Genomic tracking of SARS-COV-2 variants in Myanmar

BackgroundIn December 2019, the COVID-19 disease started in Wuhan, China. WHO declared a pandemic on March 12, 2020, and the disease started in Myanmar on March 23, 2020. December brought variants around the world, threatening the healthcare systems. To counter those threats, Myanmar started the COVID-19 variant surveillance program in late 2020. MethodsWhole genome sequencing was done six times between January 2021 and March 2022. We chose 83 samples with a PCR threshold cycle of less than 25. Then, we used MiSeq FGx for sequencing and Illumina DRAGEN COVIDSeq pipeline, command line interface, GISAID, and MEGA version 7 for data analysis. Result and DiscussionJanuary 2021 results showed no variant. The second run during the rise of cases in June 2021 showed multiple variants like Alpha, Delta, and Kappa. There is only Delta in the third run at the height of mortality in August, and Delta alone continued until the fourth run in December. After the world reported the Omicron variant in November, Myanmar started a surveillance program. The fifth run in January 2022 showed both Omicron and Delta variants. The sixth run in March 2022 showed only Omicron BA.2. Amino acid mutation at receptor binding domain (RBD) of Spike glycoprotein started since the second run coupling with high transmission, recurrence, and vaccine escape. We also found the mutation at the primer targets used in current RT-PCR platforms. ConclusionThe occurrence of multiple variants and mutations claimed vigilance at ports of entry and preparedness for effective control measures. Genomic surveillance with the observation of evolutionary data is required to predict imminent threats of the current disease and diagnose emerging infectious diseases.

How Myanmar Is Working to Maintain Essential Services for People Living With HIV and Key Populations During the Covid-19 Pandemic.

BACKGROUND: Maintaining essential HIV services has being a Global challenge during the COVID-19 crises. Myanmar has 54 million inhabitants. Neighbor of China, Thailand, India and Bangladesh it was impacted by COVID-19, but came up with a comprehensive and effective response, following WHO recommendations. The HIV Prevalence is 0.58% and it is concentrated among key population. A HIV Contingency Plan was developed to face this challenge. METHODOLOGY: The programme-based cross-sectional descriptive study with analysis of routinely collected data from MoHS data system, between 2019 and 2020 was conducted, comparing first six months of 2019 and 2020. RESULTS: HIV outreach activities and HIV testing were slightly affected after detection of first COVID-19 case, till mid May 2020. After that, outreach activities resumed. Introduction of HIV self-testing was initiated. 72% of more than 21,000 PWID on MMT were receiving take home dose up to 14 days and 60% of ART patients were receiving 6 months ARV dispensing. CONCLUSION: Essential HIV services were maintained.

Assessment of post-harvest losses and carbon footprint in intensive lowland rice production in Myanmar.

This paper examines how a move from traditional post-harvest operations of smallholder rice farms in the Ayeyarwaddy delta, Myanmar, to improved post-harvest operations affected income, energy efficiency and greenhouse gas emissions (GHGE). Harvest and post-harvest losses were investigated in a field experiment with 5 replications per scenario. A comparative analysis on energy efficiency and cost-benefits was conducted for different practices of rice production from cultivation to milling. GHGE of different practices were also considered using a life-cycle assessment approach. The study demonstrates that the mechanized practices increased the net income by 30-50% compared with traditional practices. Despite using additional energy for machine manufacturing and fuel consumption, the mechanized practices significantly reduced postharvest losses and did not increase the total life-cycle enegy and GHGE. Combine harvesting helped to significantly reduce harvesting loss in a range of 3 to 7% (by weight of the rice product). Improved post-harvest management practices with a flatbed dryer and hermetic storage reduced the discoloration of rice grains by 3 to 4% and increased head-rice recovery by 20 to 30% (by weight of rice product). The research findings provide empirical evidence that improved post-harvest management of rice in the Ayeyarwaddy delta, compared to traditional post-harvest operations by smallholder farmers, reduce post-harvest losses and improve the quality of rice. The findings provide valuable information for policy makers involved in formulating evidence-based mechanization policies in South and Southeast Asia.

Protective Factors and Biological Sex Differentiate Profiles of Teen Substance Users in Myanmar.

Background. Reports on worldwide drug use include some information on risk factors, but virtually no information on protective factors, which are an important component of prevention programs. Aims. This study investigated protective factors and biological sex differences associated with patterns of substance use among adolescents in Myanmar, a country in Southeast Asia. Method. Myanmar high school students (N = 1,918; Mage = 15.35, SD = 1.07, range = 14-18; 56% female) completed a version of the Communities That Care survey validated for use in this population. Results. Latent class analysis revealed "Low Users" (38%), "Normative Users" (47%), and "Poly Drug Users" (15%) classes for males, and "Low Users" (80%), "Glue/Over-the-Counter Medication Users" (14%), and "High Users" (6%) classes for females. Univariate analyses indicated that belief in the moral order and positive family attachment differentiated profiles for both males and females; opportunities for prosocial family involvement, prosocial peer behavior, and opportunities to talk with teachers were additionally significant for males only. Logistic regression analysis comparing males in the "Low Users" and "Normative Users" classes indicated that opportunities for prosocial family involvement was protective after accounting for significant demographic and risk factors. In contrast, analyses comparing other classes of males or females found that once significant demographic and risk factors were controlled, protective factors did not discriminate classes. Conclusions. These data suggest that sex-specific prevention and intervention strategies may be more successful than universal approaches, and that attention to both risk and protective factors in prevention programming is warranted.

Human exposure to trace elements in central Cambodia: Influence of seasonal hydrology and food-chain bioaccumulation behaviour.

Exposure to mercury and other trace elements remains an important public health concern, worldwide. The present study involved a comprehensive field study to determine concentrations of fourteen trace elements (Al, As, Cr, Co, Cd, Cu, Fe, Hg, Mn, Ni, Pb, Se, V and Zn) in surface water and different fish species from Tonlé Sap Lake in central Cambodia, during both the dry and wet seasons. Total arsenic (tAs) and Mn in surface water during the dry season exceeded WHO drinking water guidelines. Total mercury (tHg) concentrations (µg/g wet wt.) in fish during the wet season (GM = 0.055; CI95 = 0.01-0.26) were approximately 15 times higher (P < 0.05) compared to those during the dry season (GM = 0.0035; CI95 = 0.0004-0.033). Mean target hazard quotients (THQs) for inorganic arsenic (iAs), methyl mercury (MeHg), Mn and Pb were > 1, with estimated maximum values greatly exceeding 1. Mean THQs of Zn, Cd, Ni and Se were very near 1, with estimated maximum values exceeding 1. The MeHg THQ (min-max range: 0.16-9.09) during the wet season was 7 times higher than in the dry season (min-max range: 0.05-1.35). Concentrations of Hg and other trace elements varied widely between fish species. The findings suggest that exposure of some trace elements via water and food is of concern in this region. High consumption rates of fish and rice key factors related to trace element exposure. Seasonal hydrology and species-specific bioaccumulation behaviour in the Tonlé Sap Lake watershed also play an important role. The generated information will be useful to better mitigate trace element exposure in this region.

Gene expression of MAGE-A3 and PRAME tumor antigens and EGFR mutational status in Taiwanese non-small cell lung cancer patients.

AIM: To determine the frequency of expression of the tumor-associated antigens (TAAs) melanoma-associated antigen A3 (MAGE-A3) and preferentially expressed antigen of melanoma (PRAME) and the rate of EGFR mutations in a Taiwanese non-small cell lung cancer (NSCLC) population including only adenocarcinomas and squamous cell carcinomas. Furthermore, to investigate associations between TAA expression and EGFR mutations and to evaluate these TAAs as prognostic markers for overall survival. The occurrence of single nucleotide polymorphisms in MAGEA3 and PRAME was also assessed. METHODS: Archival fresh-frozen tumor tissue specimens were tested by quantitative reverse transcription polymerase chain reaction assays to detect MAGE-A3 and PRAME expression. EGFR mutations were detected by mass spectroscopy and single nucleotide polymorphisms by gene sequencing. RESULTS: Of the 156 adenocarcinomas examined, 3.3% expressed MAGE-A3, 32.2% expressed PRAME and 62.8% had EGFR mutations. Of the 128 squamous cell carcinomas, 29.8% expressed MAGE-A3, 59.2% expressed PRAME and 20.5% harbored EGFR mutations. TAA expression was similar across subgroups determined by patient or tumor characteristics. There was no association between TAA expression and EGFR mutation status and TAA expression was found not to be a prognostic marker for survival. Single nucleotide polymorphisms were identified, one of which with a possible impact on MAGE-A3 expression. CONCLUSIONS: In this NSCLC population, expression of MAGE-A3 and PRAME was more frequent in squamous cell carcinomas than in adenocarcinomas tumors. EGFR mutations were not associated with TAA expression for either histology and were three times more frequent in adenocarcinomas than in squamous cell carcinomas tumors.

The prevalence of expression of MAGE-A3 and PRAME tumor antigens in East and South East Asian non-small cell lung cancer patients.

INTRODUCTION: Treatment of non-small cell lung cancer (NSCLC) is an important and often unmet medical need regardless of the disease stage at the time of first diagnosis. Antigen-specific immunotherapy may be a feasible therapeutic option if tumor associated antigens (TAAs) that can be targeted by the patient's immune system are identified. The study objective (NCT01837511) was to investigate the expression rates of MAGE-A3 and PRAME in tumors from East Asian NSCLC patients, and the associations between TAA expression and clinico-pathologic patient characteristics. METHODS: Archived formalin-fixed paraffin-embedded tumor tissue specimens were tested for MAGE-A3 and PRAME expression by quantitative reverse transcription polymerase chain reaction. Exploratory analyses of the impact of patient and tumor characteristics on antigen expression were performed by multivariate logistic regression analyses. RESULTS: A total of 377 specimens were tested and a valid expression result was obtained for 86.5% and 92.6% for MAGE-A3 and PRAME, respectively. Of the specimens with valid test results, 26.4% expressed MAGE-A3, 49.9% PRAME, 20.0% both and 57.5% expressed at least one TAA. The same pattern of associations between antigen expression and patient and tumor characteristics was found for both TAAs: higher rates of antigen-positive tumors were found in squamous cell carcinomas compared to adenocarcinomas, and for smokers compared to non-smokers. CONCLUSIONS: Expression of MAGE-A3 and PRAME suggests an association with tumor histology and the patient's smoking status. The rates of TAA-positive tumors found in these East and South East Asian NSCLC patients indicate that both antigens may serve as targets for antigen-specific immunotherapies.