Displaying publications 1 - 20 of 27 in total

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  1. Khor, C. C., Tan, T. L.
    Medicine & Health, 2017;12(2):363-367.
    MyJurnal
    The Morel-Lavallee lesion is a rare soft tissue injury that occurs due to traumatic shearing force on skin surface causing separation of skin and subcutaneous tissue resulting in hematoma. This case report depicts a 22-year-old gentleman who was involved in a motor vehicle accident. He complained of pain and swelling over lower back. He was treated for soft tissue injury and admitted for pain control. One day post-trauma, he complained of increased swelling over the back. His hemoglobin dropped from 12.2g/dL to 10.7g/dL. Diagnosis of Morel-Lavallae lesion was made. Initially no surgical intervention was planned. However, in view of worsening of swelling, bedside aspiration was performed and subsequently a pigtail catheter was inserted to drain the hematoma. In total, 2.05 litre of liquefied hematoma was drained. Thus, Morel-Lavallee lesion is an uncommon soft tissue injury that can cause significant bleeding following trauma.
    Keywords: degloving injuries, hematoma, trauma
  2. Khor CC, Tan TL
    Medicine & Health, 2018;13(1):227-231.
    MyJurnal
    Acupuncture is a form of complementary medicine that has been practiced in China for thousands of years. Adverse effect of acupuncture is rarely reported in local literature. This is a case of a patient who developed bilateral pneumothorax following an acupuncture session. A 63-year-old lady with no significant medical illness presented with sudden onset of shortness of breath half an hour following acupuncture and massage session by traditional medicine practitioner. On examination, she was tachypnoiec and there was reduced air entry bilaterally on lung auscultation. Urgent portable chest X-ray was done and it showed bilateral pneumothorax. Bilateral chest tubes were inserted. Patient was discharged well following five days of hospitalization. As acupuncture is gaining popularity among Malaysian population, medical practitioners need to increase their awareness and knowledge regarding the adverse effect of such alternative practice.
  3. Aziz MS, Abdullah MZ, Khor CY
    ScientificWorldJournal, 2014;2014:482363.
    PMID: 25225638 DOI: 10.1155/2014/482363
    An efficient simulation technique was proposed to examine the thermal-fluid structure interaction in the effects of solder temperature on pin through-hole during wave soldering. This study investigated the capillary flow behavior as well as the displacement, temperature distribution, and von Mises stress of a pin passed through a solder material. A single pin through-hole connector mounted on a printed circuit board (PCB) was simulated using a 3D model solved by FLUENT. The ABAQUS solver was employed to analyze the pin structure at solder temperatures of 456.15 K (183(°)C) < T < 643.15 K (370(°)C). Both solvers were coupled by the real time coupling software and mesh-based parallel code coupling interface during analysis. In addition, an experiment was conducted to measure the temperature difference (ΔT) between the top and the bottom of the pin. Analysis results showed that an increase in temperature increased the structural displacement and the von Mises stress. Filling time exhibited a quadratic relationship to the increment of temperature. The deformation of pin showed a linear correlation to the temperature. The ΔT obtained from the simulation and the experimental method were validated. This study elucidates and clearly illustrates wave soldering for engineers in the PCB assembly industry.
  4. Yap KL, Ooi YE, Khor CM, Wong SH
    Malays J Pathol, 1992 Dec;14(2):105-10.
    PMID: 1338997
    The group A rotavirus staphylococcal co-agglutination test was evaluated and its sensitivity and specificity compared with an in-house enzyme-linked immunosorbent assay (ELISA) and a commercial latex agglutination test (Rotalex). In addition, the storage stability of the staphylococcal reagents was ascertained. Examination of 136 clarified suspensions of diarrhoeal faeces by the staphylococcal co-agglutination test revealed a high proportion of false positives (26%) and uninterpretable results (34%) due to non-specific agglutination. Non-specific agglutination could be removed effectively by prior absorption of the clarified faecal specimens with unsensitized staphylococci. The staphylococcal co-agglutination test was less sensitive and specific than the in-house enzyme-linked immunosorbent assay but was comparable to the Rotalex slide latex agglutination test. The staphylococcal reagents have a shelf life of at least 29 weeks.
  5. Yap KL, Wong YH, Khor CM, Ooi YE
    Can J Microbiol, 1992 Sep;38(9):996-9.
    PMID: 1334446
    A 12-month study was carried out on the molecular epidemiology of rotavirus in urban and suburban Malaysian children. Analysis of faecal samples from 973 hospitalized diarrhoeic children by polyacrylamide gel electrophoresis detected 268 rotaviruses (28%). All isolates were group A rotaviruses, which produced 22 electropherotypes: 16 (91.5%) with long RNA migration patterns and 6 (8.5%) with short patterns. One of the long-pattern electropherotypes was the predominant strain (71.1% of the total electropherotypes) isolated during this study. Although 3 other strains were detected sporadically over the study period, 16 others were present only during the first 7 months and 2 others were confined to the last 5 months. Long- and short-pattern electropherotypes were found to co-circulate extensively. There was a significant association of short-pattern electropherotypes with infection in older children. In addition, the prevalence of vomiting and mean duration of diarrhoea were significantly associated with different electropherotypes.
  6. Khoo HY, Lee HY, Khor CS, Tan KK, AbuBakar S
    Trop Biomed, 2021 Dec 01;38(4):613-621.
    PMID: 35001928 DOI: 10.47665/tb.38.4.105
    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.
  7. Jaafar MS, Hamid O, Khor CS, Yuvaraj RM
    Malays J Med Sci, 2002 Jan;9(1):28-33.
    PMID: 22969315 MyJurnal
    The relationship between left ventricular mass (LVM) and the mean arterial blood pressure (MAP) was investigated, using M-Mode echocardiography. MAP was higher in hypertensive patients (p<0.05, n=9) compared to that of controlled subjects. The results showed that LVM index for hypertensive patients was significantly higher (p<0.05, n=9) than that for the normal group. LVM index correlates fairly (r=0.6) with MAP for hypertensive patients. The results also show that the increase of intraventricular septal wall thickness (IVST) was due to hypertension. The LVM (r =0.9) and IVST (r=0.75) of the normal subjects were linearly dependent on the body surface area (BSA). The hypertensive group revealed a non-linear relationship to the BSA.
  8. Lee YM, Fock K, See SJ, Ng TM, Khor C, Teo EK
    J Gastroenterol Hepatol, 2000 Jun;15(6):622-5.
    PMID: 10921415
    BACKGROUND: The aim of this study was to determine the prevalence rates of inflammatory bowel disease in the different races in Singapore.

    METHODS: The patients studied consisted of 58 people with an established diagnosis of ulcerative colitis (UC) and Crohn's disease (CD) as determined by a combination of clinical, radiological, endoscopic and histological criteria. The patients were residents of a well-defined geographical area in the northern part of Singapore and had been referred to the single regional hospital. Epidemiological data including sex, age, ethnicity, family history and disease type and extent were collected from case records and patient interviews.

    RESULTS: There were 37 UC and 21 CD patients. Of the patients with UC, 67.5% were Chinese, 13.5% were Malay and 19% were Indian. The CD group consisted of 81% Chinese, 9.5% Malay and 9.5% Indian patients. The study population from which the patients were drawn was approximately 0.5 million in size.

    CONCLUSIONS: The overall prevalence of UC was 6 per 100,000 and of CD was 3.6 per 100,000 in Singapore. There were disproportionately more Indians suffering from UC, with a prevalence of 16.2 per 100,000 in comparison with six per 100,000 for Chinese and seven per 100 000 for Malays. The relative risk of UC in Indians is 2.9-fold greater than for the Chinese (CI= 1.25-6.7) which was statistically significant. This trend was not seen for CD.

  9. 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. Khor CS, Lee HY, Abd-Majid MA, Khoo HY, Khoo JJ, AbuBakar S
    Trop Biomed, 2024 Jun 01;41(2):224-229.
    PMID: 39154278 DOI: 10.47665/tb.41.2.015
    Serological evidence has shown the presence of several mosquito-borne arbovirus infections among the inhabitants of the forest fringe areas of the tropics. Among these infections, Japanese encephalitis, dengue fever, chikungunya fever and Zika fever could be targeted for vaccination to overcome severe infection and limit the disease transmission. Seroprevalence data among this high-risk population are needed to provide an estimate of the potential cost-effectiveness of any vaccine programme targeting these infections. The present study was conducted at six indigenous people (Orang Asli) villages and FELDA (Federal Land Development Authority) settlements located at the forest fringes of Malaysia. All participants consented and provided blood samples and demographic data for the study. The blood samples were tested for the presence of antibodies against CHIKV, DENV, JEV and ZIKV individually using ELISA. Results obtained were also analysed to determine the predictors for CHIKV, DENV, JEV and ZIKV seropositivity. Among the 585 samples tested, 33.0% (N=193), 41.7% (N=244), 10.3% (N=60) and 21.0% (N=123) were positive for CHIKV IgG, DENV IgG, JEV IgG and ZIKV IgG, respectively. Approximately one-third (N=220, 37.6%) of the participants were tested negative for IgG antibodies against all four arboviruses. Age of participants and type of settlement were found to be a significant predictor for CHIKV, DENV, JEV and ZIKV seropositivity. Level of education was a significant predictor for CHIKV, DENV and ZIKV seropositivity. Gender, however, was not found to be a significant predictor for infection with any of these viruses. These findings reaffirmed the significant presence of infection involving these major arboviruses among the group of people living within the forest fringe areas of Peninsular Malaysia. Hence, any future consideration of vaccination for these infections must take into consideration the marginalized and underserved communities living at the forest fringe areas of the tropics where these infections are present.
  11. Ishak MI, Daud R, Noor SNFM, Khor CY, Roslan H
    Acta Bioeng Biomech, 2022;24(3):147-159.
    PMID: 38314490
    PURPOSE: The aim of this study was to evaluate the mechanical stimuli transfer at the bone-implant interface via stress and strain energy density transfer parameters. This study also aimed to investigate the effect of different implant stiffness and parafunctional loading values on the defined mechanical stimuli transfer from the implant to the surrounding bone.

    METHODS: A three-dimensional finite element model of two-piece threaded dental implant with internal hexagonal connection and mandibular bone block was constructed. Response surface method through face-centred central composite design was applied to examine the influence of two independent factors variables using three levels. The analysis model was fitted to a second-order polynomial equation to determine the response values.

    RESULTS: The results showed that the implant stiffness was more effective than the horizontal load value in increasing the stress and strain energy density transfers. The interaction between both factors was significant in decreasing the likelihood of bone resorption. Decreasing the implant stiffness and horizontal load value led to the increased stress transfer and unexpected decrease in the strain energy density, except at the minimum level of the horizontal load. The increase in the implant stiffness and horizontal load value (up to medium level) have increased the strain energy transfer to the bone.

    CONCLUSIONS: The stress and strain energy density were transferred distinctively at the bone-implant interface. The role of both implant stiffness and parafunctional loading is important and should be highlighted in the preoperative treatment planning and design of dental implant.

  12. Muhammad M, Loong SK, Khor CS, Mohd-Azami SNI, Kafle A, Useh U, et al.
    Trop Biomed, 2024 Mar 01;41(1):78-83.
    PMID: 38852137 DOI: 10.47665/tb.41.1.010
    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.
  13. Yap KL, Yasmin AM, Wong YH, Ooi YE, Tan SC, Jegathesan M, et al.
    Med J Malaysia, 1992 Dec;47(4):303-8.
    PMID: 1303484
    A 1 year longitudinal study of 156 Malaysian children from urban and suburban areas in the Klang Valley revealed that the incidence rate of diarrhoea was 23.6 per 100 person-year with abnormal faeces reported on 0.26% of the total days of observation. Diarrhoea cases were detected in children from all socioeconomic classes. Rotavirus was isolated from 12% of the diarrheic children and asymptomatic rotavirus infection occurred in 3.2% of the children. All rotaviruses isolated were group A rotaviruses with long electrophoretypic pattern.
  14. Faizal WM, Ghazali NNN, Khor CY, Badruddin IA, Zainon MZ, Yazid AA, et al.
    Comput Methods Programs Biomed, 2020 Nov;196:105627.
    PMID: 32629222 DOI: 10.1016/j.cmpb.2020.105627
    BACKGROUND AND OBJECTIVE: Human upper airway (HUA) has been widely investigated by many researchers covering various aspects, such as the effects of geometrical parameters on the pressure, velocity and airflow characteristics. Clinically significant obstruction can develop anywhere throughout the upper airway, leading to asphyxia and death; this is where recognition and treatment are essential and lifesaving. The availability of advanced computer, either hardware or software, and rapid development in numerical method have encouraged researchers to simulate the airflow characteristics and properties of HUA by using various patient conditions at different ranges of geometry and operating conditions. Computational fluid dynamics (CFD) has emerged as an efficient alternative tool to understand the airflow of HUA and in preparing patients to undergo surgery. The main objective of this article is to review the literature that deals with the CFD approach and modeling in analyzing HUA.

    METHODS: This review article discusses the experimental and computational methods in the study of HUA. The discussion includes computational fluid dynamics approach and steps involved in the modeling used to investigate the flow characteristics of HUA. From inception to May 2020, databases of PubMed, Embase, Scopus, the Cochrane Library, BioMed Central, and Web of Science have been utilized to conduct a thorough investigation of the literature. There had been no language restrictions in publication and study design of the database searches. A total of 117 articles relevant to the topic under investigation were thoroughly and critically reviewed to give a clear information about the subject. The article summarizes the review in the form of method of studying the HUA, CFD approach in HUA, and the application of CFD for predicting HUA obstacle, including the type of CFD commercial software are used in this research area.

    RESULTS: This review found that the human upper airway was well studied through the application of computational fluid dynamics, which had considerably enhanced the understanding of flow in HUA. In addition, it assisted in making strategic and reasonable decision regarding the adoption of treatment methods in clinical settings. The literature suggests that most studies were related to HUA simulation that considerably focused on the aspects of fluid dynamics. However, there is a literature gap in obtaining information on the effects of fluid-structure interaction (FSI). The application of FSI in HUA is still limited in the literature; as such, this could be a potential area for future researchers. Furthermore, majority of researchers present the findings of their work through the mechanism of airflow, such as that of velocity, pressure, and shear stress. This includes the use of Navier-Stokes equation via CFD to help visualize the actual mechanism of the airflow. The above-mentioned technique expresses the turbulent kinetic energy (TKE) in its result to demonstrate the real mechanism of the airflow. Apart from that, key result such as wall shear stress (WSS) can be revealed via turbulent kinetic energy (TKE) and turbulent energy dissipation (TED), where it can be suggestive of wall injury and collapsibility tissue to the HUA.

  15. Chan YF, Wee KL, Chiam CW, Khor CS, Chan SY, Amalina W MZ, et al.
    Trop Biomed, 2012 Sep;29(3):451-66.
    PMID: 23018509 MyJurnal
    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.
  16. Abd Majid MA, Khoo JJ, Lim FS, Khor CS, Loong SK, Low VL, et al.
    Trop Biomed, 2020 Dec 01;37(4):884-895.
    PMID: 33612742 DOI: 10.47665/tb.37.4.884
    This study was carried out to determine from bacterial profiling to the bacterial profiles of head lice among the Orang Asli communities. The head lice were collected from Orang Asli community volunteers. The surface sterilized head lice pools were subjected to genomic DNA extraction while next generation sequencing of the 16S rRNA gene was performed using the Illumina MiSeq platform. Six female and three male head lice identified as Pediculus humanus capitis were collected. A total of 111 368 number of NGS sequencing reads were recorded while another 223 bacterial taxa sequences were obtained. Symbiotic bacteria showed the highest number of reads, with Arsenophonus and Rhodococcus sequences being the most abundant genera in the female and male samples, respectively. The female head lice contained a more distinct microbial diversity. Amongst the pathogenic bacterial species sequences noted were the methicillin-resistant Staphylococcus aureus, Streptobacillus moniliformis, Haemophilus influenzae, Bordetella pertussis and Acinetobacter baumannii. The 16S rRNA genome sequencing revealed a number of rare and pathogenic bacterial species within the head lice of the Orang Asli. The socio-economic practices of the community which involved forest foraging and hunting, and their poor living conditions potentially facilitated the transmission of zoonotic bacterial pathogens, including those found within the head lice. Hence, there is the possibility that the head lice could serve as vectors for the transmission of pathogenic bacteria. This study highlighted the diverse microbial community found within the head lice's gut of the Orang Asli, with the detection of multiple rare and pathogenic bacteria capable of causing severe infections.
  17. Khoo JJ, Lim FS, Tan KK, Chen FS, Phoon WH, Khor CS, et al.
    J Med Entomol, 2017 09 01;54(5):1444-1448.
    PMID: 28874019 DOI: 10.1093/jme/tjx131
    Spirochetes from the Borrelia genus are known to cause diseases in humans, namely Lyme disease and relapsing fever. These organisms are commonly transmitted to humans by arthropod vectors including ticks, mite, and lice. Here, we report the molecular detection of a Borrelia sp. from a Haemaphysalis hystricis Supino tick collected from wildlife in an Orang Asli settlement in Selangor, Malaysia. Phylogenetic analyses of partial 16s rRNA and flaB gene sequences revealed that the Borrelia sp. is closely related to the relapsing fever group borreliae, Borrelia lonestari, Borrelia miyamotoi, and Borrelia theileri, as well as a number of uncharacterized Borrelia sp. from ticks in Portugal and Japan. To our knowledge, this is the first report of a Borrelia sp. detected in H. hystricis, and in Malaysia. The zoonotic potential of this Borrelia sp. merits further investigation.
  18. Faizal WM, Ghazali NNN, Badruddin IA, Zainon MZ, Yazid AA, Ali MAB, et al.
    Comput Methods Programs Biomed, 2019 Oct;180:105036.
    PMID: 31430594 DOI: 10.1016/j.cmpb.2019.105036
    Obstructive sleep apnea is one of the most common breathing disorders. Undiagnosed sleep apnea is a hidden health crisis to the patient and it could raise the risk of heart diseases, high blood pressure, depression and diabetes. The throat muscle (i.e., tongue and soft palate) relax narrows the airway and causes the blockage of the airway in breathing. To understand this phenomenon computational fluid dynamics method has emerged as a handy tool to conduct the modeling and analysis of airflow characteristics. The comprehensive fluid-structure interaction method provides the realistic visualization of the airflow and interaction with the throat muscle. Thus, this paper reviews the scientific work related to the fluid-structure interaction (FSI) for the evaluation of obstructive sleep apnea, using computational techniques. In total 102 articles were analyzed, each article was evaluated based on the elements related with fluid-structure interaction of sleep apnea via computational techniques. In this review, the significance of FSI for the evaluation of obstructive sleep apnea has been critically examined. Then the flow properties, boundary conditions and validation of the model are given due consideration to present a broad perspective of CFD being applied to study sleep apnea. Finally, the challenges of FSI simulation methods are also highlighted in this article.
  19. 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.
  20. Ong J, Ong AML, Ong S, Xin X, Lee YY, Pausawasdi N, et al.
    J Gastroenterol Hepatol, 2021 Nov;36(11):3056-3068.
    PMID: 34159640 DOI: 10.1111/jgh.15594
    BACKGROUND AND AIM: The coronavirus disease 2019 pandemic has impacted gastroenterology practices worldwide; however, its protracted effects within Southeast Asia were unknown. The primary aim of the study was to determine the impact of the pandemic on clinical demands including burnout among gastroenterologists within the region. The secondary aim was to identify risk factors for burnout and determine regional stressors.

    METHODS: This was a mixed-methods study. Gastroenterologists were surveyed electronically between September 1 and December 7, 2020, via gastroenterology and endoscopy societies of Brunei, Indonesia, Malaysia, Philippines, Singapore, and Thailand. Quantitative and qualitative data were collected. The 22-item Maslach Burnout Inventory-Human Services Survey (MBI-HSS) was used to detect burnout. Quantitative data were non-parametric; non-parametric methods were used for statistical comparisons. Logistic regression was used to determine risk factors for burnout. Content analysis method was used to analyze qualitative data. Ethical approval was obtained.

    RESULTS: A total of 73.0% reported that they were still significantly affected by the pandemic. Of these, 40.5% reported increased workload and 59.5% decreased workload. Statistically significant differences in weekly working hours, endoscopy, and inpatient volumes were present. No differences were observed in outpatient volumes, likely because of telemedicine. Burnout was common; however, 50.1% of gastroenterologists were unaware of or did not have access to mental health support. This, as well as depression, being a trainee, and public sector work, increased burnout risk significantly.

    CONCLUSION: The effects of the pandemic are multifaceted, and burnout is common among Southeast Asian gastroenterologists. Safeguards for mental health are suboptimal, and improvements are urgently needed.

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