Retrospective Analysis of Clostridioides difficile Infection Rates in Hospitalized Patients during COVID-19 Pandemic. A Unicenter Study in Reus, Spain (preprint)

.Background: Clostridioides difficile infections (CDI) vary in severity from mild diarrhea to life-threatening conditions like pseudomembranous colitis or toxic megacolon, often leading to sepsis and death. The COVID-19 pandemic prompted changes in healthcare practices, potentially affecting CDI incidence, though reported data are inconclusive. We studied factors influencing CDI incidence and outcomes at a university hospital throughout the COVID-19 pandemic years. Methods: We conducted a retrospective study on all adult hospitalized CDI cases from January 1, 2020, to December 31, 2022. We collected demographic information, comorbid conditions, and concurrent infections. Results: While overall CDI and COVID-19 rates decreased in 2022, a nota-ble increase in CDI infections was observed among oncological patients and those undergoing some aggressive treatments, such as colon or gastroscopies. The prevalence of comorbidities remained unmodified, and there were declines in prior gastrointestinal surgeries and proton pump inhibitor prescriptions. Factors associated with patient fatality or prolonged hospitaliza-tion included older age, cancer, chronic kidney disease, higher Charlson and McCabe indices, elevated C-reactive protein, and low albumin concentrations. Conclusion: Our study shows the evolving landscape of CDI during the COVID-19 pandemic and emphasizes the impact of de-layed diagnoses and treatments exacerbated by telemedicine adoption. Identified risk factors for CDI-related mortality or prolonged hospital stays underscore the importance of targeted inter-ventions in high-risk populations.

Multi-ancestry GWAS of diarrhea during acute SARS-CoV2 infection identifies multiple novel loci and contrasting etiological roles of irritable bowel syndrome subtypes (preprint)

A substantial proportion of acute SARSCoV2 infection cases exhibit gastrointestinal symptoms, yet the genetic determinants of these extrapulmonary manifestations are poorly understood. Using survey data from 239,866 individuals who tested positively for SARSCoV2, we conducted a multi-ancestry GWAS of 80,289 cases of diarrhea occurring during acute COVID19 infection (33.5%). Six loci (CYP7A1, LZFTl1/CCR9, TEME182, NALCN, LFNG, GCKR) met genomewide significance in a trans-ancestral analysis. The top significant GWAS hit mapped to the CYP7A1 locus, which plays an etiologic role in bile acid metabolism and is in high LD (r2= 0.93) with the SDCBP gene, which was previously implicated in antigen processing and presentation in the COVID-19 context. Another association was observed with variants in the LZTFL1/CCR9 region, which is a known locus for COVID19 susceptibility and severity. PheWAS showed a shared association across three of the six SNPs with irritable bowel syndrome (IBS) and its subtypes. Mendelian randomization showed that genetic liability to IBS-diarrhea increased (OR=1.40,95%,CI[1.33,1.47]), and liability to IBS-constipation decreased (OR=0.86, 95%CI[0.79,0.94]) the relative odds of experiencing COVID19+ diarrhea. Our genetic findings provide etiological insights into the extrapulmonary manifestations of acute SARSCoV2 infection.

The Aftermath of COVID-19: Exploring Long-Term Effects on the Organ Systems (preprint)

Background: Post-acute sequelae of SARS-CoV-2 infection (PASC) is a complicated disease that affects millions of people all over the world. Previous studies have shown that PASC impacts 10% of SARS-CoV-2 infected patients of which 50-70% are hospitalized. It has also been shown that 10-12% of those vaccinated against COVID-19 were affected with PASC and its complications. The severity and the later development of PASC symptoms is positively associated with the early intensity of the infection. Results: The generated health complications caused by PASC involve a vast variety of organ systems. Patients affected by PASC have been diagnosed with neuropsychiatric and neurological symptoms. Cardiovascular system also has been involved and several diseases such as myocarditis, pericarditis, and coronary artery diseases were reported. Chronic hematological problems such as thrombotic endothelialitis and hypercoagulability were described as a condition that could increase the risk of clotting disorders and coagulopathy in PASC patients. Chest pain, breathlessness, and cough in PASC patients were associated with respiratory system in long COVID-19 causing respiratory distress syndrome. The observed immune complications were notable, involving several diseases. Renal system also was impacted and result in raising the risk of diseases such as thrombotic issues, fibrosis, and sepsis. Endocrine gland malfunction can lead to diabetes, thyroiditis, and male infertility. Symptoms such as diarrhea, nausea, loss of appetite and taste were also among reported observations due to several gastrointestinal disorders. Skin abnormalities might be an indication of infection and long-term implications such as persistent cutaneous complaints were linked to PASC. Conclusions: Long COVID is a multidimensional syndrome with considerable public health implications, affecting several physiological systems and demanding thorough medical therapy as well as more study to address its underlying causes and long-term effects.

Evaluating Nirmatrelvir-Ritonavir (Paxlovid®) in Outpatient COVID-19 Treatment: Safety, Tolerability, and Adherence Insights from Primary Healthcare Clinics (preprint)

Objective: This study aims to fill this gap by evaluating the safety, tolerability, and adherence of patients prescribed Paxlovid® in outpatient settings, focusing on its use in managing category 2 COVID-19 patients across three primary healthcare clinics in Selangor, Malaysia. Design: Retrospective cross-sectional study Setting: Data were collected from the Paxlovid® pharmacy registry and medical records at Klinik Kesihatan Seksyen 7, Klinik Kesihatan Seksyen 19, and Klinik Kesihatan Kelana Jaya between April 1, 2022, and November 30, 2022. Participants: This study analysed data from 415 category 2 COVID-19 patients aged ≥18 years old. Primary and secondary outcomes: Parameters assessed included patient demographics, dosing, current medication, changes in drug regimen, adherence, and ADR. Pharmacists follow-ups were conducted on days 3 and 5 post-medication initiation. Results: The majority (79.5%) of the cohort experienced ADR, predominantly dysgeusia, diarrhoea, body ache, vomiting, and nausea. Despite these, the ADR were generally well-tolerated, with no severe impacts reported. High adherence was observed, with 96.9% of patients completing the 5-day regimen. The primary reasons for non-adherence included adverse effect intolerability, dosing ambiguity, forgetfulness, concerns about ADR, and perceived health improvement. Notable medications interacting with Paxlovid® were simvastatin, amlodipine, and atorvastatin, and 21.7% of 23 concurrent medications were found not complying to the recommended interventions by the University of Liverpool COVID-19 Drug Interaction database. Conclusion: Nirmatrelvir-ritonavir (Paxlovid®) demonstrates a high level of safety and tolerability in outpatient COVID-19 patients, with optimal adherence observed. This study underscores the vital role of healthcare professionals in managing Paxlovid® within primary healthcare and highlights the need for broader research and direct patient involvement to enhance treatment strategies against COVID-19.

Does the severity of SARS-CoV-2 infection higher in liver transplant recipients?: A single-center experience. (preprint)

Background: Liver transplant (LT) recipients with COVID-19 have been reported as a high-risk population for severe disease through the COVID-19 pandemic. Studies have shown that liver transplantation did not significantly increase the risk of death and severe disease in patients with SARS-CoV-2 infection. Methods: From September 2020- March 2021, we collected data and serum anti-SARS-CoV-2 IgM +IgG results for 91 liver transplant recipients. Study enrolment was performed when patients presented for scheduled routine follow-up. All participants with serum anti-SARS-CoV-2 IgM+IgG completed a questionnaire querying information including clinical symptoms in the last six months. We further collected 91 patients with anti-SARS-CoV-2 IgM + IgG results. Seven patients had a known history of symptomatic COVID-19 during the previous six months. Of the 84 participants included in the study, 21 (25 %) had positive anti-SARS-Cov-2 IgM + IgG results. In addition, we applied the COVID-19 PCR test to all 21 patients, and all of them were negative. Overall, only seven patients declared flu-like upper respiratory tract infection symptoms or diarrhea in detailed inquiry. Conclusion: We documented past SARS-CoV-2 infection in 25 % of our outpatient LT recipients, and the majority were asymptomatic. There was no significant relationship between symptoms and seropositivity for SARS-COV-2.

WHAT THE COVID-19 PANDEMIC TAUGHT US IN CHILDREN (preprint)

Objective: The COVID-19 pandemic is an important cause of morbidity and mortality, which has had a negative impact worldwide. We aimed to contribute to the medical literature by sharing the knowledge and experience of pediatric patients who were diagnosed as having COVID-19 in a one-year period. Method: Patients aged 1 month to 18 years who were diagnosed as having COVID-19 in our clinic, between March 2020 and April 2020, from when COVID-19 was declared as a pandemic, were included in the study. Results: Four hundred sixty-seven children were included in the study. There were 34 (7.3%) patients under one year of age, 111 (23.8%) between 1-5 years, 98 (30.4%) between 5-10 years, 142 (30.4%) between 11-15 years, and 82 (17.6%) age over 15 years. Fever (88.2%), vomiting (32.4%), and diarrhea (29.4%) in patients aged under 1 year, sore throat (36.6%) in patients aged 11-15 years, and dysgeusia (11%), anosmia (14.6%), headache (18.3%), malaise (40.8%), myalgia (28%), and dyspnea (17.1%) in those aged over 15 years of age were found significantly more common compared with the other age groups. Thirty-five (7.5%) patients were asymptomatic, 365 (78.1%) had mild disease, 35 (7.5%) were moderate, 27 (5.8%) were severe, and five (1.07%) were critical. Leukocyte count, erythrocyte sedimentation rate, ferritin, and C-reactive protein values were significantly higher in hospitalized patients. Four patients died during the study period (0.8%, 4/494). Conclusion: Although COVID-19 has an asymptomatic and mild course in children, it should be kept in mind that it may have a severe course.

Healthcare Behaviour During a Health Crisis: The Case of Covid-19 in Madagascar (preprint)

A health crisis can affect the attitude towards healthcare seeking of the population. During the COVID-19 pandemic, two situations arose: people either sought care out of caution and vigilance, or because of the fear of contracting the virus and the health restrictions, they did not consult the healthcare facilities. This paper aims to analyse the effects of a health crisis such as that of COVID-19 on the use of healthcare in Madagascar. Two diseases, diarrhoea and fever, are considered, fever, as it is a common symptom of COVID-19, and diarrhoea, as it is one of the causes of morbidity in Madagascar and a less common symptom of the pandemic. Using data from the Multiple Indicator Cluster Survey in 2018 and the Rapid Survey on the Socio-Economic Impact of COVID-19 in Madagascar in 2020 and considering the same individuals surveyed in 2018 and 2020, after verification of the endogeneity, the absence of it was raised. Probit models without instrumental variables are used. During the pandemic, in the case of diarrhoea, faced with the fear of a pandemic, people have sought other alternatives, such as Community Health Workers (CHWs), which is considered less risky than health centres (0.33; p-value = 0.05). In the case of fever, people out of caution, prefer to consult health centres rather than self-medicate (-1.86; p-value = 0.00). People’s behaviour differs according to the symptoms of their illness, diarrhoea being less well-known and less frequent as a symptom of Covid-19 than fever.

Establishment of a real-time recombinase-aided isothermal amplification (RT-RAA) assay for the rapid detection of bovine respiratory syncytial virus (preprint)

Background Bovine respiratory syncytial virus (BRSV) is a major cause of bovine respiratory disease, resulting in significant losses to the cattle industry. For rapid detection of BRSV, reverse transcription recombinase polymerase amplification assays targeting the F gene were developed by integrating the fluorescence detection platform (RT-RAA).Results The developed RT-RAA assays allowed the exponential amplification of the target fragment in 20 min at a constant temperature of 39°C. The RT-RAA assays also showed good specificity for BRSV, with no cross-reactions with Infectious Bovine Rhinotracheitis Virus (IBRV), Bovine Parainfluenza Virus Type 3 (BPIV3), Bovine Viral Diarrhea Virus (BVDV) and Bovine Coronavirus (BCoV). With the standard RNA of BRSV serving as a template, the limit of detection for RT-RAA was 5 × 102 copies per reaction. Forty clinical samples collected from cattle with respiratory disease were tested, and the positive rate was 7.5% (3/40), consistent with results using the conventional PCR method reported previously.Conclusion An RT-RAA assay for BRSV detection was established in this study. The method is specific and sensitive and can be completed within 20 min at 39℃. These results ascertain that the developed RT-RAA assays are effective diagnostic tools for rapidly detecting BRSV in resource-limited settings, which may be applied for clinical detection of BRSV.

Temporal changes in the positivity rate of common enteric viruses among paediatric admissions in coastal Kenya, in the period spanning the COVID-19 pandemic, 2019-2022 (preprint)

Abstract Background The non-pharmaceutical interventions (NPIs) implemented to curb the spread of SARS_CoV_2 early in the COVID_19 pandemic years, disrupted the activity of other respiratory viruses. There is limited data from low and middle income countries (LMICs) to determine whether COVID_19 NPIs also impacted the epidemiology of enteric viruses. We investigated the changes in infection patterns of common enteric viruses among hospitalised children who presented with diarrhoea to a referral hospital in coastal Kenya, in the period spanning the COVID_19 pandemic. Methods A total of 870 stool samples from children under 13 years of age admitted to Kilifi County Hospital between January 2019, and December 2022 were screened for rotavirus group A (RVA), norovirus genogroup II (GII), astrovirus, sapovirus, and adenovirus type F40/41 using realtime reverse transcription polymerase chain reaction. The proportions positive across the four years were compared using the chi-squared test statistic. Results One or more of the five virus targets were detected in 282 (32.4%) cases. A reduction in the positivity rate of RVA cases was observed from 2019 (12.1%, 95% confidence interval (CI) 8.7% to 16.2%) to 2020 (1.7%, 95% CI 0.2% to 6.0%; p < 0.001). However, in the 2022, RVA positivity rate rebounded to 23.5% (95% CI 18.2% to 29.4%). For norovirus GII, the positivity rate fluctuated over the four years with its highest positivity rate observed in 2020 (16.2%; 95% C.I, 10.0% to 24.1%). No astrovirus cases were detected in 2020 and 2021, but the positivity rate in 2022 was similar to that in 2019 (3.1% (95% CI 1.5% to 5.7%) vs 3.3% (95% CI 1.4% to 6.5%)). A higher case fatality rate was observed in 2021 (9.0%) compared to the 2019 (3.2%), 2020 (6.8%) and 2022 (2.1%) (p <0.001). Conclusion Our study finds that in 2020 the transmission of common enteric viruses, especially RVA and astrovirus, in Kilifi Kenya may have been disrupted due to the COVID_19 NPIs. After 2020, local enteric virus transmission patterns appeared to return to prepandemic levels coinciding with the removal of most of the government COVID_19 NPIs.

Serological Epidemiological Survey Of Bovine Diarrhea In Large-Scale Cattle Farms In Inner Mongolia, China from 2019 to 2022 (preprint)

Bovine diarrhea is a multi-factorial disease, and remains one of the most serious health problems in cattle husbandry. However, the endemic trends of the main pathogens responsible for bovine diarrhea have not been analyzed before, therefore, the purpose of this study was to estimate the prevalence of bovine diarrhea pathogens in the large-scale cattle farms of Inner Mongolia in China, we assessed the differences in the prevalence of infection based on age and area, as well as determined local prevalence rates and the rates of mixed infections. Using stratified random sampling strategy, cattle were divided into four age stages (0-2 months, 3-6 months, 7-18 months and ＞18 months), 2,216 serum samples were collected from 38 cattle herds in 12 leagues and cities in Inner Mongolia of China. Positive rates of Bovine Viral Diarrhoea Virus (BVDV), Bovine Rotavirus (BRV), Bovine Coronavirus (BCoV), Escherichia coli K99 (E.coli K99), and M. paratuberculosis (Mptb) antibodies were detected in the samples by ELISA to determine the epidemic trends and differences of the five pathogens in Inner Mongolia. The positive rate of BVDV vaccine higher than 90% in each age category of cattle, and the prevalence rates of BRV and Mptb in other ages significantly higher than ＞18 months (P <0.05). Except BVDV, the prevalence of BCoV was the highest in 0-2 months old (74.88%), the highest positive rate in ＞18 months old is BRV (63.31%), the infection of viral pathogens were serious in Inner Mongolia. With the highest mixed infection (33.74%) being BRV and BCoV in the category of 0-2 months, and there was a mixed infection of BRV and BCoV at four age stages, Only double and triple infections were detected in cattle aged 2-6 months and 6-18 months, quadruple infections were detected in cattle aged 0-2 months and ＞18 months. Furthermore, obvious regional epidemiological differences among the five pathogens were observed, 5 pathogens were detected in 11 regions, Hulun Buir city was seriously infected with bacterial pathogens, only antibodies to viral pathogens were detected in Ulanqab city. All the above detected pathogens can trigger high mortality and poor prognosis in cattle. This study is the first to report the prevalence and characteristics of the main pathogens of bovine diarrhea in large-scale cattle farms in Inner Mongolia, China, which has practical significance for the future prevention and control of bovine diarrhea and reduce economic losses in cattle farming.

Clinical Features and Short-Term Outcomes in Virus-Induced Bradycardia: Comparison Between Covid and non-Covid Infected Patients (preprint)

Covid-19 outbreak has drawn attention to the fact that viral infections might present with clinical bradycardia. Seeking its clinical significance, not yet unveiled by the literature, we come across other viral infections that also show clinical bradycardia during its clinical course, such as dengue fever and viral diarrhea. The clinical presentation of the latest seems to be severe, often presenting with orthostatic intolerance and fatigue symptoms, requiring expert consultation irrespective of the infection stage, and in case of dengue fever, frequently during the recovery phase. Meanwhile, in Covid-19 infected patients, the bradycardia observed is mild, frugal, and usually asymptomatic. Thus, we conducted a comparison between two different groups of patients with viral infection displaying clinical bradycardia during hospital stay: Covid and non-Covid patients regarding clinical and Holter monitoring parameters. All patients had other causes of bradycardia excluded and echocardiography and cardiac biomarkers ruled out acute myocarditis. The results showed that non-Covid patients presented with significantly lower mean and minimum heart rates (HR) on Holter monitoring, as well as longer times in with HR < 50 beats per minute (bpm).  SDNN and pNN>50% were also significantly higher in non-Covid patients. The minimum systolic BP was significantly lower in non-Covid patients. The study shows that Covid-19 is not the only viral infection that may display with clinical bradycardia, but it’s much milder than other viral infections such as dengue fever and viral diarrhea. It remains unclear the mechanism throughout Covid-related bradycardia comes about.

Adverse events of COVID-19 vaccination among Japanese University Students suppressed by breakfast consumption and favorable sleeping habits (preprint)

Despite the evidence of effectiveness of vaccines in preventing SARS-CoV-2 infection-associated serious illness, hospitalization, and death, there is some hesitation towards COVID-19 vaccination in young adults because of concerns regarding adverse events. A retrospective cohort study was conducted in Gifu University students receiving the mRNA-1273 vaccine and boosters to elucidate the real incidence of adverse events and factors that prevent them. We examined the adverse events and identified potential risk factors through a self-administered questionnaire reporting their physical condition after COVID-19 vaccination. A higher number of vaccinations, female sex, and low body mass index were significantly associated with the occurrence of adverse events on the day of or after receiving the COVID-19 vaccine. Regular breakfast consumption was significantly associated with a decreased incidence of post-vaccination itching, abdominal pain, and diarrhea. Sufficient sleep duration was significantly associated with a decreased incidence of post-vaccination abdominal pain and diarrhea. Focal/systemic adverse events were highly frequent among university students after receiving the COVID-19 vaccine, with no life-threatening cases or hospitalizations. A higher number of vaccinations, female sex, and lower body mass index were associated with an increased incidence of adverse events. Contrastingly, regular breakfast and sufficient sleep were associated with fewer adverse events.

Prevalence and predictors of depression, anxiety, and stress among recovered COVID-19 patients in Vietnam.

Background: During the COVID-19 pandemic, a high prevalence of mental health distress has been reported among people who have recovered from the disease. Objectives: To assess the prevalence of depression, anxiety, and stress as well as identify predictors among recovered COVID-19 patients after more than six months of being discharged in Dong Thap Province, Vietnam. Material and methods: The cross-sectional study was conducted among 549 eligible participants recruited by stratified sampling. Data was collected using the depression, anxiety and stress scale - 21 items had Content Validity Index = 0.9, and Cronbach's alpha for depression, anxiety and stress sub-scales were 0.95, 0.81, and 0.86, respectively. Descriptive statistics were used to measure the prevalence levels and distribution of characteristics of the participant, while factors influencing depression, anxiety, and stress were predicted using binary logistic regression. Results: The overall prevalence of depression, anxiety, and stress were 24.8% (95% CI: 21.2-28.6), 41.5% (95% CI: 37.4-45.8), and 25.3% (95% CI: 21.7-29.2), respectively. The predictors of depression were living in urban area (OR = 1.97; 95% CI: 1.27-3.08), holding a bachelor's degree (OR:3.51; 95% CI: 1.13-10.8), having a high monthly income (OR: 2.57; 95% CI: 1.03-6.38), diabetes (OR: 2.21; 95% CI: 1.04-4.68), heart disease (OR: 3.83; 95% CI: 1.79-8.17), respiratory disease (OR: 3.49; 95% CI: 1.24-9.84), and diarrhea (OR: 4.07; 95% CI: 1.06-15.6). Living in the urban area (OR: 1.57; 95% CI: 1.07-2.29), having sleep disturbance (OR: 2.32; 95% CI: 1.56-3.46), and fatigue (OR: 1.57; 95% CI: 1.03-2.39) were predictors for anxiety. Having respiratory disease (OR: 3.75; 95% CI: 1.47-9.60) or diarrhea (OR: 4.34; 95% CI: 1.18-15.9) were predictors of stress. Conclusion: People who have recovered from COVID-19 should be assessed for symptoms of depression, anxiety, and stress. Primary healthcare providers should develop interventions to support their recovery.

Successful management of life-threatening post-COVID-19 cryptosporidiosis in a renal transplant patient: a case report.

Worldwide, Cryptosporidium spp. is a common parasite that affects domestic and wild animals, including humans, and causes diarrhea in both immunocompetent and immunocompromised hosts. The fecal-oral pathway accounts for the majority of its transfer. Although C. parvum and C. hominis are the most common zoonotic species in humans, other zoonotic species can also infect immunocompetent and immunocompromised people. Patients undergoing renal transplants are more likely to contract cryptosporidiosis, which can cause severe and potentially fatal diarrhea. A 41-year-old male patient who presented to the emergency department complained of a sudden onset, severe and continuous fatigue, and a feverish sensation of two-day duration. Two days prior to the current admission, the patient started to complain of weakness affecting his whole body, as well as a fever of 39°C and continuous yellowish diarrhea occurring 4-5 times daily without blood. Stool analysis revealed a cryptosporidium infection. The patient underwent surgery for kidney transplantation. The donated kidney was the left one from his brother and was attached to the patient´s right groin. As illustrated by our example, cryptosporidiosis should be considered a significant cause of acute, persistent, watery diarrhea in immunocompromised kidney transplant recipients. Patients undergoing renal transplants should be instructed to wash their hands frequently, stay away from young animals, sick people, and swimming pools in order to lower their risk of infection.

Trajectory of Gastrointestinal Symptoms in Previously Hospitalized COVID-19 Survivors: The Long COVID Experience Multicenter Study.

This multicenter cohort study used Sankey plots and exponential bar plots to visualize the fluctuating evolution and the trajectory of gastrointestinal symptoms in previously hospitalized COVID-19 survivors during the first 18 months after acute SARS-CoV-2 infection. A total of 1266 previously hospitalized COVID-19 survivors were assessed at four points: hospital admission (T0), at 8.4 months (T1), at 13.2 months (T2), and at 18.3 months (T3) after hospitalization. Participants were asked about their overall gastrointestinal symptoms and particularly diarrhea. Clinical and hospitalization data were collected from hospital medical records. The prevalence of overall gastrointestinal post-COVID symptomatology was 6.3% (n = 80) at T1, 3.99% (n = 50) at T2 and 2.39% (n = 32) at T3. The prevalence of diarrhea decreased from 10.69% (n = 135) at hospital admission (T0), to 2.55% (n = 32) at T1, to 1.04% (n = 14) at T2, and to 0.64% (n = 8) at T3. The Sankey plots revealed that just 20 (1.59%) and 4 (0.32%) patients exhibited overall gastrointestinal post-COVID symptoms or diarrhea, respectively, throughout the whole follow-up period. The recovery fitted exponential curves revealed a decreasing prevalence trend, showing that diarrhea and gastrointestinal symptoms recover during the first two or three years after COVID-19 in previously hospitalized COVID-19 survivors. The regression models did not reveal any symptoms to be associated with the presence of gastrointestinal post-COVID symptomatology or post-COVID diarrhea at hospital admission or at T1. The use of Sankey plots revealed the fluctuating evolution of gastrointestinal post-COVID symptoms during the first two years after infection. In addition, exponential bar plots revealed the decreased prevalence of gastrointestinal post-COVID symptomatology during the first three years after infection.

Misdiagnosis of Clostridioides difficile Infections by Standard-of-Care Specimen Collection and Testing among Hospitalized Adults, Louisville, Kentucky, USA, 2019-20201.

Although Clostridioides difficile infection (CDI) incidence is high in the United States, standard-of-care (SOC) stool collection and testing practices might result in incidence overestimation or underestimation. We conducted diarrhea surveillance among inpatients >50 years of age in Louisville, Kentucky, USA, during October 14, 2019-October 13, 2020; concurrent SOC stool collection and CDI testing occurred independently. A study CDI case was nucleic acid amplification test‒/cytotoxicity neutralization assay‒positive or nucleic acid amplification test‒positive stool in a patient with pseudomembranous colitis. Study incidence was adjusted for hospitalization share and specimen collection rate and, in a sensitivity analysis, for diarrhea cases without study testing. SOC hospitalized CDI incidence was 121/100,000 population/year; study incidence was 154/100,000 population/year and, in sensitivity analysis, 202/100,000 population/year. Of 75 SOC CDI cases, 12 (16.0%) were not study diagnosed; of 109 study CDI cases, 44 (40.4%) were not SOC diagnosed. CDI incidence estimates based on SOC CDI testing are probably underestimated.

Investigation of variants in genetics and virulence of Porcine Epidemic Diarrhea Virus after serial passage on Vero cells.

Porcine epidemic diarrhea virus (PEDV) is a highly contagious intestinal virus. However, the current PEDV vaccine, which is produced from classical strain G1, offers low protection against recently emerged strain G2. This study aims to develop a better vaccine strain by propagating the PS6 strain, a G2b subgroup originating from Vietnam, on Vero cells until the 100th passage. As the virus was propagated, its titer increased, and its harvest time decreased. Analysis of the nucleotide and amino acid variation of the PS6 strain showed that the P100PS6 had 11, 4, and 2 amino acid variations in the 0 domain, B domain, and ORF3 protein, respectively, compared to the P7PS6 strain. Notably, the ORF3 gene was truncated due to a 16-nucleotide deletion mutation, resulting in a stop codon. The PS6 strain's virulence was evaluated in 5-day-old piglets, with P7PS6 and P100PS6 chosen for comparison. The results showed that P100PS6-inoculated piglets exhibited mild clinical symptoms and histopathological lesions, with a 100% survival rate. In contrast, P7PS6-inoculated piglets showed rapid and typical clinical symptoms of PEDV infection, and the survival rate was 0%. Additionally, the antibodies (IgG and IgA) produced from inoculated piglets with P100PS6 bound to both the P7PS6 and P100PS6 antigens. This finding suggested that the P100PS6 strain was attenuated and could be used to develop a live-attenuated vaccine against highly pathogenic and prevalent G2b-PEDV strains.

Coinfection with porcine epidemic diarrhea virus and Clostridium perfringens type A enhances disease severity in weaned pigs.

Clostridium perfringens is a constituent of the normal gut microbiome in pigs; however, it can potentially cause pre- and post-weaning diarrhea. Nevertheless, the importance of this bacterium as a primary pathogen of diarrhea in piglets needs to be better understood, and the epidemiology of C. perfringens in Korean pig populations is unknown. To study the prevalence and typing of C. perfringens, 203 fecal samples were collected from diarrheal piglets on 61 swine farms during 2021-2022 and examined for the presence of C. perfringens and enteric viruses, including porcine epidemic diarrhea virus (PEDV). We determined that the most frequently identified type of C. perfringens was C. perfringens type A (CPA; 64/203, 31.5%). Among the CPA infections, single infections with CPA (30/64, 46.9%) and coinfections with CPA and PEDV (29/64, 45.3%) were the most common in diarrheal samples. Furthermore, we conducted animal experiments to investigate the clinical outcome of single infections and coinfections with highly pathogenic (HP)-PEDV and CPA in weaned piglets. The pigs infected with HP-PEDV or CPA alone showed mild or no diarrhea, and none of them died. However, animals that were co-inoculated with HP-PEDV and CPA showed more-severe diarrheal signs than those of the singly infected pigs. Additionally, CPA promoted PEDV replication in coinfected piglets, with high viral titers in the feces. A histopathological examination revealed more-severe villous atrophy in the small intestine of coinfected pigs than in singly infected pigs. This indicates a synergistic effect of PEDV and CPA coinfection on clinical disease in weaned piglets.

[Genetic diversity of Siberian bovine coronavirus isolates (Coronaviridae: Coronavirinae: Betacoronavirus-1: Bovine-Like coronaviruses)].

INTRODUCTION: Bovine coronaviruses (BCoVs) are causative agents of diarrhea, respiratory diseases in calves and winter cow dysentery. The study of genetic diversity of these viruses is topical issue. The purpose of the research is studying the genetic diversity of BCoV isolates circulating among dairy cattle in Siberia. MATERIALS AND METHODS: Specimens used in this study were collected from animals that died or was forcedly slaughtered before the start of the study. The target for amplification were nucleotide sequences of S and N gene regions. RESULTS: Based on the results of RT-PCR testing, virus genome was present in 16.3% of samples from calves with diarrheal syndrome and in 9.9% with respiratory syndrome. The nucleotide sequences of S gene region were determined for 18 isolates, and N gene sequences - for 12 isolates. Based on S gene, isolates were divided into two clades each containing two subclades. First subclade of first clade (European line) included 11 isolates. Second one included classic strains Quebec and Mebus, strains from Europe, USA and Korea, but none of sequences from this study belonged to this subclade. 6 isolates belonged to first subclade of second clade (American-Asian line). Second subclade (mixed line) included one isolate. N gene sequences formed two clades, one of them included two subclades. First subclade included 3 isolates (American-Asian line), and second subclade (mixed) included one isolate. Second clade (mixed) included 8 sequences. No differences in phylogenetic grouping between intestinal and respiratory isolates, as well as according to their geographic origin were identified. CONCLUSION: The studied population of BCoV isolates is heterogeneous. Nucleotide sequence analysis is a useful tool for studying molecular epidemiology of BCoV. It can be beneficial for choice of vaccines to be used in a particular geographic region.

Risk factors for complicated course and recurrence of Clostridioides Difficile infections during COVID-19 pandemic.

INTRODUCTION: The primary symptom of Clostridioides difficile infection (CDI) is diarrhea of varying severity. Both malnutrition and clinical nutrition increase the risk for contracting Clostridioides difficile (C. difficile) infection and the likelihood of relapses. Moreover, the risk for recurrence is higher if there is infection with a hypervirulent strain (NAP1/BI/027). Hypoalbuminemia predisposes to a severe course of the disease and morbidity. MATERIAL AND METHODS: Analysis was carried out of the data regarding patients hospitalized at the Regional Hospital for Infectious Diseases in Warsaw from 01 January 2020 to 31 December 2021 who were diagnosed with C. difficile infection. A severe course of infection was diagnosed when a blood test showed a leukocyte count greater than or equal to 15,000/µl and/or a creatinine concentration >1.5 mg/dl (>132.6 mmol/l). RESULTS: Clostridioides difficile infection was the reason for 185 hospitalizations (involving 108 women and 77 men), of 167 patients aged from 22 to 93 years old. There were 68 (37%) cases of recurrent infection. Seventy-five (41%) infections met the study's criteria for severe CDI, and 12 (7%) patients died. Out of the total number of hospitalizations, 41 (22%) were due SARS-CoV-2 co-infection. PCR tests detecting binary toxin revealed 34 (18%) positive results. Infection with a hypervirulent strain was an independent risk factor for the recurrence of diarrhea which had C. difficile etiology. Overall, during an episode of diarrhea, one antibacterial drug was used in 139 cases (75%), two in 27 (15%), three in 14 (8%) situations, and four - twice (1%). Among these, drugs not recommended for the treatment of CDI were used in 21 (11%) cases. The number of antibacterial drugs administered during an episode of diarrhea was an independent risk factor for the death of the infected person. Clinical nutrition was applied during 19 hospitalizations (10%), out of which 12 (63%) cases showed a severe course of C. difficile infection, while four patients (21%) died. Using clinical nutrition methods was an independent risk factor for a severe course of the disease and patient death. CONCLUSIONS: Clinical nutrition and the number of antibiotics used during an episode of diarrhea are independent risk factors for the death of a patient with CDI. Infection with a hypervirulent strain increases the risk for relapse.