Influenza A/(H1N1)pdm09 virus evolves through continuous antigenic variation in both surface antigens, such as hemagglutinin (HA) and neuraminidase (NA) proteins, which affect its pathogenicity, the effectiveness of the host immune response, and drug resistance. This study reports the evolution and dynamics of 527 HA protein sequences of influenza A/(H1N1)pdm09 Indian isolates submitted from 2009 to 2020. These isolates were aligned with a reference sequence and 22 sequences representing different clades using MEGA X, and subjected to phylogenetic analysis. The strains were predominantly grouped in clades 6B.1 and 6B.2. Prediction of glycosylation sites using the BioEdit and NetNglyc servers showed 12 glycosylation sites distributed in both the stem and globular head regions of HA. Functional evaluation showed that there were 22 deleterious mutations that could affect the function of HA. In addition, 403 unique mutations were distributed across various isolates, indicating the dynamics of antigenic variation in Indian isolates. These results provide an understanding of the frequency, phylodynamics, and impact of mutations in Indian isolates of influenza A/(H1N1)pdm09 relative to global isolates. Monitoring the genomic evolution of the virus will support studies on strain selection for vaccine development and devising control and prevention measures to manage this respiratory infection.

Crimean-Congo hemorrhagic fever (CCHF), a zoonotic disease spread by infected viruses, can be a significant cause of morbidity and mortality in endemic areas. This prospective study aimed to establish the relationship between fractional exhaled nitric oxide (FeNO) levels and clinical prognosis of CCHF. The study included 85 participants: 55 patients followed up for CCHF from May to August 2022, and 30 healthy controls. FeNO levels were measured upon hospital admission and were 7.6 ± 3.3 parts per billion (ppb) in patients with mild/moderate CCHF, 2.5 ± 2.1 ppb in patients with severe CCHF, and 6.7 ± 1.7 ppb in the healthy control group. There was no statistically significant difference in FeNO levels between the control group and patients with mild/moderate CCHF (P = 0.09), whereas patients with severe CCHF had lower FeNO levels than those in the control group and patients with mild/moderate CCHF (P < 0.001 for both). FeNO measurement may offer a noninvasive and easily applied approach for predicting the clinical course and prognosis of CCHF in the early stages of the disease.

Respiratory syncytial virus (RSV) is a major cause of acute lower respiratory tract infections (ALRTIs). In this study, we aimed to evaluate the role of viral load, cytokines, matrix metalloproteinase 9 (MMP-9), and tissue inhibitor of metalloproteinase 1 (TIMP-1) in determining the severity of RSV disease and identify potential biomarkers of disease severity. A total of 142 patients with RSV infection (aged between 2 months and 5 years) who presented with ALRTI between December 2013 and March 2016 were enrolled. Their nasopharyngeal aspirates were subjected to RSV viral load quantification, and local cytokine levels of interleukin 6 (IL-6), tumor necrosis factor α (TNF-α), IL-17A, interferon γ (IFN-γ), and IL-10 were determined using a cytokine bead array. The levels of MMP-9 and TIMP-1 in 109 aspirates were calculated using Quantikine ELISA. These parameters were compared for different disease severity categories. A higher viral load and increased levels of TNF-α, MMP-9, and MMP-9:TIMP-1 were associated with greater severity of disease; whereas levels of IL-17A, IFN-γ, and IFN-γ:IL-10 were associated with disease resolution. When defining the transition from non-severe to severe disease, MMP-9 had a sensitivity and specificity of 89.7% and 85.4%, respectively. Moreover, MMP-9:TIMP-1 had a sensitivity and specificity of 87.2% and 76.8%, respectively. Hence, MMP-9, MMP-9:TIMP-1, TNF-α, and IL-10 could serve as potential biomarkers for disease progression in RSV-infected children.

Osteomyelitis is the infection and destruction of the bone. To date, there is no universal protocol for its treatment. Receptor-interacting serine/threonine-protein kinase 2 (RIPK2) has been implicated in osteomyelitis development. However, the detailed mechanism remains unknown. Here, 6–8w wild-type or Pellino E3 Ubiquitin Protein Ligase Family Member 3 (Peli3)-deficient mice were injected with Staphylococcus aureus to induce osteomyelitis. RAW264.7 cells or bone marrow-derived macrophages isolated from mice were treated with lipopolysaccharide (LPS). Knocking down Peli3 in RAW264.7 cells increased the expression of inflammatory cytokines (interleukin-1β, interleukin-6, and tumor necrosis factor-α) after LPS stimulation. Inflammation was also activated in S. aureus-induced Peli3-deficient mice. Moreover, S. aureus-infected Peli3-deficient mice also displayed more severe symptoms of osteomyelitis than S. aureus-infected wild-type mice. Moreover, Peli3 targets and degrades RIPK2 through K48-linked ubiquitination, and negatively modulates osteomyelitis by degrading RIPK2. Our data further expands the current understanding of RIPK2 in osteomyelitis, and suggests that RIPK2 might serve as a novel therapeutic target for treating osteomyelitis.

Sapovirus (SaV) and astrovirus (AstV) are important viral causes of acute gastroenteritis. From 2016 to 2019, 172 stool samples were collected from children with gastroenteritis in Kobe, Japan for sentinel surveillance of infectious gastroenteritis. In this study, we tested 53 of the 172 stool samples that tested negative for other enteric viruses to determine the prevalence of SaV and AstV. The samples were screened for SaV and AstV using real-time polymerase chain reaction. Positive samples were genotyped by sequencing and genetic analysis of partial regions of the capsid and RNA-dependent RNA polymerase. Of the 53 samples tested, 19 (35.8%) were positive for SaV, and three (5.7%) were positive for AstV. Of the total samples, 11.0% (19/172) and 1.7% (3/172) were positive for SaV and AstV, respectively. The most frequently detected genotype of SaV was GI.1, followed by GII.3. The AstV genotypes were MAstV1.1 and MAstV1.4. This study indicates that SaV and AstV are important causes of viral gastroenteritis in children.

Methicillin-resistant Staphylococcus aureus (MRSA) USA300 is a representative community-associated MRSA (CA-MRSA) clone worldwide. Herein, we report the case of a patient with USA300 clone infection who could not be salvaged. A 25-year-old man who had sex with men presented with symptoms including fever persisting for one week and skin lesions located on the buttocks. Computed tomography imaging showed multiple nodules and consolidations, especially in the peripheral lung fields, right iliac vein thrombosis, and pyogenic myositis of medial thighs bilaterally. Blood cultures revealed MRSA bacteremia. The patient’s condition deteriorated rapidly, complicated by acute respiratory distress syndrome and infective endocarditis. Despite the intubation on the 6th hospital day, he died on the 9th day. Multilocus sequence typing of this patient’s MRSA strain revealed sequence type 8 with a staphylococcal cassette chromosome of mec type IVa, Panton-Valentine leukocidin gene, and the arginine catabolic mobile element, indicating presence of the USA300 clone. Patients with CA-MRSA skin lesions presenting with furuncles or carbuncles on the lower body are at a higher risk of severe disease. The patient’s background, appearance, and location of skin lesions are critical for the early diagnosis of severe CA-MRSA infection.

Sapovirus (SaV) infections are a public health problem because they cause acute gastroenteritis in humans of all ages, both sporadically and as outbreaks. However, only a limited amount of SaV sequence information, especially whole-genome sequences for all the SaV genotypes, is publicly available. Therefore, in this study, we determined the full/near-full-length genomic sequences of 138 SaVs from the 2001 to 2015 seasons in 13 prefectures across Japan. The genogroup GI was predominant (67%, n = 92), followed by genogroups GII (18%, n = 25), GIV (9%, n = 12), and GV (6%, n = 9). Within the GI genogroup, four different genotypes were identified: GI.1 (n = 44), GI.2 (n = 40), GI.3 (n = 7), and GI.5 (n = 1). We then compared these Japanese SaV sequences with 3,119 publicly available human SaV sequences collected from 49 countries over the last 46 years. The results indicated that GI.1, and GI.2 have been the predominant genotypes in Japan, as well as in other countries, over at least four decades. The 138 newly determined Japanese SaV sequences together with the currently available SaV sequences, could facilitate a better understanding of the evolutionary patterns of SaV genotypes.

Mpox, caused by the mpox virus (MPXV), produces symptoms similar to those of smallpox when transmitted to humans. Since 1970, this disease has been endemic, particularly in Africa. However, since May 2022, the number of patients without a history of travel to endemic areas has increased rapidly globally. Under these circumstances, in July 2022, two different real-time PCR methods were used on specimens brought to the Tokyo Metropolitan Institute of Public Health. MPXV was detected in the skin samples, and it was inferred that the virus was a West African strain. Furthermore, a more detailed analysis of the genetic characteristics of the detected MPXV using next-generation sequencing revealed that the MPXV detected in Tokyo was strain B.1, which corresponds to the same strain that is prevalent in Europe and the USA. This suggests that mpox reported for the first time in Japan was imported and related to outbreaks in Europe and the USA. Therefore, it is necessary to continue monitoring outbreaks in Japan in conjunction with global epidemics.

Human rhinovirus (HRV) infections are generally referred to as the common cold, and are the main cause of mild symptoms. HRV is less frequently implicated in the development of severe respiratory infections. This study reports a nosocomial outbreak of bronchitis and pneumonia caused by HRV in a hospital during the COVID-19 epidemic in September 2022 in Gunma Prefecture, Japan. The patient continued to be symptomatic for nine days. During this outbreak, all 15 residents displayed respiratory symptoms. HRV-A was detected in 12 of the 12 samples, and phylogenetic analysis classified the strain as HRV-A type 61. HRV, COVID-19, and other respiratory infections cannot be differentiated based solely on clinical symptoms. A surveillance system to monitor them is thus needed.