Microbiome analysis revealing microbial interactions and secondary bacterial infections in COVID-19 patients comorbidly affected by Type 2 diabetes.

The mortality of coronavirus disease 2019 (COVID-19) disease is very high among the elderly or individuals having comorbidities such as obesity, cardiovascular diseases, lung infections, hypertension, and/or diabetes. Our study characterizes the metagenomic features in severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2)-infected patients with or without type 2 diabetes, to identify the microbial interactions associated with its fatal consequences.This study compared the baseline nasopharyngeal microbiome of SARS-CoV-2-infected diabetic and nondiabetic patients with controls adjusted for age and gender. The metagenomics based on next-generation sequencing was performed using Ion GeneStudio S5 Series and the data were analyzed by the Vegan-package in R. All three groups possessed significant bacterial diversity and dissimilarity indexes (p < 0.05). Spearman's correlation coefficient network analysis illustrated 183 significant positive correlations and 13 negative correlations of pathogenic bacteria (r = 0.6-1.0, p < 0.05), and 109 positive correlations between normal flora and probiotic bacteria (r > 0.6, p < 0.05). The SARS-CoV-2 diabetic group exhibited a significant increase in pathogens and secondary infection-causing bacteria (p < 0.05) with a simultaneous decrease of normal flora (p < 0.05). The dysbiosis of the bacterial community might be linked with severe consequences of COVID-19-infected diabetic patients, although a few probiotic strains inhibited numerous pathogens in the same pathological niches. This study suggested that the promotion of normal flora and probiotics through dietary supplementation and excessive inflammation reduction by preventing secondary infections might lead to a better outcome for those comorbid patients.

Dominant clade-featured SARS-CoV-2 co-occurring mutations reveal plausible epistasis: An in silico based hypothetical model.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has evolved into eight fundamental clades with four of these clades (G, GH, GR, and GV) globally prevalent in 2020. To explain plausible epistatic effects of the signature co-occurring mutations of these circulating clades on viral replication and transmission fitness, we proposed a hypothetical model using in silico approach. Molecular docking and dynamics analyses showed the higher infectiousness of a spike mutant through more favorable binding of G614 with the elastase-2. RdRp mutation p.P323L significantly increased genome-wide mutations (p < 0.0001), allowing for more flexible RdRp (mutated)-NSP8 interaction that may accelerate replication. Superior RNA stability and structural variation at NSP3:C241T might impact protein, RNA interactions, or both. Another silent 5'-UTR:C241T mutation might affect translational efficiency and viral packaging. These four G-clade-featured co-occurring mutations might increase viral replication. Sentinel GH-clade ORF3a:p.Q57H variants constricted the ion-channel through intertransmembrane-domain interaction of cysteine(C81)-histidine(H57). The GR-clade N:p.RG203-204KR would stabilize RNA interaction by a more flexible and hypo-phosphorylated SR-rich region. GV-clade viruses seemingly gained the evolutionary advantage of the confounding factors; nevertheless, N:p.A220V might modulate RNA binding with no phenotypic effect. Our hypothetical model needs further retrospective and prospective studies to understand detailed molecular events and their relationship to the fitness of SARS-CoV-2.

Opsin expression varies across larval development and taxa in pteriomorphian bivalves.

Introduction: Many marine organisms have a biphasic life cycle that transitions between a swimming larva with a more sedentary adult form. At the end of the first phase, larvae must identify suitable sites to settle and undergo a dramatic morphological change. Environmental factors, including photic and chemical cues, appear to influence settlement, but the sensory receptors involved are largely unknown. We targeted the protein receptor, opsin, which belongs to large superfamily of transmembrane receptors that detects environmental stimuli, hormones, and neurotransmitters. While opsins are well-known for light-sensing, including vision, a growing number of studies have demonstrated light-independent functions. We therefore examined opsin expression in the Pteriomorphia, a large, diverse clade of marine bivalves, that includes commercially important species, such as oysters, mussels, and scallops. Methods: Genomic annotations combined with phylogenetic analysis show great variation of opsin abundance among pteriomorphian bivalves, including surprisingly high genomic abundance in many species that are eyeless as adults, such as mussels. Therefore, we investigated the diversity of opsin expression from the perspective of larval development. We collected opsin gene expression in four families of Pteriomorphia, across three distinct larval stages, i.e., trochophore, veliger, and pediveliger, and compared those to adult tissues. Results: We found larvae express all opsin types in these bivalves, but opsin expression patterns are largely species-specific across development. Few opsins are expressed in the adult mantle, but many are highly expressed in adult eyes. Intriguingly, opsin genes such as retinochrome, xenopsins, and Go-opsins have higher levels of expression in the later larval stages when substrates for settlement are being tested, such as the pediveliger. Conclusion: Investigating opsin gene expression during larval development provides crucial insights into their intricate interactions with the surroundings, which may shed light on how opsin receptors of these organisms respond to various environmental cues that play a pivotal role in their settlement process.

Alternative genome sequencing approaches of SARS-CoV-2 using Ion AmpliSeq Technology.

A thorough understanding of SARS-CoV-2 genetic features is compulsory to track the ongoing pandemic across multiple geographical locations of the world. Thermo Fisher Scientific USA has developed the Ion AmpliSeq SARS-CoV-2 Research Panel for the targeted sequencing of SARS-CoV-2 complete genome with high coverage and lower error rate. In this study an alternative approach of complete genome sequencing has been validated using different commercial sequencing kits to sequence the SARS-CoV-2. Amplification of cDNA with the SARS-CoV-2 primer pool was performed separately using two different master mixes: 2X environmental master mix (EM) and Platinum™ PCR SuperMix High Fidelity master mix (PM) instead of 5X Ion AmpliSeq™ HiFi Mix whereas NEBNext® Fast DNA Library Prep Set for Ion Torrent™ kit was used as an alternative to Ion AmpliSeq Library Kit Plus for other reagents. This study demonstrated a successful procedure to sequence the SARS-CoV-2 whole genome with average ∼2351 depth and 98.1% of total the reads aligned against the reference sequence (SARS-CoV-2, isolate Wuhan-Hu-1, complete genome). Although genome coverage varied, complete genomes were retrieved for both reagent sets with a reduced cost. This study proposed an alternative approach of high throughput sequencing using Ion torrent technology for the sequencing of SARS-CoV-2 in developing countries where sequencing facilities are low. This blended sequencing technique also offers a low cost protocol in developing countries like Bangladesh.

Contamination of Selected Toxic Elements in Integrated Chicken-Fish Farm Settings of Bangladesh and Associated Human Health Risk Assessments.

The presence of trace elements in the environment can contaminate a food chain of an agro farm in various ways. Integrated chicken-fish farms (i.e., where poultry chicken and fish are cultivated in same places) are getting popular nowadays to meet the demands of a balanced diet. The present study conducted a health risk assessment on the basis of selected heavy metal (i.e., Cr and Pb) and metalloid (i.e., As) contamination in this type of farm in Bangladesh. Samples of various types were collected from different farms between September 2019 and March 2020. The concentrations of the elements were checked by Flame-AAS and HG-AAS. Our findings demonstrated that the elements' concentrations in fishes were simultaneously induced by the habitation and bioaccumulation through the food chain of the farm. The concentrations of As and Pb in the chicken parts and Cr and As in some fishes were greater than the highest limits set by different permissible standards. Overall, the metal concentration obtained in different samples was in descending order: sediment > droppings > different fish parts > various species of chicken > pond water. Among the pollutants, As gave target hazard quotient (THQ) values higher than 1 for all the species, suggesting health risks from the intake of fishes and chicken. However, there was non-target cancer risk present while considering all the elements together. Notably, the study found carcinogenic risks of As, Pb, and Cr for humans due to poultry and/or fish consumption; the identified health risks associated with the integrated farming setting will be crucial in further tackling strategies. Investigation of the possible sources of heavy metals in commercial chicken feeds and regular monitoring of groundwater used for agro-farming are highly recommended to reduce the burden.

Factors determining preventive practices of the healthcare workers regarding COVID-19 in Bangladesh.

PURPOSE: Identifying the factors influencing the preventive practices of the healthcare workers (HCWs) is crucial during the ongoing coronavirus disease 2019 (COVID-19) because the HCWs are exposed to unparalleled levels of risks. Such concern is starting to be explored worldwide although there is only a single study available in Bangladesh with a limited scope of explorations of the domain. Therefore, this study aimed to identify the factors determining better preventive practices of HCWs toward COVID-19. MATERIALS AND METHODS: A cross-sectional one-to-one survey was carried out using a validated questionnaire from December 15, 2020 to March 15, 2021 among a sample of 640 HCWs from Khulna, a southwestern division of Bangladesh, consisting of ten districts. The measures included socio-demographics, knowledge, attitude, and preventive practices related information. A binary logistic regression analysis was conducted to identify factors determining preventive practices of HCWs toward COVID-19. RESULTS: More than half of the respondents (62%) were following better preventive practices. Besides, around 70% of them had better knowledge and attitudes toward the disease. Regression analysis showed a number of major determining factors of the HCWs' better preventive practices including being a nurse or other professionals (ie, radiologists and pathologists), being graduates, working in coronavirus isolation units, managing COVID-19 patients, having previous training, and having better attitudes toward COVID-19. CONCLUSION: The findings confirmed that the HCWs were generally practicing preventive manners although these trends followed were not at the standard level. So, providing guidance and information from authentic sources and organizing proper training could possibly enhance the preventive behavior in managing COVID-19 patients.

Genomic analysis of SARS-CoV-2 variants of concern identified from the ChAdOx1 nCoV-19 immunized patients from Southwest part of Bangladesh.

BACKGROUND: Bangladesh introduced ChAdOx1 nCoV-19 since February, 2021 and in six months, only a small population (12.8%) received either one or two dose of vaccination like other low-income countries. The COVID-19 infections were continued to roll all over the places although the information on genomic variations of SARS-CoV-2 between both immunized and unimmunized group was unavailable. The objective of this study was to compare the proportion of immune escaping variants between those groups. METHODS: A total of 4718 nasopharygeal samples were collected from March 1 until April 15, 2021, of which, 834 (18%) were SARS-CoV-2 positive. The minimum sample size was calculated as 108 who were randomly selected for telephone interview and provided consent. The prevalence of SARS-CoV-2 variants and disease severity among both immunized and unimmunized groups was measured. A total of 63 spike protein sequences and 14 whole-genome sequences were performed from both groups and phylogenetic reconstruction and mutation analysis were compared. RESULTS: A total of 40 respondents (37%, N = 108) received single-dose and 2 (2%) received both doses of ChAdOx1 nCoV-19 vaccine, which significantly reduce dry cough, loss of appetite and difficulties in breathing compared to none. There was no significant difference in hospitalization, duration of hospitalization or reduction of other symptoms like running nose, muscle pain, shortness of breathing or generalized weakness between immunized and unimmunized groups. Spike protein sequence assumed 21 (87.5%) B.1.351, one B.1.526 and two 20B variants in immunized group compared to 27 (69%) B.1.351, 5 (13%) B.1.1.7, 4 (10%) 20B, 2 B.1.526 and one B.1.427 variant in unimmunized group. Whole genome sequence analysis of 14 cases identified seven B.1.351 Beta V2, three B.1.1.7 Alpha V1, one B.1.526 Eta and the rest three 20B variants. CONCLUSION: Our study observed that ChAdOx1 could not prevent the new infection or severe COVID-19 disease outcome with single dose while the infections were mostly caused by B.1.351 variants in Bangladesh.

Emergence of European and North American mutant variants of SARS-CoV-2 in South-East Asia.

The SARS-CoV-2 coronavirus is responsible for the current COVID-19 pandemic, with an ongoing toll of over 5 million infections and 333 thousand deaths worldwide within the first 5 months. Insight into the phylodynamics and mutation variants of this virus is vital to understanding the nature of its spread in different climate conditions. The incidence rate of COVID-19 is increasing at an alarming pace within subtropical South-East Asian nations with high temperatures and humidity. To understand this spread, we analysed 444 genome sequences of SARS-CoV-2 available on the GISAID platform from six South-East Asian countries. Multiple sequence alignments and maximum-likelihood phylogenetic analyses were performed to analyse and characterize the non-synonymous (NS) mutant variants circulating in this region. Global mutation distribution analysis showed that the majority of the mutations found in this region are also prevalent in Europe and North America, and the concurrent presence of these mutations at a high frequency in other countries indicates possible transmission routes. Unique spike protein and non-structural protein mutations were observed circulating within confined area of a given country. We divided the circulating viral strains into four major groups and three subgroups on the basis of the most frequent NS mutations. Strains with a unique set of four co-evolving mutations were found to be circulating at a high frequency within India, specifically. Group 2 strains characterized by two co-evolving NS mutants which alter in RdRp (P323L) and spike (S) protein (D614G) were found to be common in Europe and North America. These European and North American variants have rapidly emerged as dominant strains within South-East Asia, increasing from a 0% prevalence in January to an 81% by May 2020. These variants may have an evolutionary advantage over their ancestral types and could present a large threat to South-East Asia for the coming winter.

Complete genome arrangement revealed the emergence of a poultry origin superbug Citrobacter portucalensis strain NR-12.

OBJECTIVES: Citrobacter spp. are part of normal human and animal intestinal flora. Citrobacter portucalensis (C. portucalensis) is closely related to Citrobacter freundii, which is an emerging opportunistic nosocomial pathogen. The aim of this study was to retrieve colistin-resistant Citrobacter spp. from poultry in Bangladesh. METHODS: The C. portucalensis strain NR-12 was isolated from poultry droppings and subjected to antibiotic susceptibility testing. Complete genome analysis of NR-12 was performed followed by bioinformatics. It is believed that this is one of first reports of its kind of complete genome sequence of multidrug-resistant (MDR) C. portucalensis isolated from veterinary samples. RESULTS: The C. portucalensis strain NR-12 showed resistance to polymyxin, sulfonamide, tetracycline, fluoroquinolone, and macrolide. Its complete genome revealed 13 acquired antimicrobial resistance gene markers (AMRs) conferring resistance to eight different antibiotic groups: dfrA12 (trimethoprim); sul1 and sul2 (sulfonamide); mph (A) (macrolide); tet (A) (tetracycline); qnrS1 and qnrB13 (fluoroquinolone); blaCMY-39 (extended-spectrum ß-lactamase (ESBL)), blaTEM-176 (non-ESBL) and aadA2, aph (3')-Ia, aph (3″)-Ib, aph (3')-Ic, aph (3')-Id, strA, strB) (aminoglycoside). The genome possessed a class 1 integron (IntI1) gene cassette harbouring four different antibiotic resistance genes (dfrA12, aadA2, sul1, mph (A)). The organisation of class 1 integron (IntI1) carrying MDR determinants in C. portucalensis strain NR-12 was also first reported here. Colistin-resistant genes such as mgrB, phoP, phoQ, pmrA, pmrB, eptB and arnB were also present within NR-12. CONCLUSION: C. portucalensis NR-12 was resistant to eight different antibiotics from six antimicrobial groups. To formulate a control strategy, it is important to understand this resistant mechanism.