed at least 5/20 (25.0%) and 4/17 (23.5%) nucleotide mismatches with 13 alphaviruses respectively. The amplification efficiency of qRT-PCR assay was 100.59% (95% CI= 93.06, 109.33) with a R2 score of 0.957. Its limit of detection (LOD) at 95% probability level was 16.6 CHIKV RNA copies (95% CI= 12.9, 28.9). The qRT-PCR assay was specific to CHIKV without cross-reacting with all dengue virus serotypes, Getah virus, Tembusu virus and Zika virus. The diagnostic results of qRT-PCR assay were perfectly agreed (k=1.000, p=0.003) with a commercial trioplex assay, with sensitivity of 100% (95% CI= 61, 100) and specificity of 100% (95% CI= 44, 100). Overall, the developed qRT-PCR assay is ideal for rapid, sensitive and specific detection as well as quantification of CHIKV.
  10. Fulltext Dengue death with evidence of hemophagocytic syndrome and dengue virus infection in the bone marrow
    Ab-Rahman HA, Wong PF, Rahim H, Abd-Jamil J, Tan KK, Sulaiman S, et al.
    Springerplus, 2015;4:665.
    PMID: 26558168 DOI: 10.1186/s40064-015-1463-z
    INTRODUCTION: HPS is a potentially life-threatening histiocytic disorder that has been described in various viral infections including dengue. Its involvement in severe and fatal dengue is probably more common but is presently under recognized.
    CASE DESCRIPTION: A 38-year-old female was admitted after 5 days of fever. She was deeply jaundiced, leukopenic and thrombocytopenic. Marked elevation of transaminases, hyperbilirubinemia and hypoalbuminemia were observed. She had deranged INR values and prolonged aPTT accompanied with hypofibrinogenemia. She also had splenomegaly. She was positive for dengue IgM. Five days later she became polyuric and CT brain image showed gross generalized cerebral edema. Her conditions deteriorated by day 9, became confused with GCS of 9/15. Her BMAT showed minimal histiocytes. Her serum ferritin level peaked at 13,670.00 µg/mL and her sCD163 and sCD25 values were markedly elevated at 4750.00 ng/mL and 4191.00 pg/mL, respectively. She succumbed to the disease on day 10 and examination of her tissues showed the presence of dengue virus genome in the bone marrow.
    DISCUSSION AND EVALUATION: It is described here, a case of fatal dengue with clinical features of HPS. Though BMAT results did not show the presence of macrophage hemophagocytosis, other laboratory features were consistent with HPS especially marked elevation of ferritin, sCD163 and sCD25. Detection of dengue virus in the patient's bone marrow, fifteen days after the onset of fever was also consistent with the suggestion that the HPS is associated with dengue virus infection.
    CONCLUSIONS: The findings highlight HPS as a possible complication leading to severe dengue and revealed persistent dengue virus infection of the bone marrow. Detection of HPS markers; ferritin, sCD163 and sCD25, therefore, should be considered for early recognition of HPS-associated dengue.
    KEYWORDS: Bone marrow; Dengue; Ferritin; Hemophagocytic syndrome; MAS; Macrophage
    Study site: University Malaya Medical Centre (UMMC), Kuala Lumpur, Malaysia
  11. Fulltext Colorimetric Detection of Dengue by Single Tube Reverse-Transcription-Loop-Mediated Isothermal Amplification
    Lau YL, Lai MY, Teoh BT, Abd-Jamil J, Johari J, Sam SS, et al.
    PLoS One, 2015;10(9):e0138694.
    PMID: 26384248 DOI: 10.1371/journal.pone.0138694
    Dengue is usually diagnosed by isolation of the virus, serology or molecular diagnostic methods. Several commercial kits for the diagnosis of dengue are existing, but concerns have arisen regarding to the affordability and performance characteristics of these kits. Hence, the loop-mediated isothermal amplification (LAMP) is potentially ideal to be used especially in resource limited environments. Serum was collected from healthy donors and patients diagnosed with dengue infection. RNA extracted from the serum samples were tested by reverse-transcription-LAMP assay developed based on 3'-NCR gene sequences for DENV 1-4. Results were interpreted by a turbidity meter in real time or visually at the end of the assay. Sensitivity and specificity of RT-LAMP results were calculated and compared to qRT-PCR and ELISA. RT-LAMP is highly sensitive with the detection limit of 10 RNA copies for all serotypes. Dengue virus RNA was detected in all positive samples using RT-LAMP and none of the negative samples within 30-45 minutes. With continuing efforts in the optimization of this assay, RT-LAMP may provide a simple and reliable test for detecting DENV in areas where dengue is prevalent.
  12. Fulltext Emergence of the Asian lineage dengue virus type 3 genotype III in Malaysia
    Tan KK, Zulkifle NI, Sulaiman S, Pang SP, NorAmdan N, MatRahim N, et al.
    BMC Evol. Biol., 2018 04 24;18(1):58.
    PMID: 29699483 DOI: 10.1186/s12862-018-1175-4
    BACKGROUND: Dengue virus type 3 genotype III (DENV3/III) is associated with increased number of severe infections when it emerged in the Americas and Asia. We had previously demonstrated that the DENV3/III was introduced into Malaysia in the late 2000s. We investigated the genetic diversity of DENV3/III strains recovered from Malaysia and examined their phylogenetic relationships against other DENV3/III strains isolated globally.

    RESULTS: Phylogenetic analysis revealed at least four distinct DENV3/III lineages. Two of the lineages (DENV3/III-B and DENV3/III-C) are current actively circulating whereas the DENV3/III-A and DENV3/III-D were no longer recovered since the 1980s. Selection pressure analysis revealed strong evidence of positive selection on a number of amino acid sites in PrM, E, NS1, NS2a, NS2b, NS3, NS4a, and NS5. The Malaysian DENV3/III isolates recovered in the 1980s (MY.59538/1987) clustered into DENV3/III-B, which was the lineage with cosmopolitan distribution consisting of strains actively circulating in the Americas, Africa, and Asia. The Malaysian isolates recovered after the 2000s clustered within DENV3/III-C. This DENV3/III-C lineage displayed a more restricted geographical distribution and consisted of isolates recovered from Asia, denoted as the Asian lineage. Amino acid variation sites in NS5 (NS5-553I/M, NS5-629 T, and NS5-820E) differentiated the DENV3/III-C from other DENV3 viruses. The codon 629 of NS5 was identified as a positively selected site. While the NS5-698R was identified as unique to the genome of DENV3/III-C3. Phylogeographic results suggested that the recent Malaysian DENV3/III-C was likely to have been introduced from Singapore in 2008 and became endemic. From Malaysia, the virus subsequently spread into Taiwan and Thailand in the early part of the 2010s and later reintroduced into Singapore in 2013.

    CONCLUSIONS: Distinct clustering of the Malaysian old and new DENV3/III isolates suggests that the currently circulating DENV3/III in Malaysia did not descend directly from the strains recovered during the 1980s. Phylogenetic analyses and common genetic traits in the genome of the strains and those from the neighboring countries suggest that the Malaysian DENV3/III is likely to have been introduced from the neighboring regions. Malaysia, however, serves as one of the sources of the recent regional spread of DENV3/III-C3 within the Asia region.

  13. Fulltext Dengue fever among febrile patients in Taiz City, Yemen during the 2016 war: Clinical manifestations, risk factors, and patients knowledge, attitudes, and practices toward the disease
    Alghazali KA, Teoh BT, Sam SS, Abd-Jamil J, Johari J, Atroosh WM, et al.
    One Health, 2020 Jun;9:100119.
    PMID: 32368608 DOI: 10.1016/j.onehlt.2019.100119
    The current war in Yemen has displaced millions of people from their homes into living in cramped shelters where the healthcare is limited. The breakdown of Yemen's healthcare and sanitation systems has facilitated the spread of infectious diseases including mosquito-borne diseases. The present study aimed to describe the prevalence of dengue virus (DENV) infection among the febrile patients of the Taiz governorate, Yemen as well as their knowledge, attitude and preventive practices (KAPs) regarding dengue fever (DF), and to investigate the factors associated with dengue preventive practices during the war. A total of 384 clinically dengue-suspected patients who sought health care in Taiz, Yemen during the period from July 2016 until October 2016 were recruited for the study. Serum samples were obtained and screened for the presence of DENV RNA and anti-DENV antibodies by reverse transcription-recombinase polymerase amplification (RT-RPA) and dengue IgM/IgG-capture ELISA, respectively. KAP questionnaires were obtained from all participants too. In the study, dengue was laboratory confirmed in approximately 49.3% (189/384) of the clinically suspected dengue patients. In general, 67.1% of the patients had low knowledge scores regarding DF. Low scores for knowledge about DF was significantly associated with those in the age groups of ≤20 years and 21-30 years, illiterates and patients with non-skilled jobs or jobless. The most common preventive practices reported by participants were covering stored water (78.6%) and putting a screen on the house's windows (65.3%). A low proportion of participants (6.7%) had 51-100% of good DF preventive practices. Low scores of positive attitudes toward DF was identified as a risk factor. The study participants showed poor knowledge about DF and their ways of dealing with the various aspects of DF prevention was quite limited, hence, preventive measures against the disease were less likely to be undertaken. Findings from the study highlight the peril of dengue in Taiz, Yemen, which is now comparable to that of endemic regions. The ongoing civil war with disruption in regular health services compounded by the low knowledge about DF as well as the limited DF preventive practices could result in entrenchment of dengue in Yemen.
  14. Fulltext Dengue virus type 1 clade replacement in recurring homotypic outbreaks
    Teoh BT, Sam SS, Tan KK, Johari J, Shu MH, Danlami MB, et al.
    BMC Evol. Biol., 2013;13:213.
    PMID: 24073945 DOI: 10.1186/1471-2148-13-213
    Recurring dengue outbreaks occur in cyclical pattern in most endemic countries. The recurrences of dengue virus (DENV) infection predispose the population to increased risk of contracting the severe forms of dengue. Understanding the DENV evolutionary mechanism underlying the recurring dengue outbreaks has important implications for epidemic prediction and disease control.
  15. Fulltext A reverse transcription loop-mediated isothermal amplification for broad coverage detection of Asian and African Zika virus lineages
    Teoh BT, Chin KL, Samsudin NI, Loong SK, Sam SS, Tan KK, et al.
    BMC Infect Dis, 2020 Dec 11;20(1):947.
    PMID: 33308203 DOI: 10.1186/s12879-020-05585-4
    BACKGROUND: Early detection of Zika virus (ZIKV) infection during the viremia and viruria facilitates proper patient management and mosquito control measurement to prevent disease spread. Therefore, a cost-effective nucleic acid detection method for the diagnosis of ZIKV infection, especially in resource-deficient settings, is highly required.

    METHODS: In the present study, a single-tube reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay was developed for the detection of both the Asian and African-lineage ZIKV. The detection limit, strain coverage and cross-reactivity of the ZIKV RT-LAMP assay was evaluated. The sensitivity and specificity of the RT-LAMP were also evaluated using a total of 24 simulated clinical samples. The ZIKV quantitative reverse transcription-polymerase chain reaction (qRT-PCR) assay was used as the reference assay.

    RESULTS: The detection limit of the RT-LAMP assay was 3.73 ZIKV RNA copies (probit analysis, P ≤ 0.05). The RT-LAMP assay detected the ZIKV genomes of both the Asian and African lineages without cross-reacting with other arthropod-borne viruses. The sensitivity and specificity of the RT-LAMP assay were 90% (95% CI = 59.6-98.2) and 100% (95% CI = 78.5-100.0), respectively. The RT-LAMP assay detected ZIKV genome in 9 of 24 (37.5%) of the simulated clinical samples compared to 10 of 24 (41.7%) by qRT-PCR assay with a high level of concordance (κ = 0.913, P 

  16. Detection and confirmation of dengue pre- and postintroduction of dengue NS1-antigen test at the University Malaya Medical Centre: An observational study
    Abd-Jamil J, Azizan NS, Che-Mat-Seri NA, Yaacob CN, Samsudin NI, Mahfodz NH, et al.
    J Med Virol, 2021 08;93(8):4714-4719.
    PMID: 33421159 DOI: 10.1002/jmv.26790
    Early diagnosis of dengue is important to ensure proper management of patients and effective implementation of control measures. The present study was undertaken to determine the outcome of the implementation of dengue NS1-antigen (Ag) rapid diagnostic test (RDT) in the confirmation of dengue at the first patient hospital visit at the University Malaya Medical Centre. A total of 1036 and 1097 sera from the year 2008 and 2015 were used, representing samples from before and after dengue NS1-Ag RDT was implemented as routine diagnostic at the hospital. Results showed that similar dengue confirmation percentage (56%) was made in 2008 and 2015, regardless of the main laboratory diagnostic method used. Confirmation of dengue, however, increased to 68% and 73% when dengue NS1-Ag test or dengue immunoglobulin M-capture enzyme-linked immunosorbent assay was used as the second test for the 2008 and 2015 samples, respectively. Detection of dengue virus (DENV) using multiplex reverse transcription-polymerase chain reaction (RT-PCR) showed that DENV-1 was the highest in circulation in 2008 and that both DENV-1 and DENV-2 were dominant in 2015. In summary, the present study demonstrated that the introduction and use of the dengue NS1-Ag RDT did not change or compromise confirmation of dengue, highlighting the advantage of using the method. With the reducing cost of molecular detection tools, DENV detection using RT-PCR remains a viable option for further confirmation of dengue in hospital settings.
  17. Multiplex sequencing of SARS-Cov-2 genome directly from clinical samples using the Ion Personal Genome Machine (PGM)
    Tan KK, Tiong V, Tan JY, Wong JE, Teoh BT, Abd-Jamil J, et al.
    Trop Biomed, 2021 Sep 01;38(3):283-288.
    PMID: 34362871 DOI: 10.47665/tb.38.3.069
    Various methods have been developed for rapid and high throughput full genome sequencing of SARS-CoV-2. Here, we described a protocol for targeted multiplex full genome sequencing of SARS-CoV-2 genomic RNA directly extracted from human nasopharyngeal swabs using the Ion Personal Genome Machine (PGM). This protocol involves concomitant amplification of 237 gene fragments encompassing the SARS-CoV-2 genome to increase the abundance and yield of viral specific sequencing reads. Five complete and one near-complete genome sequences of SARS-CoV-2 were generated with a single Ion PGM sequencing run. The sequence coverage analysis revealed two amplicons (positions 13 751-13 965 and 23 941-24 106), which consistently gave low sequencing read coverage in all isolates except 4Apr20-64- Hu. We analyzed the potential primer binding sites within these low covered regions and noted that the 4Apr20-64-Hu possess C at positions 13 730 and 23 929, whereas the other isolates possess T at these positions. The genome nucleotide variations observed suggest that the naturally occurring variations present in the actively circulating SARS-CoV-2 strains affected the performance of the target enrichment panel of the Ion AmpliSeq™ SARS CoV 2 Research Panel. The possible impact of other genome nucleotide variations warrants further investigation, and an improved version of the Ion AmpliSeq™ SARS CoV 2 Research Panel, hence, should be considered.
  18. Fulltext Penicillin-Susceptible, Oxidase-Negative, Nonhemolytic, Nonmotile Bacillus megaterium in Disguise of Bacillus anthracis
    Loong SK, Teoh BT, Johari J, Khor CS, Abd-Jamil J, Nor'e SS, et al.
    Case Rep Infect Dis, 2017;2017:2578082.
    PMID: 28331641 DOI: 10.1155/2017/2578082
    Bacillus anthracis is a bacterial pathogen of major concern. The spores of this bacteria can survive harsh environmental conditions for extended periods and are well recognized as a potential bioterror weapon with significant implications. Accurate and timely identification of this Bacillus species in the diagnostic laboratory is essential for disease and public health management. Biosafety Level 3 measures and ciprofloxacin treatment were instituted when B. anthracis was suspected from a patient with gangrenous foot. 16S rDNA sequencing was performed to accurately identify the suspected bacterium, due to the superiority of this method to accurately identify clinically isolated bacteria. B. megaterium was identified as the causative agent and the organism was subsequently treated as a Biosafety Level 2 pathogen.
  19. Disruption of predicted dengue virus type 3 major outbreak cycle coincided with switching of the dominant circulating virus genotype
    Tan KK, Zulkifle NI, Abd-Jamil J, Sulaiman S, Yaacob CN, Azizan NS, et al.
    Infect Genet Evol, 2017 Oct;54:271-275.
    PMID: 28698156 DOI: 10.1016/j.meegid.2017.07.008
    Dengue is hyperendemic in most of Southeast Asia. In this region, all four dengue virus serotypes are persistently present. Major dengue outbreak cycle occurs in a cyclical pattern involving the different dengue virus serotypes. In Malaysia, since the 1980s, the major outbreak cycles have involved dengue virus type 3 (DENV3), dengue virus type 1 (DENV1) and dengue virus type 2 (DENV2), occurring in that order (DENV3/DENV1/DENV2). Only limited information on the DENV3 cycles, however, have been described. In the current study, we examined the major outbreak cycle involving DENV3 using data from 1985 to 2016. We examined the genetic diversity of DENV3 isolates obtained during the period when DENV3 was the dominant serotype and during the inter-dominant transmission period. Results obtained suggest that the typical DENV3/DENV1/DENV2 cyclical outbreak cycle in Malaysia has recently been disrupted. The last recorded major outbreak cycle involving DENV3 occurred in 2002, and the expected major outbreak cycle involving DENV3 in 2006-2012 did not materialize. DENV genome analyses revealed that DENV3 genotype II (DENV3/II) was the predominant DENV3 genotype (67%-100%) recovered between 1987 and 2002. DENV3 genotype I (DENV3/I) emerged in 2002 followed by the introduction of DENV3 genotype III (DENV3/III) in 2008. These newly emerged DENV3 genotypes replaced DENV3/II, but there was no major upsurge of DENV3 cases that accompanied the emergence of these viruses. DENV3 remained in the background of DENV1 and DENV2 until now. Virus genome sequence analysis suggested that intrinsic differences within the different dengue virus genotypes could have influenced the transmission efficiency of DENV3. Further studies and continuous monitoring of the virus are needed for better understanding of the DENV transmission dynamics in hyperendemic regions.
  20. Fulltext A quantitative reverse transcription-polymerase chain reaction for detection of Getah virus
    Sam SS, Teoh BT, Chee CM, Mohamed-Romai-Noor NA, Abd-Jamil J, Loong SK, et al.
    Sci Rep, 2018 12 05;8(1):17632.
    PMID: 30518924 DOI: 10.1038/s41598-018-36043-6
    Getah virus (GETV), a mosquito-borne alphavirus, is an emerging animal pathogen causing outbreaks among racehorses and pigs. Early detection of the GETV infection is essential for timely implementation of disease prevention and control interventions. Thus, a rapid and accurate nucleic acid detection method for GETV is highly needed. Here, two TaqMan minor groove binding (MGB) probe-based quantitative reverse transcription-polymerase chain reaction (qRT-PCR) assays were developed. The qRT-PCR primers and TaqMan MGB probe were designed based on the conserved region of nsP1 and nsP2 genes of 23 GETV genome sequences retrieved from GenBank. Only the qRT-PCR assay using nsP2-specific primers and probe detected all two Malaysia GETV strains (MM2021 and B254) without cross-reacting with other closely related arboviruses. The qRT-PCR assay detected as few as 10 copies of GETV RNA, but its detection limit at the 95% probability level was 63.25 GETV genome copies (probit analysis, P ≤ 0.05). Further validation of the qRT-PCR assay using 16 spiked simulated clinical specimens showed 100% for both sensitivity and specificity. In conclusion, the qRT-PCR assay developed in this study is useful for rapid, sensitive and specific detection and quantification of GETV.
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