Human movement avoidance decisions during Coronavirus disease 2019 in Japan.

Understanding host behavioral change in response to epidemics is important to forecast the disease dynamics. To predict the behavioral change relevant to the epidemic situation (e.g., the number of reported cases), we need to know the epidemic situation at the moment of decision, which is difficult to identify from the records of actually performed human mobility. In this study, the largest travel accommodation reservation data covering half of the existed accommodations in Japan was analyzed to observe decision-making timings and how it responded to the changing epidemic situation during Japan's Coronavirus Disease 2019 until February 2023. To this end, we measured mobility avoidance index proposed in Ito et al., 2022 to indicate people's decision of mobility avoidance and quantified it using the time-series of the accommodation booking/cancellation data. We observed matches of the peak dates of the mobility avoidance and the number of reported cases, and mobility avoidance changed proportional to the logarithmic number of reported cases. We also found that the slope of mobility avoidance against the change of the logarithmic number of reported cases were similar among the epidemic waves, while the intercept of that was much reduced as the first epidemic wave passed by. People measure the intensity of epidemic by logarithm of the number of reported cases. The sensitivity of their response is established during the first wave and the people's response became weakened after the first experience, as if the number of reported cases were multiplied by a constant small factor.

A Novel Hemostatic Peptide Solution for Common Acute Gastrointestinal Bleeding Diseases: First Case Series Study on the Treatment Results of Endoscopic Hemostasis by Nonexpert Endoscopists.

INTRODUCTION: We investigated the hemostatic effect and safety of a hemostatic peptide solution for the treatment of gastrointestinal bleeding requiring emergency endoscopy. METHODS: We retrospectively examined the patient backgrounds, hemostatic results, and procedural safety in patients who were treated with a hemostatic peptide solution for hemostasis during emergency endoscopies for gastrointestinal bleeding. All hemostatic procedures were performed by nonexpert physicians with less than 10 years of endoscopic experience. All of the cases were treated at a single institution over the months from January 2022 to January 2023. RESULTS: Twenty-six consecutive patients (17 males and 9 females) with a median age of 74 (45-95) years were included. Their conditions requiring emergency endoscopy were melena in 8 patients, hematochezia in 2, hematemesis in 8, anemia in 6, and bleeding during esophagogastroduodenoscopy in 2. The sites of bleeding were the esophagus in 3 patients, the stomach in 17, the duodenum in 3, the small intestine in 2, and the colon in 1. Hemostasis was obtained with another hemostasis device used in conjunction with the hemostatic peptide solution in 13 cases and with the hemostatic peptide solution alone in 13 cases. The hemostasis success rate was 100%, with no complications. Rebleeding occurred within 1 week in 4 cases. CONCLUSION: Hemostasis with the hemostatic peptide solution was safe and provided a temporary high hemostatic effect in emergency gastrointestinal endoscopy.

Importance of second-look endoscopy after per-oral endoscopic myotomy for safe postoperative management.

OBJECTIVES: Per-oral endoscopic myotomy (POEM) is a safe and effective treatment for achalasia and esophageal motility disorders. The role of second-look endoscopy (SE) on postoperative day 1 has not been examined. This study aimed to evaluate the findings and need of SE after POEM. METHODS: This is a single-center, retrospective study. All consecutive patients who underwent POEM and SE on postoperative day 1 between December 2017 and September 2019 were included. The primary endpoint was the rate of newly-detected adverse events (nAE) during SE that required endoscopic intervention or deviation from the normal postoperative course. Multivariate logistic regression was used to identify predictors of nAE. RESULTS: Four-hundred-ninety-seven patients (mean age, 50.3 years; female, 49.9%) were included. SE identified abnormal findings in a total of 71 patients (14.3%). nAE which required endoscopic intervention or deviation from the normal postoperative course were identified in 12 patients (2.4%): eight (1.6%) entry site dehiscence; two (0.4%) submucosal hemorrhage or hematoma; and two (0.4%) dehiscence of an intraoperative perforation site after endoclip closure. Other findings such as mucosal thermal damage without perforation and small submucosal hematoma were found in 54 patients (10.9%) and five patients (1.0%), respectively. Multivariate analysis showed that longer operation time and intraoperative adverse events (AE) were associated with clinically significant nAE during SE. CONCLUSIONS: Second-look endoscopy can detect and treat nAE that may lead to severe AE. Thus, SE should be highly considered before starting oral ingestion in all cases, and especially in those who present an intraoperative AE and longer operation time.

Feasibility of a Newly Developed Thumb Control Device for Simultaneous Manipulation of the Endoscope and Treatment Devices in Endoscopic Submucosal Dissection: A Clinical Feasibility Study.

BACKGROUND/AIM: We developed a new device for the simultaneous manipulation of an endoscope and treatment devices, which we named the Smart Shooter®. The aim of this study was to validate the feasibility of using the Smart Shooter® in endoscopic submucosal dissection (ESD). METHODS: This pilot feasibility study conducted between March and June 2014 involved 20 consecutive patients who underwent ESD for superficial gastrointestinal neoplasia. The primary endpoint was a serious adverse event during the ESD procedure. The secondary endpoints were completion rate of ESD using the Smart Shooter® and a mechanical problem with the Smart Shooter® during ESD. RESULTS: A total of 20 patients underwent ESD for 23 lesions: 5 pharyngeal, 8 esophageal, 7 gastric, and 3 colonic lesions. There were no serious adverse events or mechanical problems during ESD. The completion rate of ESD using the Smart Shooter® was 82.6% (19/23). CONCLUSION: ESD using the Smart Shooter® appears to be technically feasible. CLINICAL TRIAL REGISTRATION: UMIN 000013710.

Endocytoscopy is a promising modality with high diagnostic accuracy for gastric cancer.

BACKGROUND AND STUDY AIM: Endocytoscopy (ECS) enables in vivo microscopic imaging, which allows analysis of mucosal structures at the cellular level; however, limited data are available on the validity of ECS in the stomach. The aim of this study was to evaluate the feasibility of ECS in the diagnosis of early gastric cancer. PATIENTS AND METHODS: Gastric lesions that were the targets of histopathological diagnosis by endoscopic submucosal dissection or biopsy specimen were prospectively enrolled and evaluated using a single charge-coupled device-integrated endocytoscope, following double staining with crystal violet and methylene blue. High grade ECS atypia was defined according to specific irregularities in gland structure and cell nuclei. The primary end point was the accuracy of ECS diagnosis for gastric cancer, using histopathological diagnosis as the gold standard. RESULTS: A total of 82 lesions were investigated, including 23 early gastric cancers, 10 gastric adenomas, and 49 non-neoplastic lesions. Ten lesions could not be clearly observed by ECS because of poor staining due to viscous mucus or plaque; thus, assessability rates with ECS were 88 % in total and 91 % for gastric cancer. High grade ECS atypia was observed in 86 % of assessable gastric cancers, but not in any cases of gastric adenomas or non-neoplastic lesions. The sensitivity, specificity, positive and negative predictive values of high grade ECS atypia as the criterion for the diagnosis of gastric cancer were 86 %, 100 %, 100 %, and 94 %, respectively. No serious complications occurred during or after the examinations. CONCLUSION: ECS is a clinically feasible modality to obtain in vivo histology, with high diagnostic accuracy in gastric cancer.

Ex vivo comparison study of smart Shooter®, a new endoscopic device for safe and speedy treatment.

BACKGROUND: In many endoscopic procedures, the operative view can be compromised when manipulating the treatment device because the endoscopists must release their hand from the endoscope. We have developed a new device called the Smart Shooter® (SS) for simultaneous manipulation of the endoscope and treatment device, and evaluated the utility of the SS compared with the conventional method. METHODS: The SS is a semirigid, loop-shaped channel extender that enables endoscopists to manipulate the treatment device with the thumb of the right hand while holding the endoscope with the same hand. We conducted a comparative study of gastric endoscopic submucosal dissection (ESD) and esophageal injection sclerotherapy (EIS) in a porcine model to compare the utility of the SS method with the conventional method. RESULTS: In gastric ESD, all lesions were resected en bloc with no perforation. The mean operative time was significantly shorter with the SS method than with the conventional method (287.5 ± 155.4 vs. 403.5 ± 215.6 s, p = 0.04). In esophageal EIS, 4 paravenous injections were given with the SS method and 5 were given using the conventional method. Similarly, the mean operative time was significantly shorter with the SS method than with the conventional method (19.0 ± 7.8 vs. 23.8 ± 10.0 s, p = 0.04). CONCLUSION: Use of the SS enabled a shorter operative time for gastric ESD and esophageal EIS with no adverse events. The present results suggest that the SS can contribute to safe and speedy endoscopic treatment.

Delayed bleeding after endoscopic submucosal dissection for non-ampullary superficial duodenal neoplasias might be prevented by prophylactic endoscopic closure: analysis of risk factors.

BACKGROUND AND AIM: Duodenal endoscopic submucosal dissection (ESD) is technically challenging because of anatomical specificities and, to date, has not been validated concerning the high rate of complications such as perforation and delayed bleeding. In the present study, the risk factors for delayed bleeding after duodenal ESD are presented with the goal of establishing preventive measures. METHODS: We analyzed 63 patients with non-ampullary superficial duodenal neoplasias treated by ESD from April 2005 to March 2014. To analyze the risk factors of delayed bleeding after duodenal ESD, we divided the patients into a delayed bleeding group and a non-bleeding group. To verify the risk factors of delayed bleeding after duodenal ESD, we analyzed various patient-, lesion-, and treatment-related factors. RESULTS: Delayed bleeding was experienced in 11 patients (17.5%) Univariate analysis of patient-related risk factors of delayed bleeding indicated no significant risk factor. Univariate analysis of lesion-related and treatment-related risk factors indicated only endoscopic closure as a significant risk factor. Multivariate analysis also identified endoscopic closure (not done > done: P = 0.049) as an independent factor significantly associated with delayed bleeding after duodenal ESD. Hypertension (present > absent: P = 0.055) showed a non-significant tendency of association by multivariate analysis. CONCLUSIONS: This retrospective evaluation found that endoscopic closure was associated with a reduced risk of delayed bleeding after duodenal ESD. Delayed bleeding after duodenal ESD might be prevented by prophylactic endoscopic closure.

Accuracy and concordance of endocytoscopic atypia for the diagnosis of gastric cancer.

BACKGROUND AND AIM: High-grade atypia demonstrated by endocytoscopy may be a key criterion for the diagnosis of gastric cancer. We therefore sought to verify whether endocytoscopic atypia can provide satisfactory levels of diagnostic accuracy and concordance among trainee and expert endoscopists. METHOD: A total of 100 lesions evaluated by endocytoscopy and histopathology were enrolled to create an endocytoscopic image catalog (44 early cancers, 10 low-grade adenomas, 46 non-neoplastic lesions). Four endoscopists (two trainees and two experts) independently reviewed the catalog images and evaluated each of them for the presence or absence of endocytoscopic atypia. High-grade endocytoscopic atypia, as a criterion for cancer diagnosis, was defined as the consistent observation of any of the following features: lumen absence, lumen fusion, and irregular nuclei showing the three typical features (heterogeneous shape, swelling, and disarrangement). RESULTS: High-grade endocytoscopic atypia was observed in 78 %, 18 %, and 4 % of cancers, adenomas, and non-neoplastic lesions, respectively. The sensitivity, specificity, accuracy, and positive and negative predictive values for cancer diagnosis by endocytoscopy were 78.4 %, 93.3 %, 87.3 %, 85.4 %, and 87.3 %, respectively. The concordance rate for the results of high-grade endocytoscopic atypia was good among the four endoscopists (κ value 0.682). No significant difference in diagnostic accuracy or concordance was observed between trainee and expert endoscopists. CONCLUSION: Using the defined high-grade atypia as a diagnostic criterion of cancer, endocytoscopy provided a satisfactory level of accuracy and concordance for the diagnosis of early gastric cancer, regardless of endoscopic expertise.

A new device for simultaneous manipulation of an endoscope and a treatment device during procedures: an ex vivo animal study.

BACKGROUND AND STUDY AIMS: Endoscopists must maneuver both endoscope and treatment device during procedures, requiring them to release their hand from the scope to manipulate the treatment device. Aiming to improve this situation, we developed a new device called the Thumb Drive. PATIENTS AND METHODS: The Thumb Drive comprises a controller and catheter. After attaching the controller to the endoscope's grip, the catheter is inserted into the forceps channel. The treatment device is then inserted into the Thumb Drive and fixed with its tip protruding from the endoscope tip. A single endoscopist resected 10 lesions in a porcine stomach by endoscopic submucosal dissection (ESD) using the Thumb Drive. RESULTS: All lesions were resected en bloc using this new device without any perforations. The mean incision, dissection, and operative times were 97.2 ± 48.7 seconds, 121.6 ± 53.6 seconds, and 218.8 ± 67.8 seconds, respectively. CONCLUSIONS: The Thumb Drive enables the endoscopist to manipulate the treatment device with the thumb while handling the endoscope with the right hand during ESD. Its utility should be examined in in vivo studies as a next step.

Clinicopathological features of patients with acute graft-versus-host disease of the upper digestive tract.

BACKGROUND AND AIMS: Acute graft-versus-host disease (GVHD) occurring within 100 days post-transplant is one of critical factors influencing prognosis in transplant recipients. Among cases of GVHD of the gastrointestinal (GI) tract, GVHD rarely affects the upper GI. In this study, we retrospectively examined the frequency of upper GI GVHD and diagnostic accuracy. PATIENTS AND METHODS: From among 868 patients who underwent allogeneic hematopoietic stem cell transplantation at our hospital between January 2005 and June 2012, 115 of whom underwent biopsy for upper GI symptoms. The endoscopic findings and histologic diagnosis from these 115 patients were retrospectively analyzed. RESULTS: GVHD was histologically diagnosed in 85 patients overall (9.8% of all 868 transplant recipients). Although gastric mucosal exfoliation was not commonly observed, this endoscopic finding when used as a diagnostic predictor had both a specificity and positive predictive value (PPV) of 100%. When using redness, luster, and mucosal change as predictors, specificity and PPV were relatively high, suggesting that these gastric endoscopic findings are useful in the diagnosis of upper GI GVHD. Among the duodenal endoscopic findings, erosion as a diagnostic predictor had both a high specificity and PPV. The biopsy results often lead to a diagnosis of GVHD even in cases judged to be endoscopically normal. CONCLUSIONS: Among the gastric endoscopic findings, mucosal exfoliation, although rare, and redness, luster, and mucosal change are likely to be useful diagnostic predictors of upper GI GVHD. GVHD was frequently diagnosed in patients with endoscopically normal duodenum, suggesting that biopsies are important for definitive diagnosis.

Diagnostic algorithm of magnifying endoscopy with narrow band imaging for superficial non-ampullary duodenal epithelial tumors.

BACKGROUND AND AIM: A novel diagnostic algorithm for magnifying endoscopy with narrow band imaging (ME-NBI) for superficial non-ampullary duodenal epithelial tumors (SNADET) is needed because of diagnostic difficulties. METHODS: In the present study, ME-NBI images taken prior to endoscopic treatment were retrospectively analyzed to investigate the relationship between ME-NBI findings and pathological findings. Lesions displaying a single surface pattern were classified as monotype, and those displaying multiple surface patterns as mixed type. Surface pattern was classified as preserved, micrified, or absent. In addition, vascular pattern was classified as absent, network, intrastructural vascular (ISV), or unclassified. RESULTS: According to the revised Vienna classification, 100% (23/23) of mixed-type lesions were category 4/5 tumors, whereas approximately 50% (10/23) of monotype lesions were category 3 tumors. In the monotype lesions, the probability of category 4/5 tumor was 100% (2/2) in lesions with an unclassified vascular pattern, 64.3% (9/14) in lesions with an ISV pattern, 33.3% (1/3) in lesions with an absent pattern, and 25.0% (1/4) in lesions with a network pattern. CONCLUSION: These findings suggest the possibility of developing an effective diagnostic algorithm for ME-NBI for SNADET by determining their surface pattern and vascular pattern.

Molecular Evolutionary Analyses of Shiga toxin type 2 subunit A Gene in the Enterohemorrhagic Escherichia coli (EHEC).

To better understand the molecular genetics of the Shiga toxin type 2 subunit A gene (stx2A gene), we collected many subtypes of stx2A genes and performed detailed molecular evolutionary analyses of the gene. To achieve the aim of the study, we used several bioinformatics technologies, including time-scaled phylogenetic analyses, phylogenetic distance analyses, phylodynamics analyses, selective pressure analyses, and conformational epitope analyses. A time-scaled phylogeny showed that the common ancestor of the stx2A gene dated back to around 18,600 years ago. After that, the gene diverged into two major lineages (Lineage 1 and 2). Lineage 1 comprised the stx2a-2d subtypes, while Lineage 2 comprised the stx2e, 2g, 2h, and 2o subtypes. The evolutionary rates of the genes were relatively fast. Phylogenetic distances showed that the Lineage 2 strains had a wider genetic divergence than Lineage 1. Phylodynamics also indicated that the population size of the stx2A gene increased after the 1930s and spread globally. Moreover, negative selection sites were identified in the Stx2A proteins, and these sites were diffusely distributed throughout the protein. Two negative selection sites were located adjacent to an active site of the common Stx2A protein. Many conformational epitopes were also estimated in these proteins, while no conformational epitope was found adjacent to the active site. The results suggest that the stx2A gene has uniquely evolved and diverged over an extremely long time, resulting in many subtypes. The dominance of the strains belonging to Lineage 1 suggests that differences in virulence may be involved in the prosperity of the offspring. Furthermore, some subtypes of Stx2A proteins may be able to induce effective neutralizing antibodies against the proteins in humans.

Molecular Evolutionary Analyses of the Fusion Genes in Human Parainfluenza Virus Type 4.

The human parainfluenza virus type 4 (HPIV4) can be classified into two distinct subtypes, 4a and 4b. The full lengths of the fusion gene (F gene) of 48 HPIV4 strains collected during the period of 1966-2022 were analyzed. Based on these gene sequences, the time-scaled evolutionary tree was constructed using Bayesian Markov chain Monte Carlo methods. A phylogenetic tree showed that the first division of the two subtypes occurred around 1823, and the most recent common ancestors of each type, 4a and 4b, existed until about 1940 and 1939, respectively. Although the mean genetic distances of all strains were relatively wide, the distances in each subtype were not wide, indicating that this gene was conserved in each subtype. The evolutionary rates of the genes were relatively low (4.41 × 10-4 substitutions/site/year). Moreover, conformational B-cell epitopes were predicted in the apex of the trimer fusion protein. These results suggest that HPIV4 subtypes diverged 200 years ago and the progenies further diverged and evolved.

Incidence and risk factors for very late recurrence of atrial fibrillation after radiofrequency catheter ablation.

AIMS: Although several prognostic factors for atrial fibrillation (AF) recurrence after catheter ablation (CA) have been reported, predictors of very late recurrence (VLR; initial recurrence >12 months after ablation) remain unidentified. This study investigated clinical variables predictive of VLR after CA for AF. METHODS AND RESULTS: This retrospective single-centre cohort study evaluated data from 1016 consecutive drug-refractory AF patients who underwent single CA for AF from July 2004 to May 2010. After excluding 324 patients with a short follow-up period (<1 year) and 300 patients with recurrence within a year of CA, 392 patients were included. Study subjects were divided into two groups on the basis of VLR presence. Preoperative clinical variables were evaluated as predictors of VLR using the Cox proportional hazards model. The annual rate of VLR was 7.6% after single CA. Univariate analysis revealed that hypertension [hazard ratio (HR) 1.77, 95% confidence interval (CI) 0.93-3.37, P = 0.08], obesity (HR 1.84, 95% CI 0.98-3.45, P = 0.06), long-standing persistent AF (HR 2.35, 95% CI 1.08-5.11, P = 0.03), and abnormally high preoperative C-reactive protein (CRP) levels >0.5 mg/dL (HR 4.28, 95% CI 2.03-9.03, P < 0.0001) were associated with VLR. In the multivariate model, only abnormally high preoperative CRP level was an independent predictor of VLR (HR 4.9, 95% CI 2.3-10.7, P < 0.0001). CONCLUSION: Even after a year without AF, VLR occurred annually in 7.6% cases. Continued vigilance for VLR after CA is clinically desirable, especially for patients with abnormally high preoperative CRP levels.

Immunohistochemical analysis of the DNA methyltransferase 3b expression is associated with significant improvements in the discrimination of ulcerative colitis-associated neoplastic lesions.

PURPOSE: Making a clinicopathological diagnosis of dysplasia is crucial. We herein assess the significance of the DNA methyltransferase 3b (DNMT3b) expression as a diagnostic marker of ulcerative colitis (UC)-associated neoplasia. METHODS: Thirty-one patients with long-standing and extensive UC were included in this study. The expression of DNMT3b in non-neoplastic rectal epithelium (non-dysplasia in 31 patients) and colorectal neoplasia (dysplasia in 43 patients and invasive cancer in 34 patients) was determined using immunohistochemistry. The presence of immunoreactive DNMT3b was assessed in the areas with the highest density of cells with positively staining nuclei. DNMT3b was expressed as the percentage of positive cells relative to the total number of cells counted under high power magnification. RESULTS: The DNMT3b expression in neoplastic rectal epithelium (0.76, range 0.59-0.84) was increased compared to that observed in non-neoplastic epithelium (0.32, range 0.18-0.67, P < 0.001). A ROC curve analysis confirmed 0.68 to be the best diagnostic cut-off value for the DNMT3b expression in neoplastic epithelium (area under the curve = 0.810). The sensitivity of the diagnostic test was 66.2 %, the specificity was 86.7 %, the positive predictive value was 95.7 % and the negative predictive value was 36.1 %. The positive likelihood ratio was 4.98 and the negative likelihood ratio was 0.20. The accuracy was 69.9 %. CONCLUSIONS: An immunohistochemical analysis of the DNMT3b expression was associated with significant improvements in the discrimination of UC-associated neoplastic lesions.

Molecular evolutionary analyses of the fusion protein gene in human respirovirus 1.

Few evolutionary studies of the human respiratory virus (HRV) have been conducted, but most of them have focused on HRV3. In this study, the full-length fusion (F) genes in HRV1 strains collected from various countries were subjected to time-scaled phylogenetic, genome population size, and selective pressure analyses. Antigenicity analysis was performed on the F protein. The time-scaled phylogenetic tree using the Bayesian Markov Chain Monte Carlo method estimated that the common ancestor of the HRV1 F gene diverged in 1957 and eventually formed three lineages. Phylodynamic analyses showed that the genome population size of the F gene has doubled over approximately 80 years. Phylogenetic distances between the strains were short (< 0.02). No positive selection sites were detected for the F protein, whereas many negative selection sites were identified. Almost all conformational epitopes of the F protein, except one in each monomer, did not correspond to the neutralising antibody (NT-Ab) binding sites. These results suggest that the HRV1 F gene has constantly evolved over many years, infecting humans, while the gene may be relatively conserved. Mismatches between computationally predicted epitopes and NT-Ab binding sites may be partially responsible for HRV1 reinfection and other viruses such as HRV3 and respiratory syncytial virus.

Pathogen Profiles in Outpatients with Non-COVID-19 during the 7th Prevalent Period of COVID-19 in Gunma, Japan.

The identification of pathogens associated with respiratory symptoms other than the novel coronavirus disease 2019 (COVID-19) can be challenging. However, the diagnosis of pathogens is crucial for assessing the clinical outcome of patients. We comprehensively profiled pathogens causing non-COVID-19 respiratory symptoms during the 7th prevalent period in Gunma, Japan, using deep sequencing combined with a next-generation sequencer (NGS) and advanced bioinformatics technologies. The study included nasopharyngeal swabs from 40 patients who tested negative for severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2) using immuno-chromatography and/or quantitative reverse transcription polymerase chain reaction (qRT-PCR) methods. Comprehensive pathogen sequencing was conducted through deep sequencing using NGS. Additionally, short reads obtained from NGS were analyzed for comprehensive pathogen estimation using MePIC (Metagenomic Pathogen Identification Pipeline for Clinical Specimens) and/or VirusTap. The results revealed the presence of various pathogens, including respiratory viruses and bacteria, in the present subjects. Notably, human adenovirus (HAdV) was the most frequently detected virus in 16 of the 40 cases (40.0%), followed by coryneforms, which were the most frequently detected bacteria in 21 of the 40 cases (52.5%). Seasonal human coronaviruses (NL63 type, 229E type, HKU1 type, and OC43 type), human bocaviruses, and human herpesviruses (human herpesvirus types 1-7) were not detected. Moreover, multiple pathogens were detected in 50% of the subjects. These results suggest that various respiratory pathogens may be associated with non-COVID-19 patients during the 7th prevalent period in Gunma Prefecture, Japan. Consequently, for an accurate diagnosis of pathogens causing respiratory infections, detailed pathogen analyses may be necessary. Furthermore, it is possible that various pathogens, excluding SARS-CoV-2, may be linked to fever and/or respiratory infections even during the COVID-19 pandemic.

Molecular Evolutionary Analyses of the Spike Protein Gene and Spike Protein in the SARS-CoV-2 Omicron Subvariants.

To better understand the evolution of the SARS-CoV-2 Omicron subvariants, we performed molecular evolutionary analyses of the spike (S) protein gene/S protein using advanced bioinformatics technologies. First, time-scaled phylogenetic analysis estimated that a common ancestor of the Wuhan, Alpha, Beta, Delta variants, and Omicron variants/subvariants diverged in May 2020. After that, a common ancestor of the Omicron variant generated various Omicron subvariants over one year. Furthermore, a chimeric virus between the BM.1.1.1 and BJ.1 subvariants, known as XBB, diverged in July 2021, leading to the emergence of the prevalent subvariants XBB.1.5 and XBB.1.16. Next, similarity plot (SimPlot) data estimated that the recombination point (breakpoint) corresponded to nucleotide position 1373. As a result, XBB.1.5 subvariants had the 5' nucleotide side from the breakpoint as a strain with a BJ.1 sequence and the 3' nucleotide side as a strain with a BM.1.1.1 sequence. Genome network data showed that Omicron subvariants were genetically linked with the common ancestors of the Wuhan and Delta variants, resulting in many amino acid mutations. Selective pressure analysis estimated that the prevalent subvariants, XBB.1.5 and XBB.1.16, had specific amino acid mutations, such as V445P, G446S, N460K, and F486P, located in the RBD when compared with the BA.4 and BA.5 subvariants. Moreover, some representative immunogenicity-associated amino acid mutations, including L452R, F486V, R493Q, and V490S, were also found in these subvariants. These substitutions were involved in the conformational epitopes, implying that these mutations affect immunogenicity and vaccine evasion. Furthermore, these mutations were identified as positive selection sites. These results suggest that the S gene/S protein Omicron subvariants rapidly evolved, and mutations observed in the conformational epitopes may reduce the effectiveness of the current vaccine, including bivalent vaccines such as mRNA vaccines containing the BA.4/BA.5 subvariants.

Molecular Evolutionary Analyses of the Pseudomonas-Derived Cephalosporinase Gene.

Despite the increasing evidence of the clinical impact of Pseudomonas-derived cephalosporinase (PDC) sequence polymorphisms, the molecular evolution of its encoding gene, blaPDC, remains elusive. To elucidate this, we performed a comprehensive evolutionary analysis of blaPDC. A Bayesian Markov Chain Monte Carlo phylogenetic tree revealed that a common ancestor of blaPDC diverged approximately 4660 years ago, leading to the formation of eight clonal variants (clusters A-H). The phylogenetic distances within clusters A to G were short, whereas those within cluster H were relatively long. Two positive selection sites and many negative selection sites were estimated. Two PDC active sites overlapped with negative selection sites. In docking simulation models based on samples selected from clusters A and H, piperacillin was bound to the serine and the threonine residues of the PDC active sites, with the same binding mode for both models. These results suggest that, in P. aeruginosa, blaPDC is highly conserved, and PDC exhibits similar antibiotic resistance functionality regardless of its genotype.

Molecular Evolutionary Analyses of the RNA-Dependent RNA Polymerase (RdRp) Region and VP1 Gene in Human Norovirus Genotypes GII.P6-GII.6 and GII.P7-GII.6.

To understand the evolution of GII.P6-GII.6 and GII.P7-GII.6 strains, the prevalent human norovirus genotypes, we analysed both the RdRp region and VP1 gene in globally collected strains using authentic bioinformatics technologies. A common ancestor of the P6- and P7-type RdRp region emerged approximately 50 years ago and a common ancestor of the P6- and P7-type VP1 gene emerged approximately 110 years ago. Subsequently, the RdRp region and VP1 gene evolved. Moreover, the evolutionary rates were significantly faster for the P6-type RdRp region and VP1 gene than for the P7-type RdRp region and VP1 genes. Large genetic divergence was observed in the P7-type RdRp region and VP1 gene compared with the P6-type RdRp region and VP1 gene. The phylodynamics of the RdRp region and VP1 gene fluctuated after the year 2000. Positive selection sites in VP1 proteins were located in the antigenicity-related protruding 2 domain, and these sites overlapped with conformational epitopes. These results suggest that the GII.6 VP1 gene and VP1 proteins evolved uniquely due to recombination between the P6- and P7-type RdRp regions in the HuNoV GII.P6-GII.6 and GII.P7-GII.6 virus strains.