Genomic diversity of SARS-CoV-2 in Malaysia.

BACKGROUND: More than a year after its first appearance in December 2019, the COVID-19 pandemic is still on a rampage in many parts of the world. Although several vaccines have been approved for emergency use, the emergence and rapid spread of new SARS-CoV-2 variants have sparked fears of vaccine failure due to immune evasion. Massive viral genome sequencing has been recommended to track the genetic changes that could lead to adverse consequences. METHODS: We sequenced SARS-CoV-2 respiratory isolates from the National Public Health Laboratory, Malaysia and examined them together with viral genomes deposited in GISAID by other Malaysian researchers, to understand the evolutionary trend of the virus circulating in the country. We studied the distribution of virus lineages and site-wise mutations, analysed genetic clustering with the goeBURST full Minimum Spanning Tree algorithm, examined the trend of viral nucleotide diversity over time and performed nucleotide substitution association analyses. RESULTS: We identified 22 sub-lineages, 13 clonal complexes, 178 sequence types and seven sites of linkage disequilibrium in 277 SARS-CoV-2 genomes sequenced between January and December 2020. B.1.524 was the largest lineage group. The number of mutations per genome ranged from 0 to 19. The mean genomic diversity value over 12 months was 3.26 × 10-4. Of 359 mutations detected, 60.5% of which were non-synonymous, the most frequent were in the ORF1ab (P4715L), S (D614G and A701V) and N (S194L) genes. CONCLUSION: The SARS-CoV-2 virus accumulated an abundance of mutations in the first year of the COVID-19 pandemic in Malaysia. Its overall genetic diversity, however, is relatively low compared to other Asian countries with larger populations. Continuous genomic and epidemiological surveillance will help to clarify the evolutionary processes determining viral diversity and impacting on human health.

The SCIDOTS Project: evidence of benefits of an integrated tobacco cessation intervention in tuberculosis care on treatment outcomes.

BACKGROUND: There is substantial evidence to support the association between tuberculosis (TB) and tobacco smoking and that the smoking-related immunological abnormalities in TB are reversible within six weeks of cessation. Therefore, connecting TB and tobacco cessation interventions may produce significant benefits and positively impact TB treatment outcomes. However, no study has extensively documented the evidence of benefits of such integration. SCIDOTS Project is a study from the context of a developing nation aimed to determine this. METHODS: An integrated TB-tobacco intervention was provided by trained TB directly observed therapy short-course (DOTS) providers at five chest clinics in Malaysia. The study was a prospective non-randomized controlled intervention using quasi-experimental design. Using Transtheoretical Model approach, 120 eligible participants who were current smokers at the time of TB diagnosis were assigned to either of two treatment groups: conventional TB DOTS plus smoking cessation intervention (integrated intervention or SCIDOTS group) or conventional TB DOTS alone (comparison or DOTS group). At baseline, newly diagnosed TB patients considering quitting smoking within the next 30 days were placed in the integrated intervention group, while those who were contemplating quitting were assigned to the comparison group. Eleven sessions of individualized cognitive behavioral therapy with or without nicotine replacement therapy were provided to each participant in the integrated intervention group. The impacts of the novel approach on biochemically validated smoking cessation and TB treatment outcomes were measured periodically as appropriate. RESULTS: A linear effect on both 7-day point prevalence abstinence and continuous abstinence was observed over time in the intervention group. At the end of 6 months, patients who received the integrated intervention had significantly higher rate of success in quitting smoking when compared with those who received the conventional TB treatment alone (77.5% vs. 8.7%; p < 0.001). Furthermore, at the end of TB treatment (6 months or later), there were significantly higher rates of treatment default (15.2% vs. 2.5%; p = 0.019) and treatment failure (6.5% vs. 0%; p = 0.019) in the DOTS group than in the SCIDOTS group. CONCLUSION: This study provides evidence that connecting TB-tobacco treatment strategy is significant among TB patients who are smokers. The findings suggest that the integrated approach may be beneficial and confer advantages on short-term outcomes and possibly on future lung health of TB patients who quit smoking. This study may have important implications on health policy and clinical practice related to TB management among tobacco users.

Tobacco use prevalence, knowledge, and attitudes among newly diagnosed tuberculosis patients in Penang State and Wilayah Persekutuan Kuala Lumpur, Malaysia.

BACKGROUND: There is sufficient evidence to conclude that tobacco smoking is strongly linked to tuberculosis (TB) and a large proportion of TB patients may be active smokers. In addition, a previous analysis has suggested that a considerable proportion of the global burden of TB may be attributable to smoking. However, there is paucity of information on the prevalence of tobacco smoking among TB patients in Malaysia. Moreover, the tobacco-related knowledge, attitudes, and behaviors of TB patients who are smokers have not been previously explored. This study aimed to document the prevalence of smoking among newly diagnosed TB patients and to learn about the tobacco use knowledge and attitudes of those who are smokers among this population. METHODS: Data were generated on prevalence rates of smoking among newly diagnosed TB patients in the State of Penang from January 2008 to December 2008. The data were obtained based on a review of routinely collated data from the quarterly report on TB case registration. The study setting comprised of five healthcare facilities (TB clinics) located within Penang and Wilayah Persekutuan, Kuala Lumpur health districts in Malaysia, which were involved in a larger project, known as SCIDOTS Project. A 58-item questionnaire was used to assess the tobacco use knowledge, attitudes and behaviors of those TB patients who were smokers. RESULTS: Smoking status was determinant in 817 of 943 new cases of TB from January to December 2008. Of this, it was estimated that the prevalence rates of current- and ex-smoking among the TB patients were 40.27% (329/817) and 13.95% (114/817), respectively. The prevalence of ever-smoking among patients with TB was estimated to be 54,220 per 100,000 population. Of 120 eligible participants for the SCIDOTS Project, 88 responded to the survey (73.3% response rate) and 80 surveys were analyzed (66.7% usable rate). The mean (+/- SD) total score of tobacco use knowledge items was 4.23 +/- 2.66 (maximum possible score=11). More than half of the participants (51.3%) were moderately dependent to nicotine. A moderately large proportion of the respondents (41.2%) reported that they have ever attempted to quit smoking, while more than half (56.3%) have not. Less than half (47.5%) of the study participants had knowledge about the body system on which cigarette smoking has the greatest negative effect. The majority wrongly believed that smokeless tobacco can increase athletic performance (60%) and that it is a safe and harmless product (46.2%). An overwhelming proportion (>80%) of the patients believed that: smoking is a waste of money, tobacco use is very dangerous to health, and that smokers are more likely to die from heart disease when compared with non-smokers. The use of smokeless tobacco was moderately prevalent among the participants with 28.8% reporting ever snuffed, but the use of cigar and pipe was uncommon. CONCLUSION: Smoking prevalence rate is high among patients with TB in Malaysia. These patients generally had deficiencies in knowledge of tobacco use and its health dangers, but had positive attitudes against tobacco use. Efforts should be geared towards reducing tobacco use among this population due to its negative impact on TB treatment outcomes.