The Role of SARS-CoV-2 Spike Protein in Long-term Damage of Tissues and Organs, the Underestimated Role of Retrotransposons and Stem Cells, a Working Hypothesis.

Coronavirus disease-2019 (COVID-19) is a respiratory disease in which Spike protein from SARS-CoV-2 plays a key role in transferring virus genomic code into target cells. Spike protein, which is found on the surface of the SARS-CoV-2 virus, latches onto angiotensin-converting enzyme 2 receptors (ACE2r) on target cells. The RNA genome of coronaviruses, with an average length of 29 kb, is the longest among all RNA viruses and comprises six to ten open reading frames (ORFs) responsible for encoding replicase and structural proteins for the virus. Each component of the viral genome is inserted into a helical nucleocapsid surrounded by a lipid bilayer. The Spike protein is responsible for damage to several organs and tissues, even leading to severe impairments and long-term disabilities. Spike protein could also be the cause of the long-term post-infectious conditions known as Long COVID-19, characterized by a group of unresponsive idiopathic severe neuro- and cardiovascular disorders, including strokes, cardiopathies, neuralgias, fibromyalgia, and Guillaume-Barret's like-disease. In this paper, we suggest a pervasive mechanism whereby the Spike proteins either from SARS-CoV-2 mRNA or mRNA vaccines, tend to enter the mature cells, and progenitor, multipotent, and pluripotent stem cells (SCs), altering the genome integrity. This will eventually lead to the production of newly affected clones and mature cells. The hypothesis presented in this paper proposes that the mRNA integration into DNA occurs through several components of the evolutionarily genetic mechanism such as retrotransposons and retrotransposition, LINE-1 or L1 (long interspersed element-1), and ORF-1 and 2 responsible for the generation of retrogenes. Once the integration phase is concluded, somatic cells, progenitor cells, and SCs employ different silencing mechanisms. DNA methylation, followed by histone modification, begins to generate unlimited lines of affected cells and clones that form affected tissues characterized by abnormal patterns that become targets of systemic immune cells, generating uncontrolled inflammatory conditions, as observed in both Long COVID-19 syndrome and the mRNA vaccine.

The Sub-Molecular and Atomic Theory of Cancer Beginning: The Role of Mitochondria.

Life as we know it is made of strict interaction of atom, metabolism, and genetics, made around the chemistry of the most common elements of the universe: hydrogen, oxygen, nitrogen, sulfur, phosphorus, and carbon. The interaction of atomic, metabolic, and genetic cycles results in the organization and de-organization of chemical information of what we consider living entities, including cancer cells. In order to approach the problem of the origin of cancer, it is therefore reasonable to start from the assumption that the atomic structure, metabolism, and genetics of cancer cells share a common frame with prokaryotic mitochondria, embedded in conditions favorable for the onset of both. Despite years of research, cancer in its general acceptation remains enigmatic. Despite the increasing efforts to investigate the complexity of tumorigenesis, complementing the research on genetic and biochemical changes, researchers face insurmountable limitations due to the huge presence of variabilities in cancer and metastatic behavior. The atomic level of all biological activities it seems confirmed the electron behavior, especially within the mitochondria. The electron spin may be considered a key factor in basic biological processes defining the structure, reactivity, spectroscopic, and magnetic properties of a molecule. The use of magnetic fields (MF) has allowed a better understanding of the grade of influence on different biological systems, clarifying the multiple effects on electron behavior and consequently on cellular changes. Scientific advances focused on the mechanics of the cytoskeleton and the cellular microenvironment through mechanical properties of the cell nucleus and its connection to the cytoskeleton play a major role in cancer metastasis and progression. Here, we present a hypothesis regarding the changes that take place at the atomic and metabolic levels within the human mitochondria and the modifications that probably drive it in becoming cancer cell. We propose how atomic and metabolic changes in structure and composition could be considered the unintelligible reason of many cancers' invulnerability, as it can modulate nuclear mechanics and promote metastatic processes. Improved insights into this interplay between this sub-molecular organized dynamic structure, nuclear mechanics, and metastatic progression may have powerful implications in cancer diagnostics and therapy disclosing innovation in targets of cancer cell invasion.

Searching for a Link between Bone Decay and Diabetes Type 2.

The current commentary describes the possible existing link between metabolic diseases such as diabetes type 2 and the degenerative patterns of bones via the molecular mechanism that inhibits the mesenchymal stem cells' differentiation into osteoblasts and osteocytes.

The Distribution of Dengue Virus Serotype in Quang Nam Province (Vietnam) during the Outbreak in 2018.

Objectives: Quang Nam province in the Centre of Vietnam has faced an outbreak of dengue hemorrhagic fever (DHF) in 2018. Although DHF is a recurrent disease in this area, no epidemiological and microbiological reports on dengue virus serotypes have been conducted mainly due to lack of facilities for such a kind of advanced surveillance. The aim of this study was to detect different dengue virus serotypes in patients' blood samples. Design and Methods: Suspected cases living in Quang Nam province (Vietnam) and presenting clinical and hematological signs of dengue hemorrhagic fever were included in the study. The screening was performed, and the results were compared by using two methodologies: RT real-time PCR (RT-rPCR) and the Dengue NS1 rapid test. Results: From December 2018 to February 2019, looking both at RT-rPCR [+] and NS1 [+] methodologies, a total of 488 patients were screened and 336 were positive for dengue virus detection (74 children and 262 adults); 273 of these patients (81.3%) underwent viral serotype identification as follows: 12.82% (35/273) D1 serotype, 17.95% (49/273) D2, 0.37% (1/273) D3, 68.50 (187/283) D4, and 0.37% (1/273) D2+D4 serotypes. The RT-rPCR outcomes showed higher sensitivity during the first three days of infection compared to NS1 (92.3% vs. 89.7%). The NS1 increased sensitivity after the first 3 days whilst the RT-rPCR decreased. Conclusions: Advanced surveillance with dengue virus serotypes identification, if performed routinely, may help to predict and prevent further DHF epidemics based on the exposure of the different serotypes during different periods that lead to the intensification of disease severity as a consequence of antibody-dependent enhancement (ADE).

Coronavirus (SARS-CoV-2) Pandemic: Future Challenges for Dental Practitioners.

In the context of the SARS-CoV-2 (Severe acute respiratory syndrome coronavirus 2) pandemic, the medical system has been subjected to many changes. Face-to-face treatments have been suspended for a period of time. After the lockdown, dentists have to be aware of the modalities to protect themselves and their patients in order not to get infected. Dental practitioners are potentially exposed to a high degree of contamination with SARS-CoV-2 while performing dental procedures that produce aerosols. It should also be noted that the airways, namely the oral cavity and nostrils, are the access pathways for SARS-CoV-2. In order to protect themselves and their patients, they have to use full personal protective equipment. Relevant data regarding this pandemic are under evaluation and are still under test. In this article, we made a synthesis about the way in which SARS-CoV-2 spreads, how to diagnose a novel corona virus infection, what the possible treatments are, and which protective personal equipment we can use to stop its spreading.

Assessment of carbapenem-resistant Enterobacteriaceae-plate formula and quality control procedure.

AIMS: To assess a cost-effective in-house selective plate formula for actively screening carbapenem-resistant Enterobacteriaceae (CRE). METHODOLOGY AND RESULTS: The in-house formula included CHROMagarTM Orientation, meropenem, and ingredients present in the Mac-Conkey formula, such as bile salts and crystal violet (pH 6.9-7.2). American Type Culture Collection strains and 200 clinical strains were used to validate the plate formula. The CRE plates had a sensitivity of 97.4% and a specificity of 98.8% with ATCC andor clinical strains used in the quality control procedure. A point prevalence survey among the 18 inpatients at Viet-Tiep hospital ICU using fecal swabs plated at the in-house agar plate showed a CRE prevalence of 44.4%. CONCLUSION: The in-house plate had high sensitivity and specificity, particularly for Escherichia coli and the KESC group (Klebsiella spp., Enterobacter spp., Serratia marscescens, and Citrobacter spp.), and it may be widely applied as an alternative to other ready-to-use commercial plates. SIGNIFICANCE AND IMPACT OF THE STUDY: The formula developed in the present study may facilitate the early detection and isolation of CRE and decrease transmission, particularly in low- and middle-income countries with a high rate of CRE colonization and limited access to ready-to-use commercial plates.

Antimicrobial susceptibility and clarithromycin resistance patterns of Helicobacter pylori clinical isolates in Vietnam.

Helicobacter pylori is a gastric pathogen that causes several gastroduodenal disorders such as peptic ulcer disease and gastric cancer.  Eradication efforts of H. pylori are often hampered by antimicrobial resistance in many countries, including Vietnam.  Here, the study aimed to investigate the occurrence of antimicrobial resistance among H. pylori clinical isolates across 13 hospitals in Vietnam.  The study further evaluated the clarithromycin resistance patterns of H. pylori strains.  In order to address the study interests, antimicrobial susceptibility testing, epsilometer test and PCR-based sequencing were performed on a total of 193 strains isolated from patients, including 136 children (3-15 years of age) and 57 adults (19-69 years of age).  Antimicrobial susceptibility testing showed that the overall resistance to amoxicillin, clarithromycin, levofloxacin, metronidazole, and tetracycline was 10.4%, 85.5%, 24.4%, 37.8%, and 23.8% respectively.  The distribution of minimum inhibitory concentrations (MICs) of clarithromycin-resistant strains was 85.5% with MIC >0.5 µg/mL.  The majority of the clarithromycin resistant isolates (135 of 165 subjects) have MICs ranging from 2 µg/mL to 16 µg/mL.  Furthermore, sequencing detection of mutations in 23S rRNA gene revealed that strains resistant and susceptible to clarithromycin contained both A2143G and T2182C mutations.  Of all isolates, eight clarithromycin-resistant isolates (MIC >0.5 µg/mL) had no mutations in the 23S rRNA gene.  Collectively, these results demonstrated that a proportion of clarithromycin-resistant H. pylori strains, which are not related to the 23S rRNA gene mutations, could be potentially related to other mechanisms such as the presence of an efflux pump or polymorphisms in the CYP2C19 gene.  Therefore, the present study suggests that providing susceptibility testing prior to treatment or alternative screening strategies for antimicrobial resistance is important for future clinical practice.  Further studies on clinical guidelines and treatment efficacy are pivotal for successful eradication of H. pylori infection.

Enhanced isolation and culture of highly efficient psychrophilic oil-degrading bacteria from oil-contaminated soils in South Korea.

It is known that isolation of oil-degrading bacterial strains is difficult at low temperatures, and the biodegradation efficiency of oil-contaminated soil is significantly reduced in cold weather. In this study, 14 strains were isolated from oil-contaminated soil that grew well at 10°C by using a newly developed culture method. 11 of the 14 isolates were successfully cultured in mineral salts medium containing 1,500 ppm of oil components, 500 ppm each kerosene, gasoline, and diesel as carbon sources, at 10°C for 2 weeks. The oil degradation efficiencies of these 11 isolates ranged from 36% to 100%, as measured by total petroleum hydrocarbon (TPH) degradation analyses. Three strains (Pseudomonas simiae G1-10O, P. taiwanensis Y1-4, and P. koreensis Gwa2) displayed complete degradation (100%), and six others (R frederiksbergensis G2-2, P arsenicoxydans Y2-1, R umsongensis Gwa3, P. migulae Gwa5, RhodococcusjialingiaeY 1-l , and R. qingshengii Y2-2) showed relatively high degradation efficiencies (> 70%). This study suggests that these isolates can be effectively utilised in thetreatment of oil-contaminated soil in landfarming, especially during winter.

Nine additional complete genome sequences of HCV genotype 6 from Vietnam including new subtypes 6xb and 6xc.

We completely sequenced nine HCV-6 variants from Vietnam. They are grouped into six lineages beyond the 24 assigned subtypes, 6a-6xa, and 14 unclassified lineages that have been recently described with full-length genomes. Co-analysis with reference sequences in the NS5B region identified additional 22 such lineages, which made the total taxonomic number of HCV-6 increased to 66 that might be recognized at the subtype level. Because two of these six lineages revealed in this study each had >3 epidemiologically unlinked isolates identified, we proposed to assign them new subtypes 6xb and 6xc in following the eXtended format recently recommended in the expanded HCV nomenclature.

The genetic diversity and evolutionary history of hepatitis C virus in Vietnam.

Vietnam has a unique history in association with foreign countries, which may have resulted in multiple introductions of the alien HCV strains to mix with those indigenous ones. In this study, we characterized the HCV sequences in Core-E1 and NS5B regions from 236 Vietnamese individuals. We identified multiple HCV lineages; 6a, 6 e, 6h, 6k, 6l, 6 o, 6p, and two novel variants may represent the indigenous strains; 1a was probably introduced from the US; 1b and 2a possibly originated in East Asia; while 2i, 2j, and 2m were likely brought by French explorers. We inferred the evolutionary history for four major subtypes: 1a, 1b, 6a, and 6 e. The obtained Bayesian Skyline Plots (BSPs) consistently showed the rapid HCV population growth from 1955 to 1963 until 1984 or after, corresponding to the era of the Vietnam War. We also estimated HCV growth rates and reconstructed phylogeographic trees for comparing subtypes 1a, 1b, and HCV-2.

Niabella thaonhiensis sp. nov., isolated from the forest soil of Kyonggi University in Korea.

Strain NHI-24(T) was isolated from forest soil by a polycarbonate membrane transwell plate. It is a Gram-negative, rod-shaped, non-motile, non-spore-forming bacterium. Phylogenetic analysis based on 16S rRNA gene sequence data indicated that strain NHI-24(T) is closely related to members of the genus Niabella: N. drilacis E90(T) (97.7 %), N. tibetensis 15-4(T) (96.7 %), N. aurantiaca R2A15-11(T) (96.5 %), N. hirudinis E96(T) (95.8 %), N. soli JS13-8(T) (94.7 %), N. ginsengisoli NBRC106414(T) (94.4 %), and N. yanshanensis CCBAU 05354(T) (94.2 %). Growth temperatures range widely, from 15 to 37 °C, with 30 °C as the optimum. Salt tolerance ranges from 0 to 2 %. The strain grows at pH 6.5-11.0, with an optimal range of pH 7.0-9.5. Cells produce flexirubin-type pigments, and the predominant menaquinone is MK-7. The major fatty acids of strain NHI-24(T) are iso-C15:0 (36.72 %), iso-C15:1 G (20.8 %), and summed feature 3 (C16:1 ω7c/C16:1 ω6c; 15.2 %). DNA-DNA hybridization values between strain NHI-24(T) and members of the genus Niabella range from 37 to 53 %. Based on these results, it is proposed that strain NHI-24(T) represents a novel species of the genus Niabella with the name Niabella thaonhiensis (= KACC 17215(T) = KEMB 9005-018(T) = JCM 18864(T)).

Measles Epidemics Among Children in Vietnam: Genomic Characterization of Virus Responsible for Measles Outbreak in Ho Chi Minh City, 2014.

BACKGROUND: Measles remains poorly controlled in Southeast Asia, including Vietnam. OBJECTIVES: The aim of this study was to characterize genes of virus responsible for a measles outbreak among children in Vietnam in 2014. STUDY DESIGN: Throat swab samples were collected from 122 pediatric patients with suspected measles. Furthermore, peripheral blood mononuclear cells (PBMCs) from 31 of these cases were also collected. Measles virus (MV) RNA was obtained directly from the clinical specimens, amplified by PCR, and then the N and H genes were sequenced. RESULTS: MV RNA was detectable in throat swabs from all 122 patients tested. Positive-strand viral RNA, which indicates the intermediate replicative form of MV, was also detected in PBMCs from all 31 cases from whom these cells were collected. One hundred and eighteen strains with the N gene were obtained by RT-PCR and sequenced. Using phylogenetic analysis with measles reference sequences, all of the Vietnamese strains were found to be genotype D8. However, all strains formed a distinct cluster within the genotype D8 group (D8-VNM) suggesting their own lineage. This distinct cluster was supported by a branch with a 99% bootstrap value and 3.3% nucleotide divergence in the N-450 region of the N gene from the D8 reference strain. Notably, all of the D8-VNM variant strains represented unique amino acid sequences consisting of R442, S451 and G452 in the N-450 region of the N gene. CONCLUSIONS: Measles viruses responsible for outbreaks in Southern Vietnam belonged to a genotype D8 variant group which had unique amino acid sequences in the N gene. Our report provides important genomic information about the virus for measles elimination in Southeast Asia.

Cultivation of unculturable soil bacteria.

Despite the abundance of bacterial species in soil, more than 99% of these species cannot be cultured by traditional techniques. In addition, the less than 1% of bacteria that can be cultured are not representative of the total phylogenetic diversity. Hence, identifying novel species and their new functions is still an important task for all microbiologists. Cultivating techniques have played an important role in identifying new species but are still low-throughput processes. This review discusses the issues surrounding cultivation, including achievements, limitations, challenges, and future directions.