Bioinformatic analysis of defective viral genomes in SARS-CoV-2 and its impact on population infection characteristics.

DVGs (Defective Viral Genomes) are prevalent in RNA virus infections. In this investigation, we conducted an analysis of high-throughput sequencing data and observed widespread presence of DVGs in SARS-CoV-2. Comparative analysis between SARS-CoV-2 and diverse DNA viruses revealed heightened susceptibility to damage and increased sequencing sample heterogeneity within the SARS-CoV-2 genome. Whole-genome sequencing depth variability analysis exhibited a higher coefficient of variation for SARS-CoV-2, while DVG analysis indicated a significant proportion of recombination sites, signifying notable genome heterogeneity and suggesting that a large proportion of assembled virus particles contain incomplete RNA sequences. Moreover, our investigation explored the sequencing depth and DVG content differences among various strains. Our findings revealed that as the virus evolves, there is a notable increase in the proportion of intact genomes within virus particles, as evidenced by third-generation sequencing data. Specifically, the proportion of intact genome in the Omicron strain surpassed that of the Delta and Alpha strains. This observation effectively elucidates the heightened infectiousness of the Omicron strain compared to the Delta and Alpha strains. We also postulate that this improvement in completeness stems from enhanced virus assembly capacity, as the Omicron strain can promptly facilitate the binding of RNA and capsid protein, thereby reducing the exposure time of vulnerable virus RNA in the host environment and significantly mitigating its degradation. Finally, employing mathematical modeling, we simulated the impact of DVG effects under varying environmental factors on infection characteristics and population evolution. Our findings provide an explanation for the close association between symptom severity and the extent of virus invasion, as well as the substantial disparity in population infection characteristics caused by the same strain under distinct environmental conditions. This study presents a novel approach for future virus research and vaccine development.

[Clinical Characteristics of Nontuberculous Mycobacterium Infection Cases in Sichuan, China in 2016-2021: A Retrospective Study].

Objective: To study the distribution of nontuberculous mycobacterium (NTM) strains, clinical characteristics and drug sensitivity data of NTM infections so as to provide support for the prevention and treatment of diseases caused by NTM infection in Sichuan. Methods: The clinical data of NTM infection cases treated at the Public Health Clinical Center of Chengdu between July 2016 and July 2021 were collected and the characteristics of the infections were retrospectively reviewed. Results: There were differences in sex, age and underlying diseases among the NTM infection cases in Sichuan. Specifically, young and middle-aged men aged between 20 and 40 were susceptible to AIDS, older men aged over 60 were susceptible to lung diseases, and middle-aged and older women over 40 were susceptible to bronchiectasis. Respiratory tract was the main route of NTM infection. The dominant strain in Sichuan was M. chelonae/ abscessus. The drug resistance rate of M. avium and M. chelonae/ abscessus were relatively higher. Conclusion: For NTM infection patients with different demographic characteristics and underlying diseases, the NTM infection sites, strains, and drug resistance are also different. Definite etiological diagnosis is essential to the treatment of NTM infection. We should highlight the importance of adopting individualized treatment for different NTM infections.

Infection Characteristics of Clonorchis sinensis Metacercariae in Fish from Republic of Korea.

The infection nature of Clonorchis sinensis metacercariae (CsMc) in freshwater fish hosts is closely related to the transmission of human clonorchiasis. This article reviewed the infection characteristics of CsMc in freshwater fish in the Republic of Korea (Korea). The status of CsMc infection was examined in a total of 17,792 cyprinid fish of 49 species in 9 water systems, which included Hantan-/Imjin-gang, Han-gang, Geum-gang, Mangyeong-gang, Yeongsan-gang, Tamjin-gang, Seomjin-gang, Nakdong-gang, and streams in the east coastal areas from 2010 to 2020. The infection status of CsMc was examined according to cyprinid fish species and water systems, after which analyzed by endemicity and susceptibility index. The high endemicity was shown in the cyprinid fish from 3 regions (6.1%) in the upper reaches of Nakdong-gang, such as Banbyeon-cheon (stream), Yongjeon-cheon, and Wi-cheon. The moderate levels were observed in fishes from 8 regions (16.3%), and low endemicity was shown in fishes from 20 regions (40.8%). No CsMc were detected in fish from 18 regions (36.7%). The susceptibility of CsMc in index fish, Puntungia herzi, was found to be a reliable index without examination of other fish species. CsMc infection rates were closely related to subfamily groups in the cyprinid fish hosts in a highly endemic area. In Korea, a total of 58 fish species in 10 families has been listed as the second intermediate hosts for C. sinensis. This review provides several novel features of CsMc infection and clarifies the species of second intermediate freshwater fish host in Korea.

3D-Printed Hydrogels in Orthopedics: Developments, Limitations, and Perspectives.

Three-dimensional (3D) printing has been used in medical research and practice for several years. Various aspects can affect the finished product of 3D printing, and it has been observed that the impact of the raw materials used for 3D printing is unique. Currently, hydrogels, including various natural and synthetic materials, are the most biologically and physically advantageous biological raw materials, and their use in orthopedics has increased considerably in recent years. 3D-printed hydrogels can be used in the construction of extracellular matrix during 3D printing processes. In addition to providing sufficient space structure for osteogenesis and chondrogenesis, hydrogels have shown positive effects on osteogenic and chondrogenic signaling pathways, promoting tissue repair in various dimensions. 3D-printed hydrogels are currently attracting extensive attention for the treatment of bone and joint injuries owing to the above-mentioned significant advantages. Furthermore, hydrogels have been recently used in infection prevention because of their antiseptic impact during the perioperative period. However, there are a few shortcomings associated with hydrogels including difficulty in getting rid of the constraints of the frame, poor mechanical strength, and burst release of loadings. These drawbacks could be overcome by combining 3D printing technology and novel hydrogel material through a multi-disciplinary approach. In this review, we provide a brief description and summary of the unique advantages of 3D printing technology in the field of orthopedics. In addition, some 3D printable hydrogels possessing prominent features, along with the key scope for their applications in bone joint repair, reconstruction, and antibacterial performance, are discussed to highlight the considerable prospects of hydrogels in the field of orthopedics.

Difference Analysis Between Canine Adenovirus Types 1 And 2.

Canine adenoviruses (CAdVs) include type 1 (CAdV-1, virulent strain) and type 2 (CAdV-2, attenuated strain). In recent years, the incidences of CAdV infections are increasing. However, they are difficult to distinguish when the symptoms are untypical. It is pivotal to find the differences between the two virus types for scientific, epidemiological, and specific treatment. CAdV-1 (virulent strain) and CAdV-2 (attenuated strain) induced canine hepatitis (ICH) and tracheobronchitis (ITB), respectively, but the clinical symptom is not obvious. CAdV-1 and CAdV-2 have the same genome structure, diameter, morphological features, and cytopathic features, but the same character hinder the diagnose time of the serotypes. CAdV-1 and CAdV-2 have a difference in the genome sequence, coding proteins, viral activity, hemagglutination patterns. After infection, pathogenicity and transmission route are different between the two serotypes. Sequence alignment, PCR, Real time-PCR assay are useful methods to distinguish the two serotypes. The attenuated live CAdV-2 vaccine is currently used to protect against CAdV-1, but it also has a risk. The further research should focus on the pathogenicity mechanism and the useful vaccine for the two serotypes of canine adenovirus.

Retrospective Analysis of the Clinical Characteristics of Candida auris Infection Worldwide From 2009 to 2020.

INTRODUCTION: Candida auris is an emerging multidrug-resistant fungus that may cause infections with a high mortality rate. The first case of C. auris infection was reported in 2009 and infections have been reported in 44 countries. The fungus now represents a major global public health threat. We analyzed cases from the emergence of C. auris infections up until the end of 2020. It is hoped that the results of this analysis will raise awareness in scientists to promote protection and control research pertaining to this pathogen. METHODS: PubMed and Web of Science databases were searched for all papers related to C. auris infections up until December 31, 2020. We sorted and organized these data into the following categories: date of publication, patient age and sex, underlying diseases, risk factors for infection, patient mortality information, drug sensitivity information of C. auris isolates, and genetic classification. The χ2 test was used to screen for factors that may affect patient mortality. RESULTS: A total of 912 patients were included in the analysis. There's a higher proportion of men and a high proportion of patients were premature babies and elderly people. The proportions of patients with underlying diseases such as diabetes, kidney disease, trauma, and ear disease were also high. More than half of patients had a history of central venous catheter use and a history of broad-spectrum antibiotic use. The χ2 test revealed that only kidney disease (P < 0.05) was an important risk factor for mortality in C. auris-infected patients. CONCLUSIONS: A comprehensive understanding of C. auris was achieved following this retrospective analysis, including the characteristics of C. auris-infected patients. In recent years, increasing numbers of multidrug-resistant C. auris isolates have been identified, and the high mortality rates associated with infection merit greater attention from the medical world.

Application of RNAscope technology to studying the infection dynamics of a Chinese porcine epidemic diarrhea virus variant strain BJ2011C in neonatal piglets.

The highly virulent porcine epidemic diarrhea virus (PEDV) variants cause the death of mainly neonatal piglets, but how the viruses spread within the gastro-intestinal tract in a temporal and spatial manner has remained poorly characterized but is critical to understand the viral pathogenesis. In this study, we used the Chinese PEDV epidemic strain BJ2011C as a model organism and took advantage of the newly developed RNAscope in situ hybridization technology to investigate the tempo-spatial infection dynamics in neonatal piglets. We found that the PEDV strain BJ2011C could quickly colonize the small intestine, which occurred in just 6 h post infection, with virus shedding starting at 6 hpi and peaking at 24 hpi. Jejunum was the first target tissue for infection and then ileum, followed by infrequent infection of duodenum. In these tissues, the virus nucleic acids were mainly present in the villous epithelial cells but not in crypt cells. Interestingly, the viral RNAs were not detectable by RNAscope in large intestines although tissue damages could be discerned by H & E staining. Overall, our results provide useful information about spread dynamics and tissue preference of PEDV epidemic strain BJ2011C.

Analysis of human papillomavirus infection characteristics and genotypes in Shenyang area of Liaoning province / 中华实验和临床病毒学杂志

Objective@#To investigate the distribution of human papillomavirus (HPV) infection characteristics and genotypes in Shenyang area of Liaoning province.@*Methods@#HPV genes were detected in cervical exfoliated cells from 55, 548 patients by amplification and diversion hybridization.@*Results@#A total of 9, 566 patients were positive for HPV infection with a positive rate of 17.22%. Additionally, the positive rate of high risk HPV infection was 14.57% and the positive rate of single genotype HPV infection was 13.63%. Totally, 12, 360 HPV viruses were detected. Among them, 10, 879 HPV viruses were classified into high risk genotypes (10, 879 out of 12, 360, 88.02%). The genotypes in women with ages less than 20 were 16/11/6/51/58/52 genotypes; the susceptible HPV genotypes in other women were 16/58/52/53/39/51/81 genotypes.@*Conclusions@#HPV infections in Shenyang are mainly infections with high risk viruses and single infection. The infection rate and genotype distribution of HPV are different in different age groups. More suitable HPV vaccine prophylaxis can be taken according to the epidemic characteristics of HPV in this area.

Infection characteristics of patients in acute gastroenteritis outbreaks caused by noroviruses / 中华实验和临床病毒学杂志

Objective@#To analyze the infection characteristics of patients in acute gastroenteritis outbreaks caused by noroviruses.@*Methods@#Between April 2014 and March 2016, the clinical data and samples were collected from the patients in acute gastroenteritis outbreaks caused by noroviruses in Beijing. Noroviruses were detected and genotyped using real time RT-PCR, and the infection characteristics of norovirus gastroenteritis were analyzed using the descriptive epidemiological method.@*Results@#A total of 1743 clinical diagnosed cases of norovirus gastroenteritis were collected, and children under 12 years old accounted for 77.68% (1354/1743). The detection rate of noroviruses was 73.98% (509/688). The detection rates of noroviruses in fecal, swab and vomitus samples were gradually decreased (χ2=67.798, P<0.001). Among these clinical diagnosed cases, vomiting was the most common symptom (93.98%), followed by abdominal pain (40.34%), diarrhea (30.35%) and fever (27.94%). The most common symptom of patients under 6 years old was vomiting(98.14%), whereas diarrhea was most common among over 18 years old patients (68.12%). With the increase of age of the patients, the incidence of vomiting was gradually decreased (χ2=100.913, P<0.001), whereas the incidence of diarrhea was gradually increased (χ2=261.164, P<0.001). There was no statistical difference in vomiting, diarrhea and abdominal pain symptoms between patients infected with genogroup Ⅰ and Ⅱ noroviruses, and patients infected with genogroup Ⅱ (34.49%, 149/432) had the higher incidence rate of fever than that of genogroup Ⅰ (18.18%, 14/77) (χ2=7.985, P<0.01).@*Conclusions@#Noroviruses mainly infected children under 12 years old in acute gastroentertis outbreaks. The most common symptom of patients with acute gastroenteritis caused by noroviruses was vomiting, and the incidences of vomiting and diarrhea were significantly correlated with age of the patients. Patients infected with genogroup Ⅱ had the higher incidence rate of fever than genogroup Ⅰ infection.

Antibiotic resistance and infective charsacteristics of Stenotrophomonas maltophilia infection in children / 国际检验医学杂志

Objective To provide the basis for clinical treatment and prevention of Stenotrophomonas maltophilia infection ,ana‐lyze the characteristics of the bacteria infection and drug‐resistant strains of the area children .Methods Statistical analysis of 52 ca‐ses detected Stenotrophomonas maltophilia culture positive patients clinical data from September 2011 to September 2012 ,and the antibiotic susceptibility test results .Results Clinical data analysis showed that patients infected with Stenotrophomonas maltophilia had no difference on age and gender ,in the detection department was given priority to with of NICU and PICU ,82 .7% of infected children with SMA had a history of invasive procedures ,95 .92% of children with SMA had a history of penicillium carbon alkene drug use ,infection SMA patients in hospital for a long time with an average of (22 .3 ± 19 .0) days .Laboratory data analysis showed that Stenotrophomonas maltophilia main detection in sputum specimen type (63 .5% ) ,four kinds of commonly used clinical drug re‐sistance was higher ,sulfa drugs up to 21 .9% .Conclusion Stenotrophomonas maltophilia infection in children is closely related to carbapenem drug use and the invasive operation ,drug resistance in severe cases ,the rational use of antibiotics are crucial to treat‐ment .