Consensus insertion/deletions and amino acid variations of all coding and noncoding regions of the SARS-CoV-2 Omicron clades, including the XBB and BQ.1 lineages.

The currently dominant Omicron variant of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has swiftly diverged into clades. To predict the probable impact of these clades, the consensus insertions/deletions (indels) and amino acid substitutions of the whole genome of clades were compared with the original SARS-CoV-2 strain. The evolutionary history of representatives of clades and lineages was inferred using the maximum-likelihood method and tested using the bootstrap method. The indels and polymorphic amino acids were found to be either clade-specific or shared among clades. The 21K clade has unique indels and substitutions, which probably represent reverted indels/substitutions. Three variations that appear to be associated with SARS-CoV-2 attenuation in the Omicron clades included a deletion in the nucleocapsid gene, a deletion in the 3'untranslated region, and a truncation in open reading frame 8. Phylogenetic analysis showed that the Omicron clades and lineages form three separate clusters.

Assessment of Cell Cycle and Induction of Apoptosis by Shiga-like Toxin Produced by Escherichia coli O157:H7 in T47D Breast Cancer Cells Using Flow Cytometry.

BACKGROUND: The low general toxicity against tumors expressing globotriaosylceramide (Gb3) and Shiga-like toxins produced by E. coli have been proposed as an anti-cancer therapy because of their specific target. This study aimed to determine the potency of the local strains of E. coli O157:H7 isolated from humans and cattle as a new breast cancer therapy by analyzing the cell cycle's inhibition and apoptosis induction. MATERIAL AND METHODS: Approximately 10 cultured T47D cells were subjected to Shiga-like toxin produced by four local isolates of E. coli O157:H7, including KL-48 (2) from humans, and SM-25 (1), SM-7 (1), DS-21 (4) from cattle. Using ATCC 43894 as a control, the treatment was observed for 24 h by two replications. In addition, a FITC-Annexin V and PI assay were used to observe apoptosis and necrosis effect, as well as to analyze the cell cycle using propidium iodide (PI) staining. RESULTS: The results showed the toxicity effect of Shiga in the human T47 D cells line. The viability of the cells is subjected to Shiga-like toxins produced by KL-48 (2), SM7 (1), ATCC 43894, SM-25 (1), and DS-21 (4) isolates decreased with 15.20, 16.36, 22.17,  22.64, and 33.86%, in contrary to control of 94.36%. These were supported by the cells entering the late apoptosis of the cell cycle through each isolate with 67.66, 62.60, 63.68, 63.90, and 54.74%, and a control of 0.01%. Also, the necrosis cell for each treatment of 12.73, 19.3, 10.84, 10.53, and 4.86% was higher than the control of 5.51%. These were confirmed by the higher percentage of the cells treated with toxins of KL-48 (2), SM7(1), ATCC 43894, SM-25 (1), and DS-21 (4), which entered G0-G1 of the cell cycle phase with 66.41, 63.37, 61.52, 55.36, and 47.28%, respectively, than control of 40.69%. Additionally, the toxicity effect was supported by an increase in the cells entering the S and the G2-M phase of the cycle for each treatment. CONCLUSION: It is concluded that the Shiga-like toxin produced by E. coli O157:H7 local isolates can be developed as a drug against breast cancer based on its effect to arrest induction of the cell cycle and inducing apoptosis.

Factors associated with anti-retroviral therapy adherence among patients living with HIV during the COVID-19 pandemic: A cross-sectional study.

Background: The coronavirus disease (COVID-19) pandemic causes fear and anxiety symptoms on some vulnerable populations such as patients living with human immunodeficiency virus (HIV) (PLWH). Physical distancing (during consultation in the clinic) and isolation restrictions will likely have a negative impact on/disruption to all care continuum services of HIV diseases although healthcare services and access to anti-retroviral therapy (ART) have continued to operate. Objective: To investigate the factors associated with ART adherence among PLWH during the COVID-19 pandemic. Methodology: A cross-sectional study was conducted on 324 PLWH who had been on ART for at least 6 months between June 2020 and January 2021. A semi-structured questionnaire was used to interview participants to collect data on sociodemographic characteristics and other factors. Results: Of 324 PLWH taking ART, 264 (81.48%) had high adherence (≥95%) and 60 (18.52%) had low adherence (< 95%). Factors independently associated with high ART adherence were employment status (adjusted odds ratio (AOR): 0.030, 95% confidence interval (CI): 0.010-0.088; p < 0.001), type of antiretroviral (ARV) (AOR: 3.101, 95% CI: 1.137-8.456; p = 0.027), family support (AOR: 0.157, 95% CI: 0.052-0.475; p = 0.001), the perception that the COVID-19 pandemic negatively impacts the ability to attend clinics (AOR: 7.339, 95% CI: 1.46-36.79; p = 0.015), and the perception that the COVID-19 pandemic negatively impacts the ability to take ART (AOR: 10.611, 95% CI: 2.98-37.72; p < 0.001). Conclusions: During the COVID-19 pandemic, factors associated with high ART adherence among PLWH attending the Hospital of Wangaya in Denpasar, Bali, Indonesia were employment status, ART type [non-fixed dose combination (FDC)], family support, and the perception that the COVID-19 pandemic negatively impacts the ability to attend clinics and to take ART.

Preliminary study of coronavirus disease 2019 on pets in pandemic in Denpasar, Bali, Indonesia.

BACKGROUND AND AIM: Coronavirus disease 2019 (COVID-19) is an acute infectious respiratory disease caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) and has spread rapidly globally, resulting in a pandemic. In humans, the main routes of transmission are respiratory droplets and close contact with infected individuals or through contact with an object infected with the virus, followed by touching mouth, nose, or eyes. It is assumed that SARS-CoV-2 was originated in wild animals and was then transmitted to humans. Although some wildlife and domestic animals can be naturally or experimentally infected with the virus, the intermediate hosts that transmitted it to humans are still unknown. Understanding the dynamics of SARS-CoV-2 associated with possible zoonotic transmission of intermediate hosts is considered critical. Reportedly, cats or dogs living with COVID-19-positive humans tested positive for the disease, suggesting that the virus was transmitted to the animals from humans. Information regarding the epidemiological investigation and comprehensive studies is limited. Therefore, it is still unclear how high is the correlation of infection in humans and pet animals, especially those living together. The aim of this study was to investigate the possibility of SARS-CoV-2 infection in the pets of patients with COVID-19 who were hospitalized at the Wangaya hospital, Denpasar, Bali, Indonesia. MATERIALS AND METHODS: A total of seven clinically asymptomatic pets (six dogs of different races and sexes and a cat [age, 360-2920 days]) were included in this study. These animals belonged to patients with confirmed SARS-CoV-2 infection from August to November 2020. Nasal swab and nasopharyngeal samples were collected from the pets individually under anesthetic condition and were collected 6-12 days after confirmed SARS-CoV-2 infection in owners and hospitalization at the Wangaya Hospital. The swab samples were then processed for RNA isolation and tested using reverse transcription-polymerase chain reaction (RT-PCR) for SARS-CoV-2, in accordance with the World Health Organization manual 2020. RESULTS: RT-PCR results for all seven RNA samples, prepared from the swab samples, were negative. For the samples, all PCR products were below the threshold limit, suggesting no genetic material belonging to the samples tested. CONCLUSION: This was the first preliminary study of COVID-19 on pets in pandemic using RT-PCR. The study tested a very limited quantity of samples, and all of them were negative. However, the way in which the samples were prepared was considered appropriate. Therefore, in further studies, testing of more samples of pets of more individuals with confirmed SARS-CoV-2 infection is required.

Shiga-Like Toxin Produced by Local Isolates of Escherichia coli O157:H7 Induces Apoptosis of the T47 Breast Cancer Cell Line.

PURPOSE: It has been suggested that Shiga-like toxins produced by Escherichia coli O157:H7 could be used as novel therapeutic agents against malignant tumors. In addition, the antitumor potency of local isolates from Indonesia, which are known to be less toxic than the control isolate ATCC 43894, has not yet been tested. The study aimed to analyze local strains of E. coli O157:H7 as a proapoptosis agent on the T47 breast cancer cell line. METHODS: As many as 30 culture cells of T47D breast cancer cell line were subjected to purified extracts of Shiga-like toxin originating from 5 local isolates of E. coli O157:H7: KL-48(2), SM-25(1), SM-7(1), DS-21(4), and 1 isolate ATCC 43894 which was used as a control. Toxin production of each isolate was detected using a sandwich enzyme-linked immunosorbent assay, and the treatment of cell lines was observed for 24 hours, with 2 replications; 3-(4,5-dimethylthiazolyl-2)-2,5-diphenyltetrazolium bromide tests and acridine orange/ethidium bromide double staining assays were used for detection and analyses of apoptosis. RESULTS: The study showed 2 local strains of E. coli O157:H7 (codes KL-48(2) and SM-25(1)) had toxins positive at titer 5 and 10 µg/100 µL. These titers were lower than the control isolate ATCC 43894, but they had a necrosis effect higher (P < .05), ie, 80.3%, than control isolate, ie, 63.3%. Other local strain SM-25(1) also had a good necrosis effect. It has a nondifferent necrosis effect (P > .05) with the control isolate ATCC 43894, ie, 13.0% from 13.3%. CONCLUSION: This study concludes that the Shiga toxin produced by E. coli O157:H7 local isolate (Indonesia) has potential as a proapoptotic and/or necrotic agent for treating T47 breast cancer cell lines, as effectively as ATCC 43894 control isolates.

Structure of cytotoxic associated antigen A protein of Helicobacter pylori from Bali and Lombok isolates of Indonesia.

BACKGROUND AND AIM: Helicobacter pylori is a well-known zoonotic agent with worldwide distribution. In Indonesia, only one report regarding the variation within the cytotoxic associated antigen A (CagA) protein of H. pylori has been described in the literature, which was conducted in Manado, South Sulawesi. There remains no report concerning the structure of this protein, particularly for the Bali and Lombok isolates. The objective of this study was to investigate the diversity of H. pylori CagA amino acid sequences of Bali and Lombok isolates, to predict their molecular structures and conduct toxicity examination of CagA on gastric cells. MATERIALS AND METHODS: A total of 36 samples were used in equal proportions for each pathologic condition. DNA extraction was performed to subculture H. pylori Bali isolates. The amplification of the CagA 3' variable region was carried out using the primers P1 (5'-GATAACAGGCAAGCTTTTTGAGG-3') and P2 (5'-CTGCAAAAGATTGTTTGGCAG-3'). The W2, W9, and W35 fragments were selected as a representation of H. pylori Bali isolates, which were modeled through the threading modeling approach using I-TASSER. RESULTS: According to the 12 CagA sequences obtained and phylogenetic analyses, the H. pylori strain originating from Bali can be grouped within the East Asian genotypes and is identical to the Lombok strain. In addition, the Bali isolates are phylogenetically more closely related to Southeast Asian strains, particularly the Filipino strain. The relationship between degree of inflammation induced and CagA-positive infection was not statistically significant. CONCLUSION: The structure of the H. pylori Bali isolate is identical to that of Lombok isolate, which belongs to the same group of East Asian genotypes, and bacterial virulence is not related to structure.

Factors Associated with Oral Candidiasis in People Living with HIV/AIDS: A Case Control Study.

BACKGROUND: Oral candidiasis (OC) is the most frequent opportunistic infection of the oral cavity caused by Candida species overgrowth. A wide variety of risk factor that contributes to yeast infection especially candidiasis. It might be acting as an early marker for people living with HIV/AIDS (PLWHA). There are some risk factors for PLWHA associated OC at Wangaya hospital in Denpasar, Bali, Indonesia. AIM: To identify risk factors of OC in PLWHA at Wangaya Hospital in Denpasar, Bali, Indonesia. SETTINGS AND DESIGN: Case control study was conducted from March 1, 2016 and July 30, 2019, included 448 participants (207 cases and 241 controls). Consecutive recruitment was employed. METHODS: Cases were PLWHA (18 to 60 years old) with OC and controls without OC. Diagnosis of OC based on the clinical features which are the pseudomembranous candidiasis; oral thrush. An interviewer administered a structured questionnaire used to collect information on risk factors. Statistical analysis used: bivariate analysis was performed on all variables. Chi-square test with statistically significant was at a level of 0.05. RESULTS: The participants included 207 (46.20%) PLWHA with OC and 241 (53.80%) PLWHA who did not have OC. The majority participants, 293 (65.40%) were male. OC was associated with age [p = 0.03; OR = 0.66 (95% CI:0.45-0.95)]; sex [p = 0.002; OR = 1.88 (95% CI:1.26-2.80)]; Xerostomia [p = 0.000; OR = 4.15 (95% CI:2.76-6.23)]; smoking [p = 0.000; OR = 6.83 (95% CI: 4.46-10.44)]; alcohol consumption [p = 0.000; OR = 5.76 (95% CI: 3.74-8.83)]; antibiotic usage [p = 0.000; OR = 4.49 (95% CI: 2.93-6.90)]; CD4 count [p = 0.000; OR = 3.29 (95% CI:2.24-4.86)]; HIV clinical stage [p = 0.000; OR = 3.58 (95% CI 2.39-5.37)]. No significant association between prothesis with OC. CONCLUSION: We found that age, sex, xerostomia, smoking, alcohol consumption, antibiotic usage, CD4 counts and advanced HIV Clinical stage (AIDS) were significant associated risk factors for OC in PLWHA.

Factors Associated With Adherence To Anti-Retroviral Therapy Among People Living With HIV/AIDS At Wangaya Hospital In Denpasar, Bali, Indonesia: A Cross-Sectional Study.

BACKGROUND: Acquired Immunodeficiency Syndrome (AIDS) is a major public health problem. Recently AIDS was considered as a manageable chronic disease. High adherence to Anti-Retroviral Therapy (ART) is necessary to achieve undetectable viral load, reduce morbidity, mortality and to improve the quality of life. It is also preventing the drug resistance, reducing the transmission and finally leading to live longer and healthier. OBJECTIVES: To assess the factor associated with ART adherence among people living with HIV/AIDS (PLWHA) at Wangaya Hospital, in Denpasar, Bali, Indonesia. METHODOLOGY: A cross-sectional study was carried out during January 2015-December 2017 among 202 PLWHA taking ART for at least 6 months. The participants were interviewed using a semi-structured questionnaire to obtain data on socio-demographic characteristics. The data were analyzed using SPSS software for windows version 24.0. Chi-square test was done, the precision value of 95% (p<0.05) was considered statistically to be significant. RESULTS: A total of 202 PLWHA taking ART, 170 (84.16%) were reported with high adherence (≥95%), 32 (15.84%) were low adherence (<95%). Factors found to be independently associated with high adherence to ART were employment status/occupation (p = 0.011), type of ARV (due to adverse effect of ART) (p = 0.002) and family support (p < 0.001). CONCLUSION: This study found that the factor associated with ART adherence among PLWHA who visited Wangaya Hospital, in Denpasar, Bali, Indonesia, was employment status, type of ARV and family support.

Antigen of 49.6-kDa subunitpili protein of Helicobacter pylori as a potential biomarker for early and rapid detection of the infection.

BACKGROUND AND AIM: Helicobacter pylori infection has been identified as a major cause of peptic ulcer diseases, including gastric and duodenal ulcers, gastritis, chronic and gastric carcinoma, and even gastric lymphoma. In vitro studies using Western blotting analysis, hemagglutination test, adherence inhibition assays, and immunocytochemical staining revealed that the 49.6-kDa subunit pili protein of H. pylori was considered an immunogenic protein. This study aimed to develop a serological diagnostic test using 49.6 kDa for detecting antibodies against H. pylori proteins in an early phase of the infection. MATERIALS AND METHODS: An in-house immunochromatographic test (ICT) kit was developed and used to test a panel of sera sample obtained from a randomly selected symptomatic patient, in which 40 sera were H. pylori positive and 40 sera were H. pylori negative. RESULTS: The results showed that ICT with 49.6 kDa as an antigen was highly sensitive and specific for detecting anti-H. pylori immunoglobulin G antibodies in human serum, with a high negative predictive value. CONCLUSION: The developed test could be used to exclude H. pylori infection in symptomatic patients.