1.Comparative genetic analysis of VP4, VP1 and 3D gene regions of enterovirus 71 and coxsackievirus A16 circulating in Malaysia between 1997-2008
Chan, Y.F. ; Wee, K.L. ; Chiam, C.W. ; Khor, C.S. ; Chan, S.Y. ; Wan Nor Amalina, W.M.Z. ; Sam, I.C.
Tropical Biomedicine 2012;29(3):451-466
Three genomic regions, VP4 capsid, VP1 capsid and 3D RNA polymerase of human enterovirus 71 (EV-71) and coxsackievirus A16 (CV-A16) were sequenced to understand the evolution of these viruses in Malaysia. A total of 42 EV-71 and 36 CV-A16 isolates from 1997-2008 were sequenced. Despite the presence of many EV-71 subgenotypes worldwide, only subgenotypes B3, B4, B5, C1 and C2 were present in Malaysia. Importation of other
subgenotypes such as C3, C4/D and C5 from other countries was infrequent. For CV-A16, the earlier subgenotype B1 was replaced by subgenotypes B2a and the recent B2c. Subgenotype B2a was present throughout the study while B2c only emerged in 2005. No genetic signatures
could be attributed to viral virulence suggesting that host factors have a major role in determining the outcome of infection. Only three EV-71 B3 isolates showed non-consistent phylogeny in the 3D RNA polymerase region which indicated occurrence of recombination in
EV-71. High genetic diversity was observed in the Malaysian EV-71 but Malaysian CV-A16 showed low genetic diversity in the three genomic regions sequenced. EV-71 showed strong purifying selection, but that occurred to a lesser extent in CV-A16.
2.Sunlight exposure might account for the relatively low COVID-19 morbidity and mortality in tropical countries
Muhammad, M. ; Loong, S.K. ; Khor, C.S. ; Mohd-Azami, S.N.I. ; Kafle, A. ; Useh, U. ; Bello, B. ; AbuBakar, S.
Tropical Biomedicine 2024;41(No.1):78-83
The present study aimed at exploring whether sunlight exposure might account for the relative
difference in COVID-19-related morbidity and mortality between tropical and non-tropical countries.
A retrospective observational study was designed and data from the World Health Organization
weekly COVID-19 epidemiological update was compiled. We examined the total number of confirmed
COVID-19 cases per 100 000 population, as well as the total number of COVID-19-related mortalities
per 100 000 population. Solar variables data were obtained from the Global Solar Atlas website
(https://globalsolaratlas.info/). These data were analyzed to determine the association of sunlight
exposure to COVID-19-related morbidity and mortality in tropical and non-tropical countries. Results
revealed a statistically significant decrease in the number of confirmed COVID-19 cases per 100 000
population (P<0.001), as well as the number of COVID-19-related mortalities per 100 000 population
(P<0.001) between tropical and non-tropical countries. Analyses of sunlight exposure data found that
specific photovoltaic power output, global horizontal irradiation, diffuse horizontal irradiation and
global tilted irradiation at optimum angle were significantly inversely correlated to COVID-19-related
morbidity and mortality. This suggests that stronger sunlight exposure potentially leads to lower
COVID-19-related morbidity and mortality. Findings from this study suggest that the relatively low
COVID-19-related morbidity and mortality in tropical countries were possibly due to better sunlight
exposure that translates into adequate vitamin D status.
3.Evaluation of commercial serological assays in Malaysia for detection of anti-Zika virus antibodies
Khoo, H.Y. ; Lee, H.Y. ; Khor, C.S. ; Tan, K.K. ; AbuBakar, S.
Tropical Biomedicine 2021;38(No.4):613-621
The recommended test guidelines for Zika virus (ZIKV) include using both molecular and
serological tools. While the molecular tools are useful for detecting acute infection, the
serological tools are useful for the detection of previous infections. Nevertheless, detection
of ZIKV-specific antibodies remains a challenge due to the high cross-reactivity between
ZIKV and other flaviviruses such as dengue virus (DENV) and Japanese encephalitis virus
(JEV). The objective of this study is to evaluate the commercially available enzyme-linked
immunosorbent assay (ELISA) for the detection of ZIKV IgG. In this study, we evaluated 6
commercially available anti-ZIKV IgG ELISA kits. Pre-characterized serum panels consisting
of 70 sera were selected for the evaluation. The diagnostic accuracy of each ELISA kits was
determined and compared to the gold standard, Foci Reduction Neutralization Test (FRNT).
The present study established that the performance of the NS1-based anti-ZIKV IgG ELISA kit
was superior to that which uses of the E protein as antigen. Overall, commercial ZIKV IgG
ELISA showed varying test performances, with some achieving moderate to high test
sensitivities and specificities. When compared against the FRNT, the test sensitivities ranged
from 7.1% to 78.6%, whereas, the test specificities ranged from 40.0% to 100%. Limitation to
the study includes the cross reactivity between flavivirus and specificity of the kit in
addressing the cross reactivity.
4.Development of a TaqMan minor groove binding probe-based quantitative reverse transcription polymerase chain reaction for the detection and quantification of Zika virus
Chin, K.L. ; Teoh, B.T. ; Sam, S.S. ; Loong, S.K. ; Tan, K.K. ; Azizan, N.S. ; Lim, Y.K. ; Khor, C.S. ; Nor&rsquo ; e, S.S. ; Abd-Jamil, J. ; AbuBakar, S.
Tropical Biomedicine 2022;39(No.4):518-523
5.A TaqMan minor groove binder probe-based quantitative reverse transcription polymerase chain reaction for detection and quantification of chikungunya virus
Lim, Y.Z. ; Teoh, B.T. ; Sam, S.S. ; Azizan, N.S. ; Khor, C.S. ; Nor&rsquo ; e, S.S. ; Abd-Jamil, J. ; AbuBakar, S.
Tropical Biomedicine 2023;40(No.3):313-319
6.Multiplex sequencing of SARS-Cov-2 genome directly from clinical samples using the Ion Personal Genome Machine (PGM)
Tan, K.K. ; Tiong, V. ; Tan, J.Y. ; Wong, J.E. ; Teoh, B.T. ; Abd-Jamil, J. ; Johari, J. ; Nor&rsquo ; e, S.S. ; Khor, C.S. ; Yaacob, C.N. ; Zulkifli, M.M.S. ; CheMatSeri, A. ; Mahfodz, N.H. ; Azizan, N.S. ; AbuBakar, S.
Tropical Biomedicine 2021;38(No.3):283-288
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 4Apr20-64Hu. 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.