Virus Coinfection Research Articles

Investigation of the safety and protective efficacy of an attenuated and marker M. bovis-BoHV-1 combined vaccine in bovines.

Bovine respiratory disease (BRD) is one of the most common diseases in the cattle industry worldwide; it is caused by multiple bacterial or viral coinfections, of which Mycoplasma bovis (M. bovis) and bovine herpesvirus type 1 (BoHV-1) are the most notable pathogens. Although live vaccines have demonstrated better efficacy against BRD induced by both pathogens, there are no combined live and marker vaccines. Therefore, we developed an attenuated and marker M. bovis-BoHV-1 combined vaccine based on the M. bovis HB150 and BoHV-1 gG-/tk- strain previously constructed in our lab and evaluated in rabbits. This study aimed to further evaluate its safety and protective efficacy in cattle using different antigen ratios. After immunization, all vaccinated cattle had a normal rectal temperature and mental status without respiratory symptoms. CD4+, CD8+, and CD19+ cells significantly increased in immunized cattle and induced higher humoral and cellular immune responses, and the expression of key cytokines such as IL-4, IL-12, TNF-α, and IFN-γ can be promoted after vaccination. The 1.0× 108 CFU of M. bovis HB150 and 1.0 × 106 TCID50 BoHV-1 gG-/tk- combined strain elicited the most antibodies while significantly increasing IgG and cellular immunity after challenge. In conclusion, the M. bovis HB150 and BoHV-1 gG-/tk- combined strain was clinically safe and protective in calves; the mix of 1.0 × 108 CFU of M. bovis HB150 and 1.0 × 106 TCID50 BoHV-1 gG-/tk- strain was most promising due to its low amount of shedding and highest humoral and cellular immune responses compared with others. This study introduces an M. bovis-BoHV-1 combined vaccine for application in the cattle industry.

Cytomegalovirus colitis as intestinal obstruction in an immunocompetent adolescent: a case report and literature review

BackgroundCytomegalovirus infection manifests varying clinical characteristics and severity in diverse populations with different immune statuses. The signs and symptoms of gastrointestinal involvement are nonspecific. Here, we present a case of cytomegalovirus colitis in an immunocompetent adolescent, which manifested as intestinal pseud-obstruction.Case presentationA 15-year-old man who had contracted novel coronavirus infection one month earlier was admitted to our hospital with fever, abdominal pain, and hematochezia. His abdomen was distended, and laboratory evaluation revealed a decrease in the blood count, an increase in inflammatory indicators and hepatic impairment. Imaging shows bowel wall thickening and dilatation of the colon. A diagnosis of intestinal infection combined with acute intestinal pseud-obstruction was made. Diarrhea persisted despite conservative treatment with empirical antibiotics. A colonoscopy was performed. Pathology confirmed cytomegalovirus infection. Ganciclovir therapy was initiated, and subsequent review showed a good recovery.ConclusionsThe case was diagnosed as cytomegalovirus colitis. We reviewed the reports of 9 cases of bowel obstruction, including our own, and found that the majority of the adult patients were elderly with underlying disease. Clinical and endoscopic manifestations are typically nonspecific, and imaging shows typical signs of intestinal obstruction. The final diagnosis was confirmed by pathology. Most of them have a good prognosis. We suggest that cytomegalovirus colitis can also lead to intestinal obstruction and that viral reactivation in immunocompetent individuals may be associated with inflammatory conditions and viral coinfection, particularly with the novel coronavirus.

Cocirculation and coinfection of multiple respiratory viruses during autumn and winter seasons of 2023 in Beijing, China: A retrospective study.

China experienced severe epidemics of multiple respiratory pathogens in 2023 after lifting "Zero-COVID" policy. The present study aims to investigate the changing circulation and infection patterns of respiratory pathogens in 2023. The 160 436 laboratory results of influenza virus and respiratory syncytial virus (RSV) from February 2020 to December 2023, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) from June 2020 to December 2023, Mycoplasma pneumoniae, adenovirus, and human rhinovirus from January 2023 to December 2023 were analyzed. We observed the alternating epidemics of SARS-CoV-2 and influenza A virus (IAV), as well as the out-of-season epidemic of RSV during the spring and summer of 2023. Cocirculation of multiple respiratory pathogens was observed during the autumn and winter of 2023. The susceptible age range of RSV in this winter epidemic (10.5, interquartile range [IQR]: 5-30) was significantly higher than previously (4, IQR: 3-34). The coinfection rate of IAV and RSV in this winter epidemic (0.695%) was significantly higher than that of the last cocirculation period (0.027%) (p < 0.001). Similar trend was also found in the coinfection of IAV and SARS-CoV-2. The present study observed the cocirculation of multiple respiratory pathogens, changing age range of susceptible population, and increasing coinfection rates during the autumn and winter of 2023, in Beijing, China.

A nanomaterial for the delivery of dsRNA as a strategy to alleviate viral infections in maize

The current methods for pest managements in cereal crops rely mainly on the applications of conventional chemicals, which are known to have low pest control efficiencies and are less environmentally friendly. The primary aim of this research endeavor was to devise a specific, efficient and eco-friendly biological agent capable of mitigating maize lethal necrosis (MLN), a viral disease that affected maize productivity and mainly caused by coinfection of maize chlorotic mottle virus (MCMV) and sugarcane mosaic virus (SCMV). Through this study, we have found that silencing Ferredoxin 3 (ZmFd3) expression in maize can significantly reduce the damages caused by MCMV and/or SCMV infections. Based on this finding, we have developed a liposome nanoparticles (LNPs)-mediated nanotechnology to suppress MCMV and/or SCMV infections. Using this nanotechnology, we have confirmed that the cationic/anionic liposomes (CLPs and ALPs) can be used to package and promote ZmFd3-dsRNA spread in maize plants. Through leaf spray, we have determined that the anti-MCMV and anti-SCMV activities of ZmFd3@CLPs and ZmFd3@ALPs nanoparticles can reach 52.46 ∼ 79.83 % at 6 days post virus inoculation (dpi). Because ZmFd3 is involved in hypersensitive response (HR), and can interact with MCMV p7b and SCMV HC-Pro, we designed an FHP-dsRNA to target ZmFd3, MCMV p7b, and SCMV HC-Pro transcripts for silencing in plants simultaneously. The result showed that both FHP@CLPs and FHP@ALPs nanoparticles can provide excellent, although short, protection to maize and sorghum plants to MCMV and SCMV infections. Overall, this study has developed a novel nanotechnology that can be used to mitigate virus infection in cereal crops through RNA interference (RNAi).

Efficacy of Newer Nucleos(t)ide Analogs After Hepatitis B Immunoglobulin Discontinuation Against Hepatitis B and D Recurrence in Liver Transplant Recipients.

The use of nucleos(t)ide analogs (NAs) with a high genetic barrier to resistance, namely entecavir and tenofovir, has improved the efficacy of antiviral prophylaxis against hepatitis B virus (HBV) recurrence after liver transplantation (LT). However, the optimal duration and dosage of hepatitis B immunoglobulin (HBIG) administration, particularly in patients transplanted for HBV and hepatitis D virus (HDV) coinfection, remains controversial. We evaluated 28 patients transplanted for HBV/HDV cirrhosis. After LT, each patient received a fixed scheme of low-dose HBIG plus NA for 6 mo post-LT and then continued with long-term NA prophylaxis (entecavir: 8, tenofovir: 20 patients). During 72 mo of follow-up, reappearance of hepatitis B surface antigen at low titers was observed in 1 (3.6%) patient at 33 mo after HBIG discontinuation, which became negative after a single dose of HBIG 1000 IU/L, whereas both serum HBV DNA and HDV RNA remained persistently undetectable and without any clinical or biochemical evidence of HBV/HDV recurrence. We showed for the first time the efficacy of a short, fixed scheme of low-dose HBIG plus NA followed by long-term NA monoprophylaxis against HBV/HDV recurrence after LT, although careful follow-up is needed after HBIG discontinuation, whereas further larger studies are needed to confirm these findings.

Survival Rate and Predictors of Mortality Among TB-HIV Co-Infected Patients During Tuberculosis Treatment at Public Health Facilities in Bahir Dar City, Northwest Ethiopia.

Tuberculosis and human immunodeficiency virus co-infection pose a major public health concern, particularly in developing countries. The survival and predictors of mortality were not sufficiently studied among TB-HIV co-infected patients in Ethiopia. This study aimed to investigate the survival rate and predictors of mortality among TB-HIV co-infected patients during TB treatment at public health facilities in Bahir Dar, Northwest Ethiopia. A retrospective follow-up study was conducted among 401 TB-HIV co-infected patients who were treated for tuberculosis between July 2018 and June 2022 at public health facilities in Bahir Dar city, Ethiopia. Data were collected using a structured checklist from patient charts. Data entry and analysis were done using EpiData 3.1 and Stata version 15, respectively. A Cox proportional Hazard regression model was used to identify predictors of mortality. Predictors with P < 0.05 in the multivariable regression were considered statistically significant. Among the 401 TB-HIV co-infected patients, 59 (14.7%) died during the follow-up period. Predictors like lower BMI (AHR = 3.00, 95% CI = 1.44, 6.28), extrapulmonary TB infection (AHR = 3.30, 95% CI = 1.50, 7.29), presence of opportunistic infection (AHR = 5.07, 95% CI = 2.55, 10.08), functional status (bedridden: AHR = 4.49, 95% CI = 1.63, 12.33), and adherence to TB treatment (fair = AHR = 2.74, 95% CI = 1.41, 7.20, and poor = AHR = 3.75, 95% CI = 1.52, 9.23) were associated with mortality. Mortality among TB and HIV coinfected people was high at public health facilities in Bahir Dar city. This result suggested that in order to increase patient survival, it would be necessary to enhance nutritional status, increase adherence to TB treatment, and prevent opportunistic infections.

Actual data regarding the impact of viral respiratory co-infection (Covid 19 and flu/ Respiratory Syncutial Virus RSV) - A systematic review

Abstract: Background. The impact of SARS-CoV-2 infection alongside with influenza and RSV, the major viral agents in pediatric disordes, may be an important concern to the healthcare system. Clinical outcomes of the interaction are unknown. The aim of this systematic review is to contribute at establishing the prevalence of the co-infection, its clinical outcomes and potential risk factors. Methods. A systematical literature search was performed for papers published in PubMed, Scopus, Web of Science, Pedro and Cochrane Library, from January 2020 - the beginning of the COVID 19 pandemic - to June 2023. Our review was conducted in accordance with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) methods. Studies were eligible for inclusion if they approached the co-infection COVID 19 and influenza or RSV, and were available in English. Due to the fact that studies conducted on pediatric population are scarce, we included patients of all ages. Results. Out of 159 articles found, 12 were eligible for inclusion. The prevalence of co-infection was between 5% and 12 % for influenza viruses and 10% for RSV. The most common symptoms were high-grade fever, cough, headache, and shortness of breath and the most frequent complications were pneumonia and respir-atory distress. In terms of laboratory findings, co-infected patients presented with signifi-cant lymphopenia and pronounced inflammatory response, as well as a progressive ten-dency towards pneumonia and respiratory distress. Regarding the clinical outcomes of co-infection, the majority of articles indicated that simultaneous infection with SARS-CoV-2 and influenza predisposes to a more severe course of the disease(s), with a longer length of hospital stay and an increased risk of death.Conclusion. Our study underlines that the frequency of such co-infections, although not very high, predisposes to more frequent hos-pitalisations and a longer length of stay, complications including admission to intensive care and more severe outcomes, including life-threatening events. It is therefore essential to determine the epidemiological impact of such an interaction nowadays, in order to in-form and adjust treatment and control and prevention strategies, for limiting co-infection between major respiratory viruses. Due to the lack of studies on children, we were unable to identify specific features of co-infections in this population. Therefore, more studies are needed to evaluate the paediatric population and consequently, our doctoral research en-deavour is warranted.

Herpesviridae and Atypical Bacteria Co-Detections in Lower Respiratory Tract Samples of SARS-CoV-2-Positive Patients Admitted to an Intensive Care Unit.

Shortly after the emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), cases of viral, bacterial, and fungal coinfections in hospitalized patients became evident. This retrospective study investigates the prevalence of multiple pathogen co-detections in 1472 lower respiratory tract (LRT) samples from 229 SARS-CoV-2-positive patients treated in the largest intensive care unit (ICU) in Slovenia. In addition to SARS-CoV-2, (rt)RT-PCR tests were used to detect cytomegalovirus (CMV), Epstein-Barr virus (EBV), herpes simplex virus 1 (HSV-1), herpes simplex virus 2 (HSV-2), varicella zoster virus (VZV), and atypical bacteria: Chlamydia pneumoniae, Mycoplasma pneumoniae and Legionella pneumophila/spp. At least one co-detection was observed in 89.1% of patients. EBV, HSV-1, and CMV were the most common, with 74.7%, 58.1%, and 38.0% of positive patients, respectively. The median detection time of EBV, HSV-1, and CMV after initial SARS-CoV-2 confirmation was 11 to 20 days. Bronchoalveolar lavage (BAL) and tracheal aspirate (TA) samples showed equivalent performance for the detection of EBV, CMV, and HSV-1 in patients with both available samples. Our results indicate that SARS-CoV-2 infection could be a risk factor for latent herpesvirus reactivation, especially HSV-1, EBV, and CMV. However, additional studies are needed to elucidate the clinical importance of these findings.

Coinfection of Influenza A and B and Human OC43 Coronavirus in Normal Human Bronchial Epithelial Cells.

Influenza viruses and seasonal coronaviruses are pathogens transmitted via an airborne route that can cause respiratory diseases in humans that have similar symptoms such as fever, cough, and pneumonia. These two viruses can infect similar human tissues, such as the respiratory tract and nasal, bronchial, and alveolar epithelial cells. Influenza virus and seasonal coronavirus coinfections are poorly understood. Here, we coinfected normal human bronchial epithelial (NHBE) cells with influenza A/California/04/09 (IAV) or B/Victoria/504/2000 (IBV) strains and the seasonal human beta-coronavirus OC43 and evaluated viral replication capacities. We also examined changes in the expression of various cytokines/chemokines by qPCR and Luminex assay. We observed that the replication of IAV and IBV was not affected by coinfection with OC43. However, coinfection reduced OC43 titers (~3-fold) compared with infection with OC43 alone. Select cytokine/chemokine expression was increased in coinfected cells compared with all single infections with greater differences seen between coinfected cells and cells infected with OC43 alone compared with IAV- or IBV-infected cells. In addition, IL-8 and IL-1RA showed the highest expression among a panel of 22 cytokines by Luminex. As the rate of influenza and seasonal coronavirus coinfection continue to increase, our findings may help set guidelines for the treatments of the individuals coinfected with both viruses.

Molecular Epidemiology and Clinical Characteristics of an Outbreak on Respiratory Virus Coinfection in Gansu, China.

This study aims to analyze the epidemiological and pathogenic characteristics of an outbreak primarily caused by respiratory syncytial virus (RSV), human rhinovirus (HRV), and human metapneumovirus (HMPV) in a kindergarten and primary school. The outbreak was investigated by field epidemiological investigation, and the common respiratory pathogens were screened by RT-PCR detection technology. The attack rate of this outbreak was 63.95% (110/172). Main symptoms included cough (85.45%), sore throat (60.91%), and sneezing (60.00%). Multifactorial logistic regression analysis revealed that continuous handwashing and mouth and nose covering when sneezing were protective factors. All 15 collected throat swab specimens tested positive for viruses, with HMPV as the predominant pathogen (80.00%), followed by HRV (53.33%), and two cases of positive respiratory syncytial virus (13.33%). Among them, six samples showed coinfections of HMPV and HRV, and one had coinfections of HMPV and RSV, resulting in a coinfection rate of 46.67%. Genetic sequencing indicated that the HMPV genotype in this outbreak was A2c, and the HRV genotype was type A, resulting in a coinfection outbreak of HMPV, HRV, and RSV in schools and kindergartens, suggesting that multi-pathogen surveillance of respiratory tract infections should be strengthened.

Incidence of Helminthic and Viral Coinfections in Malaria Patients in the Tertiary Care Hospital Setup.

This study determines the incidence of common viral and helminth coinfections with malaria in the tertiary care hospital set up in southern Khyber Pakhtunkhwa, Pakistan. The multidimensional research included malaria patients admitted to different hospitals of district Kohat during January and December 2021. Stool samples and blood were assembled from the patients. Giemsa-stained microscopy-positive samples were processed by the immunochromatography technique (ICT) to identify Plasmodium species. Common viral infections such as viral hepatitis (A, B, and C), HIV, and dengue (DENV) were analyzed by ICT kits while SARS-CoV-2 was confirmed through real-time PCR. Furthermore, the intestinal helminths were identified using the Kato-Katz thick smear method. Among 1278 patients, 548 were diagnosed with malaria, 412 (75.2%) were positive for P. vivax infection, 115 (21%) for P. falciparum, and 21 (3.8%) for mixed malaria infection (P. vivax/P. falciparum), with a higher incidence among males (65.2%) than females (34.8%). Coinfection with helminths was positive in 215 (39.3%) malaria patients. The most common infections were caused by the Ascaris lumbricoides species (42.6%) followed by Enterobius vermicularis (31.7%) and hookworm. A total of 24.6% of malaria-positive cases were also coinfected with different viruses with higher frequencies of confection for HAV (8.2%) and DENV (6.2%), respectively. The patients revealed higher incidence of coinfections with P. falciparum (57%) as compared with P. vivax (39.2%) and mixed infections (3.7%). This study demonstrated that the study population exhibited a significant incidence of coinfections with intestinal helminth and viral malaria.

HIV and hepatitis B, C co-infection and correlates of HIV infection among men who have sex with men in Rwanda, 2021: a respondent-driven sampling, cross-sectional study

BackgroundMen who have sex with men (MSM) are a key population group disproportionately affected by HIV and other sexually transmitted infections (STIs) worldwide. In Rwanda, the HIV epidemic remains a significant public health concern, and understanding the burden of HIV and hepatitis B and C coinfections among MSM is crucial for designing effective prevention and control strategies. This study aims to determine the prevalence of HIV, hepatitis B, and hepatitis C infections among MSM in Rwanda and identify correlates associated with HIV infection within this population.MethodsWe used respondent-driven sampling (RDS) to recruit participants between November and December 2021. A face-to-face, structured questionnaire was administered. Testing for HIV infection followed the national algorithm using two rapid tests: Alere Combo and STAT PAK as the first and second screening tests, respectively. Hepatitis B surface antigen (HBsAg) and anti-HCV tests were performed. All statistics were adjusted for RDS design, and a multivariable logistic regression model was constructed to identify factors associated with HIV infection.ResultsThe prevalence of HIV among MSM was 6·9% (95% CI: 5·5–8·6), and among HIV-positive MSM, 12·9% (95% CI: 5·5–27·3) were recently infected. The prevalence of hepatitis B and C was 4·2% (95% CI: 3·0–5·7) and 0·7% (95% CI: 0·4–1·2), respectively. HIV and hepatitis B virus coinfection was 0·5% (95% CI: 0·2–1·1), whereas HIV and hepatitis C coinfection was 0·1% (95% CI: 0·0–0·5), and no coinfection for all three viruses was observed. MSM groups with an increased risk of HIV infection included those who ever suffered violence or abuse because of having sex with other men (AOR: 3·42; 95% CI: 1·87–6·25), those who refused to answer the question asking about ‘ever been paid money, goods, or services for sex’ (AOR: 10·4; 95% CI: 3·30–32·84), and those not consistently using condoms (AOR: 3·15; 95% CI: 1·31–7·60).ConclusionThe findings suggest more targeted prevention and treatment approaches and underscore the importance of addressing structural and behavioral factors contributing to HIV vulnerability, setting interventions to reduce violence and abuse against MSM, promoting safe and consensual sexual practices, and expanding access to HIV prevention tools such as condoms and preexposure prophylaxis (PrEP).

Microbiological profile of long COVID and associated clinical and radiological findings: a prospective cross-sectional study.

To study the frequency of microbiological etiology of respiratory infections in patients with long COVID and their associated clinical and radiological findings. Nasopharyngeal swabs and sputum specimens were collected from 97 patients with respiratory illness stemming from long COVID. The specimens were assessed for their microbiological profile (bacteria and virus) and their association with the overall clinical and radiological picture. In total, 23 (24%) patients with long COVID had viral infection (n = 12), bacterial infection (n = 9), or coinfection (n = 2). Microorganisms were detected at significantly higher rates in hospitalized patients, patients with moderate COVID-19, and patients with asthma (P < .05). Tachycardia (65%) was the most common symptom at presentation. A statistically significant number of patients with long COVID who had viral infection presented with cough and myalgia; and a statistically significant number of patients with long COVID who had bacterial infection presented with productive coughing (P < .05). Post-COVID fibrotic changes were found in 61% of cohort patients (31/51). A decreasing trend of respiratory pathogens (enveloped viruses and bacteria) was found in long COVID. An analysis including a larger group of viral- or bacterial-infected patients with long COVID is needed to obtain high-level evidence on the presenting symptoms (cough, myalgia) and their association with the underlying comorbidities and severity.

Breastfeeding Initiation in People With Hepatitis C Virus Infection in the United States.

To evaluate breastfeeding initiation rates among people living with and without hepatitis C virus (HCV) infection during pregnancy and to identify characteristics associated with breastfeeding initiation. We conducted a cross-sectional analysis of individuals who had a live birth in the United States from 2016 to 2021 using the National Center for Health Statistics birth certificate data. We grouped participants by whether they had HCV infection during pregnancy. Using propensity-score matching, we assessed the association between breastfeeding initiation before hospital discharge , defined as neonates receiving any parental breast milk or colostrum, and HCV infection during pregnancy in a logistic regression model. We also assessed factors associated with breastfeeding initiation among those with HCV infection. There were 96,896 reported cases (0.5%) of HCV infection among 19.0 million births that met inclusion criteria during the study period. Using propensity-score matching, we matched 87,761 individuals with HCV infection during pregnancy with 87,761 individuals without HCV infection. People with HCV infection during pregnancy were less likely to initiate breastfeeding compared with those without HCV infection (51.5% vs 64.2%, respectively; odds ratio 0.59, 95% CI, 0.58-0.60, P <.001). Characteristics associated with higher rates of breastfeeding initiation among individuals with HCV infection included a college degree (adjusted odds ratio [aOR] 1.22, 95% CI, 1.21-1.24); self-identified race or ethnicity as Native Hawaiian or Pacific Islander (aOR 1.22, 95% CI, 1.06-1.40), Asian (aOR 1.09, 95% CI, 1.06-1.13), or Hispanic (aOR 1.09, 95% CI, 1.08-1.11); private insurance (aOR 1.07, 95% CI, 1.06-1.08); nulliparity (aOR 1.09, 95% CI, 1.08-1.10), and being married (aOR 1.08, 95% CI, 1.07-1.09). Characteristics associated with not breastfeeding before hospital discharge included receiving no prenatal care (aOR 0.81, 95% CI, 0.79-0.82), smoking during pregnancy (aOR 0.88, 95% CI, 0.88-0.89), and neonatal intensive care unit admission (aOR 0.92, 95% CI, 0.91-0.93). Despite leading health organizations' support for people living with HCV infection to breastfeed, our study demonstrates low breastfeeding initiation rates in this population. Our findings highlight the need for tailored breastfeeding support for people with HCV infection and for understanding the additional effects of human immunodeficiency virus (HIV) co-infection, HCV treatment, and concurrent substance use disorders on breastfeeding initiation.

Coinfection and nonrandom recombination drive the evolution of swine enteric coronaviruses

ABSTRACT Coinfection with multiple viruses is a common phenomenon in clinical settings and is a crucial driver of viral evolution. Although numerous studies have demonstrated viral recombination arising from coinfections of different strains of a specific species, the role of coinfections of different species or genera during viral evolution is rarely investigated. Here, we analyzed coinfections of and recombination events between four different swine enteric coronaviruses that infect the jejunum and ileum in pigs, including porcine epidemic diarrhea virus (PEDV), transmissible gastroenteritis virus (TGEV), and swine acute diarrhea syndrome coronavirus (SADS-CoV), and a deltacoronavirus, porcine deltacoronavirus (PDCoV). Various coinfection patterns were observed in 4,468 fecal and intestinal tissue samples collected from pigs in a 4-year survey. PEDV/PDCoV was the most frequent coinfection. However, recombination analyses have only detected events involving PEDV/TGEV and SADS-CoV/TGEV, indicating that inter-species recombination among coronaviruses is most likely to occur within the same genus. We also analyzed recombination events within the newly identified genus Deltacoronavirus and found that sparrows have played a unique host role in the recombination history of the deltacoronaviruses. The emerging virus PDCoV, which can infect humans, has a different recombination history. In summary, our study demonstrates that swine enteric coronaviruses are a valuable model for investigating the relationship between viral coinfection and recombination, which provide new insights into both inter- and intraspecies recombination events among swine enteric coronaviruses, and extend our understanding of the relationship between coronavirus coinfection and recombination.

Clinical Characteristics and Microorganisms Isolated in Community-Acquired Pneumonia in the COVID-19 Period.

Community-acquired pneumonia is a leading cause of mortality and hospital admissions. The aetiology remains unknown in 30-65% of the cases. Molecular tests are available for multiple pathogen detection and are under research to improve the causal diagnosis. We carried out a prospective study to describe the clinical characteristics and aetiology of community-acquired pneumonia during the COVID-19 pandemic and to assess the diagnostic effectivity of the microbiological tests, including a molecular test of respiratory pathogens (FilmArray™ bioMérieux). From the 1st of February 2021 until the 31st of March 2022, 225 patients were included. Failure in microorganism identification occurred in approximately 70% of patients. Streptococcus pneumoniae was the most common isolate. There were 5 cases of viral pneumonia. The tested FilmArray exhibited a low positivity rate of 7% and mainly aided in the diagnosis of viral coinfections. Despite our extensive diagnostic protocol, there is still a low rate of microorganism identification. We have observed a reduction in influenza and other viral pneumoniae during the COVID-19 pandemic. Having a high NEWS2 score on arrival at the emergency department, an active oncohematological disease or chronic neurological conditions and a positive microbiological test result were related to worse outcomes. Further research is needed to determine the role of molecular tests in the microbiological diagnosis of pneumonia.

SARS-CoV-2 pandemic non-pharmacologic interventions temporally associated with reduced pediatric infections due to Mycoplasma pneumoniae and co-infecting respiratory viruses in Arkansas.

Non-pharmacologic interventions (NPIs) effectively curtailed the spread of SARS-CoV-2 and, fortuitously, many other aerosol-transmitted respiratory pathogens. This study included the largest data set of symptomatic, pediatric patients from within the United States spanning a period from November 2017 through December 2023, and encompassed individuals residing in both rural and urban settings. We observed a strong correlation between the implementation and cessation of NPIs with the rate of respiratory infections due to Mycoplasma pneumoniae and viral co-infections. These infections are returning to baseline levels approximately 2 years following NPI cessation. This observation was not unexpected since the replication time for viruses is exponentially faster than that of bacteria. The resurgence of M. pneumoniae and likely other atypical bacterial pathogens is currently in process. Healthcare providers should strongly consider these pathogens in individuals presenting with respiratory tract illnesses.

Accuracy of blood-based biomarkers for staging liver fibrosis in chronic liver disease: A systematic review supporting the AASLD Practice Guideline.

Blood-based biomarkers have been proposed as an alternative to liver biopsy for noninvasive liver disease assessment in chronic liver disease. Our aims for this systematic review were to evaluate the diagnostic utility of selected blood-based tests either alone, or in combination, for identifying significant fibrosis (F2-4), advanced fibrosis (F3-4), and cirrhosis (F4), as compared to biopsy in chronic liver disease. We included a comprehensive search of databases including Ovid MEDLINE(R), EMBASE, Cochrane Database, and Scopus through to April 2022. Two independent reviewers selected 286 studies with 103,162 patients. The most frequently identified studies included the simple aspartate aminotransferase-to-platelet ratio index and fibrosis (FIB)-4 markers (with low-to-moderate risk of bias) in HBV and HCV, HIV-HCV/HBV coinfection, and NAFLD. Positive (LR+) and negative (LR-) likelihood ratios across direct and indirect biomarker tests for HCV and HBV for F2-4, F3-4, or F4 were 1.66-6.25 and 0.23-0.80, 1.89-5.24 and 0.12-0.64, and 1.32-7.15 and 0.15-0.86, respectively; LR+ and LR- for NAFLD F2-4, F3-4, and F4 were 2.65-3.37 and 0.37-0.39, 2.25-6.76 and 0.07-0.87, and 3.90 and 0.15, respectively. Overall, the proportional odds ratio indicated FIB-4 <1.45 was better than aspartate aminotransferase-to-platelet ratio index <0.5 for F2-4. FIB-4 >3.25 was also better than aspartate aminotransferase-to-platelet ratio index >1.5 for F3-4 and F4. There was limited data for combined tests. Blood-based biomarkers are associated with small-to-moderate change in pretest probability for diagnosing F2-4, F3-4, and F4 in viral hepatitis, HIV-HCV coinfection, and NAFLD, with limited comparative or combination studies for other chronic liver diseases.

Heterogeneity in the prevalence of subclinical malaria, other co-infections and anemia among pregnant women in rural areas of Myanmar: a community-based longitudinal study

BackgroundDue to the low prevalence of clinically suspected malaria among pregnant women in Myanmar, little is known about its impact on mothers and newborns. Helminth and Human Immuno-deficiency Virus (HIV) co-infections cause anemia in pregnant women. This study assessed the prevalence of subclinical malaria and co-infections among pregnant women, and its association with adverse outcomes of pregnancy in the presence of infection.MethodsA prospective longitudinal study was conducted in 12 villages in two townships in Myanmar between 2013 to 2015. A total of 752 pregnant women, with a mean age of 27 years, were enrolled and followed up once a month until six weeks after childbirth. Prevalence ratio was calculated in the multivariable analysis.ResultsThe prevalence of subclinical malaria as measured by nested PCR was 5.7% for either P. falciparum or P. vivax, 2.7% prevalence of P. falciparum and 2.8% prevalence of P. vivax. Helminth infections were prevalent in 17% of women, and one woman with an HIV infection was found in our study. The burden of anemia was high, with an overall prevalence of 37% with or without helminth infection, 42% of the women were malaria positive and 43% had dual infections (both malaria and helminth). Only 11 abnormal pregnancy outcomes (7 stillbirths, 2 premature, 2 twins) were identified. Poisson regression showed that women in their first trimester had a 2.9 times higher rate of subclinical malaria compared to women in the third trimester (PR:2.9, 95%CI 1.19, 7.31, p = 0.019), women who were enrolled during the wet season were 2.5 times more likely to be malaria positive than the women enrolled in the dry season (PR: 2.5, 95%CI 1.27, 4.88, p = 0.008), and the malaria positivity rate decreased by 5% when increased in one year of woman’s age (PR:0.95, 95%CI 0.91, 0.99, p = 0.02). In the multivariable regression, the age of respondents was the only significant factor associated with subclinical malaria in pregnancy.ConclusionsA comprehensive approach of integrating interventions for malaria, anemia, and helminths should be delivered during antenatal care services for pregnant women in rural areas of Myanmar.

Cacao sustainability: The case of cacao swollen-shoot virus co-infection.

The cacao swollen shoot virus disease (CSSVD) is among the most economically damaging diseases of cacao trees and accounts for almost 15-50% of harvest losses in Ghana. This virus is transmitted by several species of mealybugs (Pseudococcidae, Homoptera) when they feed on cacao plants. One of the mitigation strategies for CSSVD investigated at the Cocoa Research Institute of Ghana (CRIG) is the use of mild-strain cross-protection of cacao trees against the effects of severe strains. In this study, simple deterministic, delay, and stochastic ordinary differential equation-based models to describe the dynamic of the disease and spread of the virus are suggested. Model parameters are estimated using detailed empirical data from CRIG. The modeling outcomes demonstrate a remarkable resemblance between real and simulated dynamics. We have found that models with delay approximate the data better and this agrees with the knowledge that CSSVD epidemics develop slowly. Also, since there are large variations in the data, stochastic models lead to better results. We show that these models can be used to gain useful informative insights about the nature of disease spread.