Epidemiological and etiological analysis of a case cluster caused by norovirus in a nursing home in Lanzhou

Objective: To understand the epidemiology and etiology of a cluster of cases with gastroenteritis in a nursing home in Anning district of Lanzhou, and to provide a scientific evidence for the prevention and control of norovirus diarrhea in community nursing centers. Methods: From January 28 to February 4 2021, an epidemiological investigation was conducted on all diarrhea cases, nursing staff and chefs in a nursing home in Anning district, Lanzhou city. Samples of patients' anal swabs, feces, vomitus were collected for norovirus detection by real-time fluorescent PCR. ORF1/ORF2 junction region of norovirus in some selected positive samples(Ct value 25) was sequenced. MEGA-X software was used to construct a phylogenetic tree for genetic evolution analysis using the neighboring method. Results: The first case was confirmed on January20,2021, and the number of cases peaked during January 25and 29.A total of 58 clinically diagnosed cases were reported,57were older people, with an incidence of(57/360,15.83%). Diarrhea(50/58,86.21%),vomiting(35/58,60.34%),nausea(13/58,22.41%)and abdominal pain(6/58,10.34%)were common symptoms, all cases were mild. Fifty-three asymptomatic cases were detected among chefs, housekeepers and nurses.A total of 163specimens were tested, the positive rate of norovirus GII was 49.08%(80/163). The positive rate of fecal samples collected from nurses, chefs and housekeepers was 48.62%(53/109), and was11.11%(2/18)in environmental surface swabs. The possibility of other pathogenic infections such as SARS-CoV-2was ruled out by further tests. Thirteen positive samples were selected for sequencing, and 9were successfully sequenced, they were all recombinant GII.4Sydney_2012 [P16]genotypes, forming an independent cluster, while in a large evolutionary branch with the 2020GII.10 [P16]and 2019GII.2 [P16]virus strains in Lanzhou city, showing a relative close genetic connection. Conclusions: GII .4Sydney_2012[P16]genotype of norovirus is found to be causative pathogen of this outbreak, and close contact is the main reason of the outbreak and persistence of the infection,so asymptomatic infections of norovirus play an important role in the disease spreading. Therefore, public health management in nursing homes and other centralized nursing facilities should be strengthened especially for asymptomatic workers in order to prevent virus transmission.

Genetic pattern of the COVID-19 course and reinfection

A new coronavirus infection (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) broke out at the end of 2019 in Wuhan (China). The disease has become a global pandemic and claimed more than 6 million lives after spreading rapidly around the world. Issues related to the complicated course of COVID-19 mechanisms continue to be the subject of active study. It is known that morbidity and mortality increase dramatically with increasing age and concomitant diseases, including obesity, diabetes, cancer, and cardiovascular diseases. Although most infected people recover, even young and otherwise healthy patients can get sick with this disease. In this regard, an urgent task is to search for specific genetic factors that can explain the predisposition of people to infection and the development of a severe COVID-19 form. Human genetic determinants can provide the scientific basis for disease prediction and the development of personalized therapies to counteract the epidemic. In addition, cases of repeated infection with SARS-CoV-2 are increasingly being registered, which occurs 1-6 months after initial infection on average and depends on the virus genome structure. Studies conducted on sequencing viral genomes have shown that some patients were re-infected with the same strain of coronavirus, while others were different. This, in turn, causes researchers concerns about the effectiveness of immunity after infection and vaccine reliability. The genetic characteristics of a person and a virus commonly determine the tendency for reinfection. It is difficult to determine the true COVID-19 reinfection prevalence, which is explained by the low detectability of asymptomatic reinfection and the fact that many patients with a mild course of the disease were not tested at an early stage of the pandemic. Therefore, the true prevalence of reinfection with COVID-19 does not reflect the current reality. There are many more cases of reinfection than are described in the literature. In this regard, the true contribution of a virus' genetic features to reinfection of COVID-19 can be determined only after population studies, and when developing immunization programs against a COVID-19, it is necessary to take into account the prevalence of reinfection in the population.

Community Health Nurses' Role in Genetic Sequencing: A Prospect for Health Team Preparedness Against Covid-19

Genetic sequencing is a scientific process of reading genetic material using advanced technology. Through genetic sequencing, we can better comprehend super-spreader events and outbreaks, and strengthen national public health responses. A better understanding of the transmission of viruses, the severity of patient illness, and mortality rates can be gained by combining this information with that from the IDSP and patient reports. Connecting the dots between the data and the host's genetics, immunology, clinical outcomes, and risk factors is also possible. Many roadblocks must be overcome before raw sequence data can be put to direct clinical application. Since DNA sequencing has so many potential applications in the field of nursing, it ought to be a required topic for students in the profession. Group wellness Preparing patients for procedures, identifying those most at risk, doing sentinel surveillance, and conducting in-depth studies are all areas in which nurses can be of assistance. The goals of this paper are twofold: (1) to present the notion of genetic sequencing and (2) to highlight the role of Community health nurses. To reduce the impact of pandemics and endemics and improve nursing care, Western countries are seeing an uptick in the participation of nurse scientists in genetic sequencing;the case of newborn screening provides a particularly apt example.Copyright © 2023, Institute of Medico-legal Publication. All rights reserved.

Combined epidemiology and genetic sequencing surveillance in the era of COVID-19 pandemic; Abu Dhabi experience, United Arab Emirates.

BACKGROUND: United Arab Emirates, has reported the first case of COVID-19 in January 2020 and by October 2022, a total of 1 Million cases and 2348 deaths due to COVID-19 have been reported. The Abu Dhabi Public Health Center, has led a novel initiative to conduct a large scale genomic surveillance project. The aim of this surveillance project is to generate data to guide public health pandemic response decision making. METHODS: Samples mainly from the community, points of entry to the emirate and healthcare facilities were collected for surveillance using both targeted PCR and/or Genome sequence analysis. Sample criteria were defined and specific metadata were collected in parallel. Using the unique identifiers and through the available datasets, epidemiological and clinical data were integrated. RESULTS: A total of 385,191 sample undertake analysis (from January 2021 to October 2022) either genotyping and/or sequence analysis. The most frequently encountered lineages in the community and among severe cases were reported. CONCLUSIONS: Genomic surveillance is a major tool essential for guiding public health measures throughout the pandemic.

Molecular dual actions of hsa-miRNA and v-miRNA in oncogenic EBV

Viruses are one of the main reasons that cause healthy cells to proliferate and become cancerous. Several viruses have been identified as causative factors for various forms of cancer. Tumor occurrence can be caused by viral oncoprotein activity, persistent infection or inflammation. The molecular process is still complicated to be understood. In recent decades, Homo sapiens cell microRNA (hsa-miRNA) has been discovered by small non-coding RNAs that affect post-transcriptional gene expression. hsa-miRNA is a key control factor for several key biological processes and has a much greater impact on the target gene group. even though they occupy a small part of the genome, they play a great role in the development of cancer. Several viruses produce this tiny RNA, which can regulate their gene expression or affect the host's gene expression. A new hypothesis is that Epstein-Barr virus (EBV) is the first cancer causing virus that is found to produce microRNAs (v-miRNAs). In addition, evidence shows that miRNA encoded by EBV contributes to the occurrence and progression of EBV-related malignancies. Generally, these compounds reduce messenger RNA (mRNA) instability, such as genes that regulate tumorigenesis mechanisms like inflammation, cell cycle control, stress response, differentiation, apoptosis, invasion, and immune pathways. Therefore, EBV-miRNAs are important in the complex interaction between host, virus and EBV tumorigenesis. In terms of malignant tumors, the combinatorial process behind EBV-miRNA still needs further study. In this article, we will introduce EBV-miRNA, including the cellular processes affected by the virus, and their ability to promote cancer.

Bioinformatics analysis of mutations in the spike protein of SARS-CoV-2 and their effects

In December 2019, a new type of pneumonia, coronavirus disease 2019 (COVID-19), caused by a novel coronavirus, SARS-CoV-2, was detected in hospitals in Wuhan, Hubei Province, China. The World Health Organization announced on 11 March 2020 that COVID-19 can be characterized as a pandemic, and since then COVID-19 has wrought havOc on public-health systems worldwide. The surface "spike" protein CS protein of SARS-CoV-2 mediates host-cell attachment and membrane fusion. The S protein is a key target for urgent development of vaccines, therapeutic antibodies, and diagnostics. To analyze the mutations and their effects on protein structure and function of the S protein, bioinformatics software has been used to analyze its nucleotide and amino-acid sequences, and Wuhan-Hu-1 (GenBank accession number: MN908947.3) was used as standard strain. As of 17 April 2020, there were 1, 002 SARS-CoV-2 strains in the GenBank database, of which 12 strains had mutations in the amino-acid sequence of the S protein. Some of these mutations could affect the physicochemical properties and secondary structures of the S protein. The R4081 mutation was located in the receptor-binding domain (RBD) and displayed on the surface, and could affect the RBD structure. The mutated amino acids 48, 74, 181, 221 and 655 were located in predicted linear epitopes of B cells, and 74, 181 and 655 mutations could greatly affect the structures and properties of linear epitopes of B cells.. The S protein of SARS-CoV-2 isolated from humans, dogs, cats and lions was highly conserved, whereas the D614G mutation was found in the isolated strain from tigers. Furthermore, the unique Flynn protease recognition site was presented in the S protein of SARS-CoV-2 compared with the coronavirus from bats. These results suggest that the S protein of SARS-CoV-2 is relatively conserved within and between species, whereas there are some mutations that can affect the physicochemical properties and structures of the S protein, which may also affect the linear epitopes of B cells. Taken together, these data provide a basis for the research and development of drugs, antibodies and vaccines against SARS-CoV-2.

Evaluation of sample pooling method for SARS CoV-2 RNA detection;A laboratory based simulated study

Real time RT-PCR is considered as the gold standard test to detect COVID-19. The use of sample pooling strategy increases testing capacity and spares resources. However, the effectiveness of sample pooling should be evaluated in the setting before being implemented. Forty five samples including 20 high positives (Ct<20), 20 low positives (Ct 20-40) and 05 negative samples were used to prepare 1:1, 1:3 and 1:5 simulated sample pools which were then subjected to viral RNA extraction followed by real time RT-PCR. Sensitivity and specificity of sample pooling technique in the detection of SARS-CoV-2 RNA was 100% without significant variation of Ct values. According to our results, pooling of up to 6 samples will not have an effect on the final result in clinical samples and hence can be adopted in the given context for the diagnosis of COVID-19 by RT-PCR.

Clinical and epidemiological characteristics of 10 cases of clustered Chlamydia pneumoniae pneumonia

OBJECTIVE: To investigate the diagnosis and clinical characteristics of 10 cases of clustered Chlamydia pneumoniae pneumonia during the prevention and control of the COVID-19 pandemic. METHODS: The clinical data of 10 patients with clustered Chlamydia pneumoniae infection in a college diagnosed and treated by the Third Medical Center of the PLA General Hospital from Mar. 10, 2021 to Mar. 17, 2021 were retrospectively analyzed, the clinical characteristics of Chlamydia pneumoniae infection were summarized, and the diagnosis and treatment plan was selected quickly and accurately. RESULTS: All 10 cases with Chlamydia pneumoniae pneumonia infection had no history of contact with live or dead birds, 80% of them had cough symptom, 50% of them had fever symptom. Laboratory test results showed that 80% of patients had white blood cell count in normal range, 60% of patients had increased c-reactive protein level to varying degrees, 70% of patients had creatine kinase above normal, creatinine and procalcitonin were all normal, and some coagulation function indexes were abnormal. Lung CT scan showed increased density of unilateral lung floccus, nodules or spots, with air bronchial signs and even consolidation. The results of respiratory tract five-link card showed that all 10 patients were positive for Chlamydia pneumoniae immunoglobulin M(IgM) antibody. The nucleic acid sequence of Chlamydia pneumoniae was detected by metagenomics next-generation sequencing(mNGS)in 2 patients after hospitalization. 10 patients were treated with moxifloxacin hydrochloride and sodium chloride injection and moxifloxacin hydrochloride tables in sequences, all of which were cured. After 1 month, the outpatient reexamination of lung CT showed that the inflammation was basically absorbed. CONCLUSION: Chlamydia pneumoniae infection can cause outbreak through respiratory transmission, which tend to occur in the spring. The combination of respiratory pathogen antibody detection and mNGS technology can improve the efficiency of clinical diagnosis and treatment.

Influencing factors of virus clearance of COVID-19 patients

Objective: To analysis the related factors that influenced the elimination of virus in patients with coronavirus disease 2019 (COVID-19), and help with its prevention and control.

Complete genome sequence and phylogenetic analysis of avian infectious bronchitis virus isolated in India

Emergence of avian infectious bronchitis virus (IBV) variants with altered tissue tropism and host range has been reported from different parts of the world. Little is known about the different IBV variants existing and emerging in India. To explore the same, an IBV isolate, namely B17 isolated from backyard chicken in Tamil Nadu was used in the present study. The complete genome of B17 was sequenced and its phylogenetic relationship with the existing vaccine strain genotypes was analysed. The phylogenetic analysis of both S1 gene and complete genome sequence grouped B17 under Mass41 genotype comprising of M41, Beaudette, H120 and H120 variant with bootstrap value of 95-100%. Further, genomic analysis of B17 revealed the possibilities of emergence of the same from H120 vaccine strain through mutations at various genes.

First isolation and identification of SARS-CoV-2 in Guangdong Province, China

In January 2020, Guangdong Province, China imported several suspected cases with SARS-CoV-2 from Wuhan City, Hubei Province. China, which were detected as SARS-CoV-2 positive in laboratory. To further understand the SARS-CoV-2 virulence, as well as drug development and epidemic prevention and control needs, we established a SARS-CoV-2 isolation procedure. Vero-E6 cells were infected with the positive bronchoalveolar-lavage sample. The cells were monitored daily for cytopathic effects using light microscopy. The presence of viral nucleic acid in the supernatant was detected by RT-PCR. RNA extracted from culture supernatants were used as a template to clone and sequence the genome. We used Illumina sequencing to characterize the virus genome and results showed that the isolated virus was SARS-CoV-2.

SARS-CoV-2 mutation hotspots incidence in different geographic regions

SARS-CoV-2 (Severe Acute Respiratory Syndrome Coronavirus 2) is RNA virus with a positive-sense single-strand that belongs to the beta-coronavirus group that causes COVID-19 (Coronavirus Disease 2019) which originally emerged in China. Viruses with RNA genomes are known by a high mutation rate potential. The mutation rate determines genome variability and evolution of the virus;therefore, allowing viruses to evade the immune system, gain more infectivity potentials, virulence modifications, and probably resistance development to antivirals. A total of 311 SARS-CoV-2 virus whole genome sequences have been retrieved from the GISAID database from 1st of January 2020 to 31th of August 2020. The sequences were analyzed for sequence purity and multiple sequence alignment together with reference sequence was conducted through using Clustal Omega that is imbedded in Jalview software and Blast tools. We recorded the occurrence of 4 newly incident high frequently occurring mutations in all six geographic regions, namely at positions 2416, 18877, 23401, and 27964. The majority of all recorded hotspots were detected in Asia, Europe, and North America. The findings of our study suggest that the SARS-CoV-2 is in continuous evolution. For the impact of these mutations, further investigations are required and to understand whether these mutations would lead to the appearance of Drug-resistance viral strains, strains with increased infectivity and pathogenicity, and also their effect on the vaccine development and immunogenesis.

Early phylodynamics analysis of the COVID-19 epidemic in France

France was one of the first countries to be reached by the COVID-19 pandemic. Here, we analyse 196 SARS-Cov-2 genomes collected between Jan 24 and Mar 24 2020, and perform a phylodynamics analysis. In particular, we analyse the doubling time, reproduction number (Rt) and infection duration associated with the epidemic wave that was detected in incidence data starting from Feb 27. Different models suggest a slowing down of the epidemic in Mar, which would be consistent with the implementation of the national lock-down on Mar 17. The inferred distributions for the effective infection duration and Rt are in line with those estimated from contact tracing data. Finally, based on the available sequence data, we estimate that the French epidemic wave originated between mid-Jan and early Feb. Overall, this analysis shows the potential to use sequence genomic data to inform public health decisions in an epidemic crisis context and calls for further analyses with denser sampling.

COVID-19 reinfection or relapse? A retrospective multicenter cohort study from Iran

Background: Returning symptomatic patients with a history of recovered COVID-19 with a new positive SARS CoV-2 PCR test after several weeks to months of a negative PCR result is challenging during the COVID-19 pandemic. Objectives: We aimed to determine such Iranian patients' clinical and laboratory characteristics and discuss possible reasons.

Molecular analysis and genome sequencing of SARS-CoV-2 during second wave 2021 revealed variant diversity in India

SARS-CoV-2 variants rapid emergence has posed critical challenge of higher transmission and immune escape causing serious threats to control the pandemic. The present study was carried out in confirmed cases of SARS-CoV-2 patients to elucidate the prevalence of SARS-CoV-2 variant strain. We performed RT-PCR using extracted RNA from the nasopharyngeal swabs of suspected Covid-19 patients. Confirmed positive cases with CT< 25 were subjected to whole-genome sequencing to track the prevalence of the virus in the Malwa region of Punjab. The presence of B.1, B.1.1.7, B.1.351, B.1.617.1, B.1.617.2, AY.1 and other unidentified variants of SARS-CoV-2 was found in the studied population. Among all the variants, B.1.1.7 (UK variant) and B.1.617.2 (delta-Indian variant) was found to be the most dominant variant in the population and was found majorly in Patiala followed by Ludhiana, SBS Nagar, Mansa and Sangrur. In addition to this, sequencing results also observed that the dominant trait was more prevalent in male population and age group 21-40 years. The B.1.1.7 and B.1.617.2 variant of SARS-CoV-2 is replacing the wild type (Wuhan Strain) and emerging as the dominant variant in Punjab.

Inadequate SARS-CoV-2 Genetic Sequencing capacity in Zimbabwe: A call to urgently address this key gap to control current and future waves.

Zimbabwe continues to confront the COVID-19 pandemic; there is an urgent need for the rapid scale-up of genomic surveillance efforts. In this piece, we express concern on the limited capacity for SARS-CoV-2 genomic surveillance in Zimbabwe due to limited skillsets and laboratory infrastructural deficiencies. We call for an urgent need for funding from the government of Zimbabwe to set up a robust genomic surveillance program to detect SARS-CoV-2 variants of concern in Zimbabwe and guide public health responses accordingly.

Wastewater-Based Epidemiology as an Early Warning System for the Spreading of SARS-CoV-2 and Its Mutations in the Population.

New methodologies based on the principle of "sewage epidemiology" have been successfully applied before in the detection of illegal drugs. The study describes the idea of early detection of a virus, e.g., SARS-CoV-2, in wastewater in order to focus on the area of virus occurrence and supplement the results obtained from clinical examination. By monitoring temporal variation in viral loads in wastewater in combination with other analysis, a virus outbreak can be detected and its spread can be suppressed early. The use of biosensors for virus detection also seems to be an interesting application. Biosensors are highly sensitive, selective, and portable and offer a way for fast analysis. This manuscript provides an overview of the current situation in the area of wastewater analysis, including genetic sequencing regarding viral detection and the technological solution of an early warning system for wastewater monitoring based on biosensors.

Viruses in Bovine Respiratory Disease in North America: Knowledge Advances Using Genomic Testing.

Advances in viral detection in bovine respiratory disease (BRD) have resulted from advances in viral sequencing of respiratory tract samples. New viruses detected include influenza D virus, bovine coronavirus, bovine rhinitis A, bovine rhinitis B virus, and others. Serosurveys demonstrate widespread presence of some of these viruses in North American cattle. These viruses sometimes cause disease after animal challenge, and some have been found in BRD cases more frequently than in healthy cattle. Continued work is needed to develop reagents for identification of new viruses, to confirm their pathogenicity, and to determine whether vaccines have a place in their control.

Dengue Fever and Severe Dengue in Barbados, 2008-2016.

Analysis of the temporal, seasonal and demographic distribution of dengue virus (DENV) infections in Barbados was conducted using national surveillance data from a total of 3994 confirmed dengue cases. Diagnosis was confirmed either by DENV-specific real time reverse transcriptase polymerase chain reaction (rRT-PCR), or non-structural protein 1 (NS1) antigen or enzyme linked immunosorbent assay (ELISA) tests; a case fatality rate of 0.4% (10/3994) was observed. The prevalence rate of dengue fever (DF) varied from 27.5 to 453.9 cases per 100,000 population among febrile patients who sought medical attention annually. DF cases occurred throughout the year with low level of transmission observed during the dry season (December to June), then increased transmission during rainy season (July to November) peaking in October. Three major dengue epidemics occurred in Barbados during 2010, 2013 and possibly 2016 with an emerging three-year interval. DF prevalence rate among febrile patients who sought medical attention overall was highest among the 10-19 years old age group. The highest DF hospitalisation prevalence rate was observed in 2013. Multiple serotypes circulated during the study period and Dengue virus serotype 2 (DENV-2) was the most prevalent serotype during 2010, whilst DENV-1 was the most prevalent serotype in 2013. Two DENV-1 strains from the 2013 DENV epidemic were genetically more closely related to South East Asian strains, than Caribbean or South American strains, and represent the first ever sequencing of DENV strains in Barbados. However, the small sample size (n = 2) limits any meaningful conclusions. DF prevalence rates were not significantly different between females and males. Public health planning should consider DENV inter-epidemic periodicity, the current COVID-19 pandemic and similar clinical symptomology between DF and COVID-19. The implementation of routine sequencing of DENV strains to obtain critical data can aid in battling DENV epidemics in Barbados.