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Myocarditis is a rare cardiomyocyte inflammatory process, typically caused by viruses, with potentially devastating cardiac sequalae in both competitive athletes and in the general population. Investigation into myocarditis prevalence in the Coronavirus disease 2019 (COVID-19) era suggests that infection with Severe acute respiratory syndrome coronavirus (SARS-CoV-2) is an independent risk factor for myocarditis, which is confirmed mainly through cardiovascular magnetic resonance imaging. Recent studies indicated that athletes have a decreased risk of myocarditis after recent COVID-19 infection compared to the general population. However, given the unique nature of competitive athletics with their frequent participation in high-intensity exercise, athletes possess distinct factors of susceptibility for the development of myocarditis and its subsequent severe cardiac complications (e.g., sudden cardiac death, fulminant heart failure, etc.). Under this context, this review focuses on comparing myocarditis in athletes versus non-athletes, owing special attention to the distinct clinical presentations and outcomes of myocarditis caused by different viral pathogens such as cytomegalovirus, Epstein-Barr virus, human herpesvirus-6, human immunodeficiency virus, and Parvovirus B19, both before and after the COVID-19 pandemic, as compared with SARS-CoV-2. By illustrating distinct clinical presentations and outcomes of myocarditis in athletes versus non-athletes, we also highlight the critical importance of early detection, vigilant monitoring, and effective management of viral and non-viral myocarditis in athletes and the necessity for further optimization of the return-to-play guidelines for athletes in the COVID-19 era, in order to minimize the risks for the rare but devastating cardiac fatality. [ABSTRACT FROM AUTHOR]

Verifying the inclusivity of molecular detection methods gives indications about the reliability of viral infection diagnosis because of the tendency of viral pathogens to undergo sequence variation. This study was aimed at selecting inclusive probes based on reverse transcription–quantitative PCR (RT-qPCR) assays for the diagnosis of the most widespread and detrimental viruses infecting honeybees, namely the acute bee paralysis virus (ABPV), the black queen cell virus (BQCV), the chronic paralysis bee virus (CBPV), the deformed wing virus variants A (DWVA) and B (DWVB), and the sacbrood virus (SBV). Therefore, previously described detection methods were re-evaluated in silico for their specificity and inclusivity. Based on this evaluation, selected methods were modified, or new ones were designed and tested in duplex RT-qPCR reactions. The limits of detection (LODs), effect of multiplexing on sensitivity and the viral RNA quantification potential in bees and hive debris were assessed. This study made available diagnostic assays able to detect an increased number of virus variants compared with previously described tests and two viral pathogens in a single PCR reaction. [ABSTRACT FROM AUTHOR]

Rabbit haemorrhage disease virus 2 (RHDV2) is a highly pathogenic lagovirus that causes lethal disease in rabbits and hares (lagomorphs). Since its first detection in Europe in 2010, RHDV2 has spread worldwide and has been detected in over 35 countries so far. Here, we provide the first detailed report of the detection and subsequent circulation of RHDV2 in New Zealand. RHDV2 was first detected in New Zealand in 2018, with positive samples retrospectively identified in December 2017. Subsequent time-resolved phylogenetic analysis suggested a single introduction into the North Island between March and November 2016. Genetic analysis identified a GI.3P-GI.2 variant supporting a non-Australian origin for the incursion; however, more accurate identification of the source of the incursion remains challenging due to the wide global distribution of the GI.3P-GI.2 variant. Furthermore, our analysis suggests the spread of the virus between the North and South Islands of New Zealand at least twice, dated to mid-2017 and around 2018. Further phylogenetic analysis also revealed a strong phylogeographic pattern. So far, no recombination events with endemic benign New Zealand rabbit caliciviruses have been identified. This study highlights the need for further research and surveillance to monitor the distribution and diversity of lagoviruses in New Zealand and to detect incursions of novel variants. [ABSTRACT FROM AUTHOR]

Real-time genome detection, classification and lineage assignment are critical for efficient tracking of emerging mutations and variants during viral pandemics such as Covid-19. For genomic surveillance to work effectively, each new viral genome sequence must be quickly and accurately associated with an existing viral family (lineage). ViRAL is a hardware-accelerated platform for real-time viral genome lineage assignment based on minhashing and Vision Transformer. Minhashing is a locality sensitive hashing based technique for finding regions of similarity within sequenced genomes. Vision Transformer is a model for image classification that employs a Transformer-like architecture over patches of images. In ViRAL, such image patches are genome fragments extracted from the regions of high similarity. ViRAL is especially efficient in lineage assignment of extremely low quality (or highly ambiguous) genomic data, i.e. when a large fraction of DNA bases are missing in an assembled genome. We implement ViRAL on CPU, GPU and a custom-designed hardware accelerator denoted ACMI. ViRAL assigns newly sequenced SARS-CoV-2 genomes to existing lineages with the top-1 accuracy of 94.2%. The probability of the correct assignment to be found among the five most likely placements generated by ViRAL (top-5 accuracy) is 99.8%. Accelerated ViRAL outperforms the fastest state-of-the-art assignment tools by $69.4\times $ . It also outperforms ViRAL GPU implementation by $19.5\times $ . ViRAL strongly outperforms the state-of-the-art solutions in assigning highly-ambiguous genomes: while state-of-the-art tools fail to assign lineage to genomes with 50% ambiguity, ViRAL achieves 77.6% assignment accuracy. We make ViRAL available to the research community through GitHub.

Pathogenic lagoviruses (Rabbit hemorrhagic disease virus, RHDV) are widely spread across the world and are used in Australia and New Zealand to control populations of feral European rabbits. The spread of the non-pathogenic lagoviruses, e.g., rabbit calicivirus (RCV), is less well studied as the infection results in no clinical signs. Nonetheless, RCV has important implications for the spread of RHDV and rabbit biocontrol as it can provide varying levels of cross-protection against fatal infection with pathogenic lagoviruses. In Chile, where European rabbits are also an introduced species, myxoma virus was used for localised biocontrol of rabbits in the 1950s. To date, there have been no studies investigating the presence of lagoviruses in the Chilean feral rabbit population. In this study, liver and duodenum rabbit samples from central Chile were tested for the presence of lagoviruses and positive samples were subject to whole RNA sequencing and subsequent data analysis. Phylogenetic analysis revealed a novel RCV variant in duodenal samples that likely originated from European RCVs. Sequencing analysis also detected the presence of a rabbit astrovirus in one of the lagovirus-positive samples. [ABSTRACT FROM AUTHOR]

The aim of this study was to evaluate the annual, seasonal and monthly trends in children with simple and complex appendicitis and their correlation to common viral pathogens in the Netherlands. A consecutive multicenter retrospective cohort study was performed between 2010 and 2019 including children (<18 years) surgically treated for appendicitis. The primary outcome was the distribution of children with simple and complex appendicitis per year, season and month. Relevant seasonal variation was defined as ≥5%. The secondary outcome was a positive correlation of the number of patients with simple and complex appendicitis to common viral pathogens (data anonymously provided by the Dutch Working Group on Clinical Virology from the Dutch Society for Clinical Microbiology (NVMM)). In total, 896 patients were included: N = 524 (58%) patients with simple and N = 372 (42%) with complex appendicitis. Of the children aged 0–5 years, 81% had complex appendicitis, versus 38% in 6–18 years (p < 0.001). An overall decline was demonstrated for both simple and complex appendicitis between 2010 and 2019. No seasonal variation was found for simple appendicitis. For complex appendicitis, the highest number of patients was found in spring, and lowest in summer (N = 372, spring 28.2 ± 5.1% versus summer 21.0 ± 5.8%, p = 0.011), but the variance was regarded as not relevant (<5% from baseline). A positive correlation was found between complex appendicitis with Adenovirus 40.41 (R = 0.356, 95%CI 0.045–0.604, p = 0.026) and simple appendicitis with Adenovirus NON 40.41 (R = 0.332, 95%CI 0.019–0.586, p = 0.039), but these correlations did not remain significant after a Bonferroni correction (p < 0.003). In conclusion, we found no relevant seasonal variation for simple or complex appendicitis, nor positive correlation with common viral pathogens. [ABSTRACT FROM AUTHOR]

High‐risk human papillomaviruses (HR‐HPVs) cause various malignancies in the anogenital and oropharyngeal regions. About 70% of cervical and oropharyngeal cancers are caused by HPV types 16 and 18. Notably, some viruses including herpes simplex virus, Epstein–Barr virus, and human immunodeficiency virus along with various bacteria often interact with HPV, potentially impacting its replication, persistence, and cancer progression. Thus, HPV infection can be significantly influenced by co‐infecting agents that influence infection dynamics and disease progression. Bacterial co‐infections (e.g., Chlamydia trachomatis) along with bacterial vaginosis‐related species also interact with HPV in genital tract leading to viral persistence and disease outcomes. Co‐infections involving HPV and diverse infectious agents have significant implications for disease transmission and clinical progression. This review explores multiple facets of HPV infection encompassing the co‐infection dynamics with other pathogens, interaction with the human microbiome, and its role in disease development. [ABSTRACT FROM AUTHOR]

Abstract Background The frequent interactions of rodents with humans make them a common source of zoonotic infections. Brandt's vole is the dominant rodent species of the typical steppe in Inner Mongolia, and it is also an important pest in grassland. Objectives: To obtain an initial unbiased measure of the microbial diversity and abundance in the blood and intestinal tracts and to detect the pathogens carried by wild Brandt's voles in Hulun Buir, Inner Mongolia. Methods Twenty wild adult Brandt's voles were trapped using live cages, and 12 intestinal samples were collected for metagenomic analysis and 8 blood samples were collected for meta‐transcriptomic analysis. We compared the sequencing data with pathogenic microbiota databases to analyse the phylogenetic characteristics of zoonotic pathogens carried by wild voles. Results A total of 122 phyla, 79 classes, 168 orders, 382 families and 1693 genera of bacteria and a total of 32 families of DNA and RNA viruses in Brandt's voles were characterized. We found that each sample carried more than 10 pathogens, whereas some pathogens that were low in abundance were still at risk of transmission to humans. Conclusion This study improves our understanding of the viral and bacterial diversity in wild Brandt's voles and highlights the multiple viral and bacterial pathogens carried by this rodent. These findings may serve as a basis for developing strategies targeting rodent population control in Hulun Buir and provide a better approach to the surveillance of pathogenic microorganisms in wildlife.

Verifying the inclusivity of molecular detection methods gives indications about the reliability of viral infection diagnosis because of the tendency of viral pathogens to undergo sequence variation. This study was aimed at selecting inclusive probes based on reverse transcription–quantitative PCR (RT-qPCR) assays for the diagnosis of the most widespread and detrimental viruses infecting honeybees, namely the acute bee paralysis virus (ABPV), the black queen cell virus (BQCV), the chronic paralysis bee virus (CBPV), the deformed wing virus variants A (DWVA) and B (DWVB), and the sacbrood virus (SBV). Therefore, previously described detection methods were re-evaluated in silico for their specificity and inclusivity. Based on this evaluation, selected methods were modified, or new ones were designed and tested in duplex RT-qPCR reactions. The limits of detection (LODs), effect of multiplexing on sensitivity and the viral RNA quantification potential in bees and hive debris were assessed. This study made available diagnostic assays able to detect an increased number of virus variants compared with previously described tests and two viral pathogens in a single PCR reaction.

Background: The frequent interactions of rodents with humans make them a common source of zoonotic infections. Brandt's vole is the dominant rodent species of the typical steppe in Inner Mongolia, and it is also an important pest in grassland. Objectives: To obtain an initial unbiased measure of the microbial diversity and abundance in the blood and intestinal tracts and to detect the pathogens carried by wild Brandt's voles in Hulun Buir, Inner Mongolia. Methods: Twenty wild adult Brandt's voles were trapped using live cages, and 12 intestinal samples were collected for metagenomic analysis and 8 blood samples were collected for meta‐transcriptomic analysis. We compared the sequencing data with pathogenic microbiota databases to analyse the phylogenetic characteristics of zoonotic pathogens carried by wild voles. Results: A total of 122 phyla, 79 classes, 168 orders, 382 families and 1693 genera of bacteria and a total of 32 families of DNA and RNA viruses in Brandt's voles were characterized. We found that each sample carried more than 10 pathogens, whereas some pathogens that were low in abundance were still at risk of transmission to humans. Conclusion: This study improves our understanding of the viral and bacterial diversity in wild Brandt's voles and highlights the multiple viral and bacterial pathogens carried by this rodent. These findings may serve as a basis for developing strategies targeting rodent population control in Hulun Buir and provide a better approach to the surveillance of pathogenic microorganisms in wildlife. [ABSTRACT FROM AUTHOR]

Rabbit haemorrhage disease virus 2 (RHDV2) is a highly pathogenic lagovirus that causes lethal disease in rabbits and hares (lagomorphs). Since its first detection in Europe in 2010, RHDV2 has spread worldwide and has been detected in over 35 countries so far. Here, we provide the first detailed report of the detection and subsequent circulation of RHDV2 in New Zealand. RHDV2 was first detected in New Zealand in 2018, with positive samples retrospectively identified in December 2017. Subsequent time-resolved phylogenetic analysis suggested a single introduction into the North Island between March and November 2016. Genetic analysis identified a GI.3P-GI.2 variant supporting a non-Australian origin for the incursion; however, more accurate identification of the source of the incursion remains challenging due to the wide global distribution of the GI.3P-GI.2 variant. Furthermore, our analysis suggests the spread of the virus between the North and South Islands of New Zealand at least twice, dated to mid-2017 and around 2018. Further phylogenetic analysis also revealed a strong phylogeographic pattern. So far, no recombination events with endemic benign New Zealand rabbit caliciviruses have been identified. This study highlights the need for further research and surveillance to monitor the distribution and diversity of lagoviruses in New Zealand and to detect incursions of novel variants.

Pathogenic lagoviruses (Rabbit hemorrhagic disease virus, RHDV) are widely spread across the world and are used in Australia and New Zealand to control populations of feral European rabbits. The spread of the non-pathogenic lagoviruses, e.g., rabbit calicivirus (RCV), is less well studied as the infection results in no clinical signs. Nonetheless, RCV has important implications for the spread of RHDV and rabbit biocontrol as it can provide varying levels of cross-protection against fatal infection with pathogenic lagoviruses. In Chile, where European rabbits are also an introduced species, myxoma virus was used for localised biocontrol of rabbits in the 1950s. To date, there have been no studies investigating the presence of lagoviruses in the Chilean feral rabbit population. In this study, liver and duodenum rabbit samples from central Chile were tested for the presence of lagoviruses and positive samples were subject to whole RNA sequencing and subsequent data analysis. Phylogenetic analysis revealed a novel RCV variant in duodenal samples that likely originated from European RCVs. Sequencing analysis also detected the presence of a rabbit astrovirus in one of the lagovirus-positive samples.

Background Viral acute respiratory tract infections (ARTIs) are a leading cause of hospitalization in infants and young children. Methods During the winter seasons of 2014–2018, hospitalized children (<18 years) with symptoms of ARTI were prospectively included at the University Hospital Heidelberg, Germany. Nasopharyngeal swabs were obtained for multiplex molecular analysis of 10 groups of respiratory viruses, and clinical data were obtained using a standardized questionnaire. Results Of 1353 children included in this study, 1142 (84.4%) were positive for ≥1 viral pathogen. Virus monoinfection was detected in 797 (69.8%) children, whereas 345 (30.2%) children had coinfections with 2–4 viral pathogens. Respiratory syncytial virus (RSV), rhinovirus, and influenza virus were the main pathogens detected. RSV-positive children had significantly more often lower ARTIs, including symptoms of severe cough, wheezing, chest indrawing, tachypnea, and pulmonary rales. Hospitalized children aged <6 months represented the largest age group with detection of ≥1 viral pathogen (455/528 [86.2%] children). Coinfection was more frequent in younger children and, particularly for RSV with rhinovirus, significantly associated with more severe respiratory symptoms (P =.01). Conclusions A better understanding of the etiology of viral ARTIs among hospitalized children plays a key role for future strategies in prevention, control, and treatment of respiratory viral infections. [ABSTRACT FROM AUTHOR]

Bovine respiratory diseases (BRD) are associated with various predisposing factors, such as physical and physiological stress factors, and bacterial and viral pathogens. These stressors and viruses suppress immune defenses, leading to bacterial growth in the upper respiratory tract and invasion of pathogens into the lower respiratory tract. Therefore, continuous monitoring of the causative pathogens would contribute to the early detection of BRD. Nasal swabs and sera from 63 clinically healthy calves were continuously collected from seven farms in Iwate prefecture from 2019 to 2021. We attempted to monitor dynamics of BRD-associated pathogens by multiplex real-time RT-PCR (RT-qPCR) using their nasal swab samples. In addition, we attempted to monitor fluctuation of antibody titers against each BRD-associated pathogen by virus neutralization test (VNT) using their sera. In contrast, nasal swabs from 89 calves infected with BRD were collected from 28 farms in Iwate prefecture from 2019 to 2021. We attempted to analyze their nasal swab samples by multiplex RT-qPCR aim to detect BRD-associated pathogens that are dominant in this region. As a result, our analyses using samples from clinically healthy calves showed that positive results by multiplex RT-qPCR were closely related to a significant increase of antibody titers by VNT in bovine coronavirus (BCoV), bovine torovirus (BToV), and bovine respiratory syncytial virus (BRSV). In addition, our data exhibited that BCoV, BToV, BRSV, bovine parainfluenza virus 3, and Mycoplasma bovis have been more frequently detected in calves infected with BRD compared to those detected in clinically healthy calves. Moreover, the data presented herein revealed co-infections by combination multiple viral pathogens with bacterial pathogens are closely involved in the onset of BRD. Taken together, our study demonstrates multiplex RT-qPCR which can simultaneously analyze multiple pathogens, including viruses and bacteria, and is useful for the early detection of BRD. [ABSTRACT FROM AUTHOR]

Background: Reindeer herding and husbandry is a traditional and important livelihood in Fennoscandia, and about 200,000 semi-domesticated reindeer are herded in Finland. Climatic changes, leading to ice-locked winter pastures, and encroachment of pasture-land have led to changes in reindeer husbandry, increasing the extent of supplementary or full ration feeding, which has become very common in Finland. Keeping reindeer in corrals or gathering them at permanent feeding sites will increase nose-to-nose contact between animals and they may be exposed to poor hygienic conditions. This may impact the epidemiology of infectious diseases, such as viral infections. The aim of this study was to investigate Finnish semi-domesticated reindeer for exposure to viral pathogens. Blood samples were collected from 596 reindeer (358 calves, 238 adults) in 2015, from nine reindeer slaughterhouses, representing most of the reindeer herding regions in Finland. Plasma samples were investigated for antibodies against a selection of known and potential reindeer viral pathogens by using enzyme linked immunosorbent assays (ELISA). Results: The screening suggested that alphaherpesvirus and gammaherpesvirus (malignant catarrhal fever virus group; MCFV) were enzootic in the reindeer population, with a seroprevalence of 46.5% (range at slaughterhouse level 28.6–64.3%) and 29.0% (range 3.5–62.2%), respectively. Whereas the seroprevalence was significantly higher for alphaherpesvirus among adult reindeer (91.2%) as compared to calves (16.8%), no age difference was revealed for antibodies against gammaherpesvirus. For alphaherpesvirus, the seroprevalence in the northernmost region, having the highest animal density (animals/km2), was significantly higher (55.6%) as compared to the southernmost region (36.2%), whereas the seroprevalence pattern for gammaherpesvirus indicated the opposite, with 8.1% in the north and 50.0% in the south. Four reindeer (0.7%) had antibodies against Pestivirus, whereas no antibodies were detected against Bluetongue virus or Schmallenbergvirus. Conclusions: Alphaherpesvirus and gammaherpesvirus (MCFV) seems to be enzootic in the Finnish reindeer population, similar to other reindeer herds in Fennoscandia, whereas the exposure to Pestivirus was low compared to findings in Norway and Sweden. The ongoing changes in the reindeer herding industry necessitate knowledge on reindeer health and diseases that may impact animal welfare and health of reindeer as well as the economy of the reindeer herding industry. [ABSTRACT FROM AUTHOR]

A winter population of around 4000–5000 wild Eurasian tundra reindeer (Rangifer t. tarandus) in the eastern part of Iceland represents descendants from 35 semi-domesticated reindeer imported to Iceland from Finnmark county, Norway, in 1787. While previous studies have indicated that they host fewer parasite species as compared to reindeer in Fennoscandia, little information exists on their exposure to reindeer viral pathogens. The aim of this study was to investigate blood from hunted reindeer for antibodies against alphaherpesvirus and gammaherpesviruses (malignant catarrhal fever viruses, MCFV), pestivirus, bluetongue virus, and Schmallenberg virus, and to investigate nasal and oral mucosal membrane swab samples for the presence of parapoxvirus-specific DNA. Blood samples collected during the hunting seasons in 2017 (n = 40), 2018 (n = 103), and 2019 (n = 138) were tested for viral antibodies using enzyme-linked immunosorbent assays (ELISA). Screening for parapoxvirus DNA was conducted on swab samples from 181 reindeer by polymerase chain reaction (PCR), targeting the B2L and GIF genes. Antibodies against pestivirus were detected in two animals from 2017, and antibodies against MCFV were detected in two reindeer from 2018. No antibodies were detected against the other viruses tested. Parapoxvirus-specific DNA was detected in nasal swab samples from two animals sampled in 2019. This study suggests that the investigated viral infections are either not present or present at a low prevalence only, probably not representing a major health threat to this reindeer population. The lack of exposure to alphaherpesvirus, an enzootic pathogen in most investigated Rangifer populations, was unexpected. [ABSTRACT FROM AUTHOR]

Aims Among fresh produce (FP)-associated foodborne infections, human noroviruses (HNoV) are the leading causative agent. The present study aimed to assess the prevalence of HNoV in FP. Methods and Results FP-associated HNoV records mined from 5 repositories until 25/05/2022 according to PRISMA standards were appraised, fitted to a generalized linear mixed-effects model and subgroup analysed by sample type, genogroup, and geographical location. Further, heterogeneity was assessed in the model coupled with a leave-one-out-cross-validation. The overall prevalence of HNoV in FP was 9.3% (95% confidence interval [CI] 3.7–21.7. HNoV prevalence was higher in fruits (9.8%[3.7–23.5]) than vegetables (9.4%[3.1–25.3]). Regarding geographical distribution, FP-associated HNoV prevalence varied from Africa (25.8%, 5.7–66.7), Asia (23.2%[4.6–65.0]), Europe (5.6%[0.7–33.9]), North America (12.4%[1.8–52.7]) to South America (7.5%[0.0–100.0]). HNoV GI overall prevalence in FP was 5.3% (2.5–11.1) and varied by sample type (fruits: 4.9%[1.7–13.2]; vegetables: 5.8%[1.6–18.8]). While the occurrence of GII in FP was 1.7% (0.7–3.9) and varied by sample type (fruits: 2.5%[1.0–6.5]; vegetables: 0.9%[0.2–4.9]), GIGII (detection of both GI and GII) was 0.3% (0.1–1.0) with 0.4% (0.1–2.2) and 0.2% (0.0–1.5) in fruits and vegetables, respectively. In all cases, the test for sample/regional prevalence differences were not significantly different with the exception of GII regional prevalence differences (p = 0.03). Conclusions This study suggests that FP represents a critical vehicle for HNoV dissemination, a global and a high risk for public health. [ABSTRACT FROM AUTHOR]

The aim of this study was to evaluate the annual, seasonal and monthly trends in children with simple and complex appendicitis and their correlation to common viral pathogens in the Netherlands. A consecutive multicenter retrospective cohort study was performed between 2010 and 2019 including children (p < 0.001). An overall decline was demonstrated for both simple and complex appendicitis between 2010 and 2019. No seasonal variation was found for simple appendicitis. For complex appendicitis, the highest number of patients was found in spring, and lowest in summer (N = 372, spring 28.2 ± 5.1% versus summer 21.0 ± 5.8%, p = 0.011), but the variance was regarded as not relevant (p = 0.026) and simple appendicitis with Adenovirus NON 40.41 (R = 0.332, 95%CI 0.019–0.586, p = 0.039), but these correlations did not remain significant after a Bonferroni correction (p < 0.003). In conclusion, we found no relevant seasonal variation for simple or complex appendicitis, nor positive correlation with common viral pathogens.

Viral enteric pathogens remain an important cause of diarrhoeal outbreaks among children in sub-Saharan Africa (SSA). Consequently, diarrhoeal illness remains a significant cause of morbidity and mortality in the under-fives in SSA. These outbreaks associated with viral pathogens tend to be seasonal and early warning systems for impending outbreaks could be very crucial for triggering preventive public health response and building public health resilience to deal with increased demand for medical services. Wastewater surveillance for pathogens is an important epidemiological component that could inform early warning systems. The objective of this rapid review was to evaluate the use of wastewater for epidemiology surveillance of enteric viral pathogens. Nine studies met the inclusion criteria. Eight viral pathogens were reviewed and analysed from 6 countries that performed wastewater analysis. Six studies explored the epidemiologic significance of viral pathogens in wastewater. The findings of this review revealed that monitoring of wastewater can provide an additional tool to determine the epidemiology of viral pathogens circulating in the community thereby providing early warning of potential outbreaks using wastewater-based epidemiology methods. Five of the included studies revealed the occurrence of viral pathogens in raw sewage and treated wastewater as an indication of inefficient elimination of viruses leading to potential release into water sources which presents a public health risk, increasing the risk of inducing gastroenteritis in the population. Six studies revealed the need for public health authorities to realise the potential benefit of environmental surveillance (ES) as an additional tool to determine the epidemiology of viral pathogens circulating in each community. Despite the significant public health challenge associated with enteric viral pathogens in sub-Saharan Africa, there remains remarkable underinvestment in potentially epidemiologically beneficial research, including wastewater-based epidemiology for these infections.

Introduction: Respiratory disease incidence is intimately associated with an animal's commensal bacteria populations (microbiome), as microbes that are involved with morbidity and mortality are commonly found in animals with no sign of disease. In addition, viral pathogens affect the immune system and appear to play an integral role in the overall incidence of bovine respiratory disease (BRD); so, an understanding of the interaction of the bacterial and viral pathogens in the upper respiratory tract (URT) may help us to understand the impact of these pathogens on development of BRD. For this research, the overall goal was to characterize bacterial and viral populations in the URT of nursing beef calves at initial vaccination and at the time of a BRD outbreak. Methods: Nasal swabs from the URT were collected at initial vaccination (average 45 days of age) and again at the time of the BRD outbreak (average 126 days of age). DNA and RNA were extracted from nasal swabs to evaluate bacterial and viral populations in the URT. Whole blood was also collected at the time of the BRD outbreak for determination of complete blood counts. To evaluate the microbiome, hypervariable regions 1 through 3 along the 16S ribosomal RNA (rRNA) gene were amplified by PCR and sequenced using nextgeneration sequencing (Illumina MiSeq) for identification of the bacterial taxa present. To evaluate the viral pathogens, multiplex reverse transcription realtime polymerase chain reaction and next-generation sequencing (Illumina NextSeq) was completed. Results: Overall, evaluation of these samples revealed that at the time of the BRD outbreak, all calves were nasally shedding bovine coronavirus and a large percentage had a coinfection with Mycoplasma sp., with Mycoplasma bovirhinis being the predominant species. Neither bovine coronavirus nor Mycoplasma sp. were present at high abundance at the earlier timepoint of initial vaccination. When comparing bacterial population diversity between the two sampling timepoints, alpha diversity was significantly greater at initial vaccination compared to the BRD outbreak (P-value <0.001). Values of leukocytes at the time of the BRD outbreak were also identified to be significantly different between calves with normal or elevated rectal temperatures (P-value <0.05). Discussion: Analysis of the respiratory microflora in the URT during initial vaccination and a BRD outbreak will provide insight into the distribution of bacterial and viral populations in nursing beef calves. [ABSTRACT FROM AUTHOR]

The fish intestinal mucosa is among the main sites through which environmental microorganisms interact with the host. Therefore, this tissue not only constitutes the first line of defense against pathogenic microorganisms but also plays a crucial role in commensal colonization. The interaction between the mucosal immune system, commensal microbiota, and viral pathogens has been extensively described in the mammalian intestine. However, very few studies have characterized these interactions in early vertebrates such as teleosts. In this study, rainbow trout (Oncorhynchus mykiss) was infected with infectious hematopoietic necrosis virus (IHNV) via a recently developed immersion method to explore the effects of viral infection on gut immunity and microbial community structure. IHNV successfully invaded the gut mucosa of trout, resulting in severe tissue damage, inflammation, and an increase in gut mucus. Moreover, viral infection triggered a strong innate and adaptive immune response in the gut, and RNA−seq analysis indicated that both antiviral and antibacterial immune pathways were induced, suggesting that the viral infection was accompanied by secondary bacterial infection. Furthermore, 16S rRNA sequencing also revealed that IHNV infection induced severe dysbiosis, which was characterized by large increases in the abundance of Bacteroidetes and pathobiont proliferation. Moreover, the fish that survived viral infection exhibited a reversal of tissue damage and inflammation, and their microbiome was restored to its pre−infection state. Our findings thus demonstrated that the relationships between the microbiota and gut immune system are highly sensitive to the physiological changes triggered by viral infection. Therefore, opportunistic bacterial infection must also be considered when developing strategies to control viral infection. [ABSTRACT FROM AUTHOR]

Akahoya is a volcanic soil rich in alumina, primarily deposited in Kyushu, Japan. We have found that Akahoya adsorbs bacteria in the water surrounding cattle grazing areas, suggesting a potential for environmental purification. This study investigated the spectrum of microorganisms adsorbed by Akahoya using a column filled with Akahoya through which a suspension of microorganisms was passed. Shirasu soil, another volcanic soil with a different chemical composition, was used as a control. Akahoya effectively adsorbed a diverse range of microorganisms including Escherichia coli , Campylobacter jejuni , Vibrio parahaemolyticus , Salmonella Enteritidis, Staphylococcus aureus , Clostridium perfringens , spores of Bacillus subtilis and Bacillus anthracis , severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), murine norovirus, and avian influenza virus (H3N2), whereas Shirasu soil did not adsorb any of the organisms examined. Moreover, bacteria naturally present in river water, such as aerobic bacteria, total coliforms, and Enterobacteriaceae as indicators of river contamination, as well as E. coli added artificially to sterilized river water, were reduced to below the detection limit (<1 CFU/mL) after being passed through Akahoya. Additionally, the number of viable E. coli continued to decrease after contact with Akahoya for 1 month, suggesting bactericidal effects. Notably, the adsorption of E. coli to Akahoya was influenced by the concentration of phosphate and the pH of the suspension due to the interaction between the surface phosphorylation of organisms and Al 2 O 3 , the major chemical component of Akahoya. The present results demonstrate the remarkable ability of Akahoya to remove phosphate and microbes, suggesting that Akahoya could be used for water purification processes.IMPORTANCEAlthough a safe and sufficient water supply is essential for the maintenance of hygienic conditions, a major challenge is to develop a comprehensive effective, sustainable, and cost-effective technological approach for the treatment and purification of contaminated water. In this study, we demonstrated that a novel volcanic soil, Akahoya, which has unlimited availability, is a highly effective adsorbent for a wide range of bacterial and viral pathogens, suggesting its potential as a sustainable resource for this purpose. It was suggested that the adsorption of microorganisms on Akahoya was mediated by phosphate groups present on the surface structures of microorganisms, which bind to the alumina component of Akahoya according to the phosphate concentration and pH of the liquid phase. The present findings highlight the exceptional ability of Akahoya to eliminate or reduce phosphate and microorganisms effectively in water purification processes, thus contributing to the development of efficient and sustainable solutions for addressing water pollution challenges.

Viral enteric pathogens remain an important cause of diarrhoeal outbreaks among children in sub-Saharan Africa (SSA). Consequently, diarrhoeal illness remains a significant cause of morbidity and mortality in the under-fives in SSA. These outbreaks associated with viral pathogens tend to be seasonal and early warning systems for impending outbreaks could be very crucial for triggering preventive public health response and building public health resilience to deal with increased demand for medical services. Wastewater surveillance for pathogens is an important epidemiological component that could inform early warning systems. The objective of this rapid review was to evaluate the use of wastewater for epidemiology surveillance of enteric viral pathogens. Nine studies met the inclusion criteria. Eight viral pathogens were reviewed and analysed from 6 countries that performed wastewater analysis. Six studies explored the epidemiologic significance of viral pathogens in wastewater. The findings of this review revealed that monitoring of wastewater can provide an additional tool to determine the epidemiology of viral pathogens circulating in the community thereby providing early warning of potential outbreaks using wastewater-based epidemiology methods. Five of the included studies revealed the occurrence of viral pathogens in raw sewage and treated wastewater as an indication of inefficient elimination of viruses leading to potential release into water sources which presents a public health risk, increasing the risk of inducing gastroenteritis in the population. Six studies revealed the need for public health authorities to realise the potential benefit of environmental surveillance (ES) as an additional tool to determine the epidemiology of viral pathogens circulating in each community. Despite the significant public health challenge associated with enteric viral pathogens in sub-Saharan Africa, there remains remarkable underinvestment in potentially epidemiologically beneficial research, including wastewater-based epidemiology for these infections. [ABSTRACT FROM AUTHOR]

We show a shift in the prevalence of respiratory viral pathogens in community-acquired pneumonia patients during the COVID-19 pandemic. Our data support the efficiency of non-pharmaceutical interventions on virus circulation except for rhinoviruses. The consequences of an altered circulation on subsequent winter seasons remain unclear and support the importance of systematic virological surveillance.

Respiratory diseases due to viral or bacterial agents, either alone or in combination, cause substantial economic burdens to the swine industry worldwide. Rapid and reliable detection of causal pathogens is crucial for effective epidemiological surveillance and disease management. This research aimed to employ the multiplex ligation-dependent probe amplification (MLPA) assay for simultaneous detection of seven distinct pathogens causing respiratory problems in swine, porcine reproductive and respiratory syndrome virus (PRRSV), swine influenza virus (SIV), porcine respiratory coronavirus (PRCV), porcine circovirus type 2 (PCV2), Pasteurella multocida , Actinobacillus pleuropneumoniae , and Glässerella parasuis. The results indicated no probe cross-reactivity among the seven target agents with other swine pathogens. The detection limits ranged from 5 to 34 copies per assay for the target organisms. The MLPA assay was evaluated with 88 samples and compared to real-time or multiplex PCR for the target pathogens. The MLPA assay demonstrated high relative test sensitivities (100 %) and reasonable to good relative specificities at 62.5 %, 95.1 %, 86.8 %, and 97.6 % for PRRSV, P. multocida , G. parasuis , and PCV2, respectively, relative to comparator PCR assays. In 71 samples where MLPA and comparator PCR assays matched exactly, infections were detected in 64 samples (90.1 %), with PRRSV being the most commonly found virus and 50.7 % of the samples showing co-infection with two to five of the pathogens. This approach serves as a valuable tool for conducting differential diagnoses and epidemiological investigations of pathogen prevalence within swine populations. • An MLPA method was developed to detect seven swine pathogens simultaneously. • PRRSV, PCV2, P. multocida and G. parasuis were detected in nasal swabs. • SIV, porcine respiratory coronavirus and A. pleuropneumoniae were also targeted. • MLPA assay is rapid for specific detection of multiple pathogens in pigs. • The assay has value in epidemiological surveillance of swine diseases. [ABSTRACT FROM AUTHOR]

Berries contaminated with human norovirus (HuNoV) have been frequently identified as a cause of foodborne gastroenteritis. To prevent virus transmission while preserving sensory and quality parameters, non-thermal treatments, such as high-pressure processing (HPP), can be applied to the berries and products thereof. Here, strawberry purees contaminated with HuNoV genogroup I (GI.3[P13]) and II (GII.4 Sydney [P16]), along with murine norovirus (MNV) and Tulane virus (TV) serving as surrogates, were exposed to HPP at several pressure-time combinations. Virus inactivation was assessed by cell culture, including the novel human intestinal enteroids (HIE) model for HuNoVs. The infectivity results showed TV more resistant than MNV to HPP, as also confirmed by kinetic mathematical modelling. Results indicated that a holding pressure of 450 MPa and an exposure time of ≥5 min are reliable operational conditions for HPP process to successfully control viral contamination. In addition, the inactivation models deduced from MNV and TV viruses were challenged with experimental HuNoV GII.4 infectivity resulting in bias factors <1 for all treatment conditions. This finding validates the proposed models for the conservative estimation of HuNoV inactivation. Our work offers a blueprint for moving forward with inactivation studies using the HIE system, which provides useful practical information on optimum treatments for the best public health outcomes. • The HIE model can be used to assess HuNoV infectivity in berry purees. • Tulane virus resulted more resistant than murine norovirus to HPP. • Weibull distribution function described virus survival for HPP inactivation. • Treatments at 450 MPa for 5 min control virus contamination in strawberry puree. [ABSTRACT FROM AUTHOR]

Disinfectants for veterinary and livestock use, plus skin antiseptics, are critical elements for the control of infectious agents, including zoonotic and antimicrobial‐resistant micro‐organisms, in managed animal species. Such agents impact animal welfare, economic performance and human health. Testing of disinfectants is needed for safety, efficacy and quality control. The present review examines the principal types of test (carrier, suspension, surface and field) that have been developed or attempted, plus the features inherent in the respective tests, particularly with respect to variability. Elements of testing that have to be controlled, or which can be manipulated, are discussed in the context of real‐world scenarios and anticipated applications. Current national and international testing regimes are considered, with an emphasis on the UK, continental Europe and North America, and with further detail provided in the Supporting Information. Challenges to disinfectant efficacy include: the nature of the biological targets (bacteria, fungi, yeasts, spores, viruses and prions), the need for economical and safe working concentrations, the physical and chemical nature of contaminated surfaces, constraints on contact times and temperatures, the presence of organic soil and other barrier or neutralising substances (including biofilms), and thoroughness of pre‐cleaning and disinfectant application. The principal challenges with veterinary disinfectant testing are the control of test variability, and relating test results to likely performance in variable field conditions. Despite some ambitions to develop standardised field tests for disinfectants, aside from skin antiseptic trials the myriad problems such tests pose with respect to cost, reproducibility and generalisability remain intractable. [ABSTRACT FROM AUTHOR]

The fish intestinal mucosa is among the main sites through which environmental microorganisms interact with the host. Therefore, this tissue not only constitutes the first line of defense against pathogenic microorganisms but also plays a crucial role in commensal colonization. The interaction between the mucosal immune system, commensal microbiota, and viral pathogens has been extensively described in the mammalian intestine. However, very few studies have characterized these interactions in early vertebrates such as teleosts. In this study, rainbow trout (Oncorhynchus mykiss) was infected with infectious hematopoietic necrosis virus (IHNV) via a recently developed immersion method to explore the effects of viral infection on gut immunity and microbial community structure. IHNV successfully invaded the gut mucosa of trout, resulting in severe tissue damage, inflammation, and an increase in gut mucus. Moreover, viral infection triggered a strong innate and adaptive immune response in the gut, and RNA−seq analysis indicated that both antiviral and antibacterial immune pathways were induced, suggesting that the viral infection was accompanied by secondary bacterial infection. Furthermore, 16S rRNA sequencing also revealed that IHNV infection induced severe dysbiosis, which was characterized by large increases in the abundance of Bacteroidetes and pathobiont proliferation. Moreover, the fish that survived viral infection exhibited a reversal of tissue damage and inflammation, and their microbiome was restored to its pre−infection state. Our findings thus demonstrated that the relationships between the microbiota and gut immune system are highly sensitive to the physiological changes triggered by viral infection. Therefore, opportunistic bacterial infection must also be considered when developing strategies to control viral infection.

Viral infections can cause rampant disease in human beings, ranging from mild to acute, that can often be fatal unless resolved. An acute viral infection is characterized by sudden or rapid onset of disease, which can be resolved quickly by robust innate immune responses exerted by the host or, instead, may kill the host. Immediately after viral infection, elements of innate immunity, such as physical barriers, various phagocytic cells, group of cytokines, interferons (IFNs), and IFN-stimulated genes, provide the first line of defense for viral clearance. Innate immunity not only plays a critical role in rapid viral clearance but can also lead to disease progression through immune-mediated host tissue injury. Although elements of antiviral innate immunity are armed to counter the viral invasion, viruses have evolved various strategies to escape host immune surveillance to establish successful infections. Understanding complex mechanisms underlying the interaction between viruses and host’s innate immune system would help develop rational treatment strategies for acute viral infectious diseases. In this review, we discuss the pathogenesis of acute infections caused by viral pathogens and highlight broad immune escape strategies exhibited by viruses.

Viral infections can cause rampant disease in human beings, ranging from mild to acute, that can often be fatal unless resolved. An acute viral infection is characterized by sudden or rapid onset of disease, which can be resolved quickly by robust innate immune responses exerted by the host or, instead, may kill the host. Immediately after viral infection, elements of innate immunity, such as physical barriers, various phagocytic cells, group of cytokines, interferons (IFNs), and IFN-stimulated genes, provide the first line of defense for viral clearance. Innate immunity not only plays a critical role in rapid viral clearance but can also lead to disease progression through immune-mediated host tissue injury. Although elements of antiviral innate immunity are armed to counter the viral invasion, viruses have evolved various strategies to escape host immune surveillance to establish successful infections. Understanding complex mechanisms underlying the interaction between viruses and host's innate immune system would help develop rational treatment strategies for acute viral infectious diseases. In this review, we discuss the pathogenesis of acute infections caused by viral pathogens and highlight broad immune escape strategies exhibited by viruses. [ABSTRACT FROM AUTHOR]

In January 2019, four cheetahs (Acinonyx jubatus) kept at a Japanese zoo intermittently showed respiratory signs following the incidence of seasonal influenza in animal caregivers. Respiratory materials (saliva, sputum and food tray swabs) were non‐invasively collected from the four cheetahs. Although we were unable to isolate the virus, the NP gene of influenza A virus was detected in three of the cheetahs but not in the fourth cheetah that had nearly recovered. From a food tray swab which tested weakly positive by a commercial influenza detection kit, we were able to obtain the whole‐genome sequence of the influenza A virus. Analysis of the genome, A/cheetah/Kanagawa/2/2019(H1N1), revealed that the virus was closely related to influenza A(H1N1)pdm09 viruses isolated from humans in Japan in the 2018–2019 winter. Production of haemagglutinin inhibition (HI) antibodies (64–128 HI) against an A(H1N1)pdm09 virus in plasma samples confirmed infection of all four cheetahs. The animals continued to produce antibodies for at least 314 days after disease onset. These findings strongly suggest that reverse zoonotic transmission of A(H1N1)pdm09 virus occurred from human to cheetah and subsequently from cheetah to cheetah in the zoo. We also show that specimens can be safely and non‐invasively collected from non‐domesticated animals and used to investigate respiratory infectious diseases. [ABSTRACT FROM AUTHOR]

Abstract Background Live fish import may lead to the unintended introduction of pathogens. We examined the monthly distribution of microbial pathogens in ornamental finfish imported into South Korea over a 6-month period. Results Vibrio alginolyticus was detected in one lemon damsel in June and July; V. vulnificus was detected in one lemon damsel, one caerulean damsel, and one pearl-spot chromis and one ocellaris clownfish in July, April, and May, respectively; Photobacterium damselae was detected in one ocellaris clownfish and one caerulean damsel in June and July, respectively; V. anguillarum was detected in one pearl-spot chromis in February; V. harveyi was detected in one ocellaris clownfish and two mandarin fish in February and April, respectively; Yersinia ruckeri was detected in a pearlscale goldfish group in June and July and in two colored carp groups in July; and Lactococcus garvieae was detected in a lemon damsel group and a sutchi catfish group in July and May, respectively. European catfish virus, the only viral pathogen detected, was found in two sutchi catfish groups in May. Conclusion This study is the first to identify pathogenic species and the presence or absence of pathogens (non-quarantine diseases) in imported ornamental finfish. These results demonstrate that various pathogens with the potential to harm indigenous fish populations can accompany ornamental finfish imported into South Korea.

Human cells are equipped with a plethora of antiviral proteins protecting them against invading viral pathogens. In contrast to apoptotic or pyroptotic cell death, which serves as ultima ratio to combat viral infections, these cell-intrinsic restriction factors may prevent or at least slow down viral spread while allowing the host cell to survive. Nevertheless, their antiviral activity may also have detrimental effects on the host. While the molecular mechanisms underlying the antiviral activity of restriction factors are frequently well investigated, potential undesired effects of their antiviral functions on the host cell are hardly explored. With a focus on antiretroviral proteins, we summarize in this review how individual restriction factors may exert adverse effects as trade-off for efficient defense against attacking pathogens.

The nature in which the coronavirus disease 2019 (COVID-19) pandemic started and spread all over the world has surprised and shocked experts and the general population alike. This has brought out a worldwide desire and serious efforts to prevent, or at least reduce, the severity of another airborne viral infection and protect individuals gathering for various reasons. Toward this main purpose, a novel method to disinfect the air, using graded, predictable, safe, and reliable dosage of ultraviolet C (UVC), with specially designed devices, is described here. Individuals exclusively breathing this disinfected air can prevent infection, thus destroying the airborne virus or any other pathogens outside the human body to prevent acute and chronic damage to the organs and provide a sense of security to congregate, use public transport, and be protected in acute and long-term healthcare facilities. The study involved designing and testing a unit with one UVC chamber and another unit with six UVC chambers both enclosed in UVC-opaque housings that could be used to destroy airborne pathogens. Wild-type severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was used as a representative pathogen. The virus was fed into these units and in both units, the virus was destroyed to undetectable levels. Such disinfected air can be made available for individuals to breathe at an individual and a community level. The two units that were studied were able to destroy the SARS-CoV-2 virus completely in UVC-opaque housings, making them safe for human use. By employing the air to bring the virus to the UVC, the problem of the virus getting protected behind structures was avoided. The individuals get to breathe totally disinfected air through a mask or a ventilator. To protect individuals who are unable or unwilling to use these units meant for individual use, the same principle can be expanded for use with air conditioners to provide community protection. It is envisaged that this method can prevent airborne infections from turning into pandemics and is a clear example of advocating prevention, rather than treatment. These units are expandable and the UVC dosage to the pathogen can be adjusted and predictable, thereby making it a standard technique to study the dosage needed to inactivate different pathogens., Competing Interests: The patents and publications listed below are relevant to this work. Patents: 1. Pisharodi M, inventor; Perumala Holdings LLC., assignee. Systems, apparatus, and methods for purifying air. United States patent US 11,052,169 B1. 2021 July 6. 2. Pisharodi M, inventor; Perumala Holdings LLC., assignee. Air purification and disinfection apparatus and methods of use. United States patent US 11,511,013 B2. 2022 Nov 29. 3. Pisharodi M, inventor; Perumala Holdings LLC., assignee. Systems, apparatus, and methods for purifying air. United States patent US 11,648,331 B2. 2023 May 16. Publications: 1. Pisharodi M, inventor; Perumala Holdings LLC., assignee. Expandable system for purification and disinfection of air. United States patent US 20230302188 A1. 2023 Sep 28. 2. Pisharodi M, inventor; Perumala Holdings LLC., assignee. Systems and methods for the preparation of vaccines utilizing predictably inactivated pathogens. United States patent US 20230081767 A1. 2023 Mar 16., (Copyright © 2024, Pisharodi et al.)

This rare case with multi-viral co-infection had been diagnosed in Au-gust 2018 in Patna, India. The depicted case was observed in seven-year-old girl child who manifested with unconsciousness along with fever, headache, weakness, body ache and irregular pupil movement. She had experienced intermittent abnormal body movement with star-ing look for every 3 hours. These symptoms were akin to epileptic sei-zures. Clinical investigations were advised with a strong suspicion of viral infection. Awfully, she was diagnosed with multi-viral co-infection including Japanese Encephalitis, Dengue, Chikungunya, Herpes Sim-plex Virus (HSV), Cytomegalovirus (CMV) and Rubella from both blood and Cerebrospinal fluid (CSF) samples. The infections were further confirmed by using reverse transcriptase polymerase chain reaction (RT-PCR). She got proper medication with antibiotic and antiviral cov-erage. She improved with complete cessation of seizures and was ad-vised to follow up after one month. Such incidences of multi-viral co-infections warrant focus on healthcare providers awareness in order to prevent its occurrence and severity of illness. [J Med Allied Sci 2019; 9(2.000): 100-102]

Background. The etiology of intussusception, the leading cause of bowel obstruction in infants, is unknown in most cases. Adenovirus has been associated with intussusception and slightly increased risk of intussusception with rotavirus vaccination has been found. We conducted a case-control study among children <2 years old in Bangladesh, Nepal, Pakistan, and Vietnam to evaluate infectious etiologies of intussusception before rotavirus vaccine introduction. Methods. From 2015 to 2017, we enrolled 1-to-1 matched intussusception cases and hospital controls; 249 pairs were included. Stool specimens were tested for 37 infectious agents using TaqMan Array technology. We used conditional logistic regression to estimate odds ratio (OR) and 95% confidence interval (CI) of each pathogen associated with intussusception in a pooled analysis and quantitative subanalyses. Results. Adenovirus (OR, 2.67; 95% CI, 1.75–4.36) and human herpes virus 6 (OR, 3.50; 95% CI, 1.15–10.63) were detected more frequently in cases than controls. Adenovirus C detection <20 quantification cycles was associated with intussusception (OR, 18.59; 95% CI, 2.45–140.89). Wild-type rotavirus was not associated with intussusception (OR, 1.07; 95% CI, 0.52–2.22). Conclusions. In this comprehensive evaluation, adenovirus and HHV-6 were associated with intussusception. Future research is needed to better understand mechanisms leading to intussusception, particularly after rotavirus vaccination. [ABSTRACT FROM AUTHOR]

Cache Valley virus (CVV) is a mosquito‐borne RNA virus detected throughout North America, Central America and parts of South America. A limited number of human case reports have described severe illness. CVV infection has been associated with outbreaks of congenital defects in small ruminants in Canada and the United States. A scoping review was conducted to identify, characterize and summarize research on CVV, and to identify research gaps. A structured search was conducted in eight electronic databases, with additional search verification and grey literature investigation. All captured studies were independently appraised by two reviewers for relevance and data characterization. The review captured 143 relevant studies investigating CVV epidemiology (n = 104), pathogenesis (n = 37), viral characteristics (n = 24), transmission (n = 14), diagnostic test performance (n = 8) and mitigation strategies (n = 2). Evidence of CVV infection was found in mosquito studies (n = 47), and serological evidence of exposure was demonstrated in animals (n = 41), as well as human (n = 20) studies. In sheep, five outbreaks of birth defects following asymptomatic dam CVV infection during the first 50 days of pregnancy were reported. Only six human cases of CVV‐associated illness were captured, with case symptoms described as initially non‐specific, progressing to more severe clinical signs (e.g., meningitis). No research was identified investigating treatment, societal knowledge and risk perception, economic burden or predictive models related to the impact of climate change on CVV. CVV circulates in mosquito and animal species across a large area of the Americas. Small ruminants are the only animals in which CVV‐associated clinical disease has been extensively studied. It is likely that human cases are under‐reported or misdiagnosed. Future research should focus on the impact of CVV infection in human and animal populations. [ABSTRACT FROM AUTHOR]

Objectives: Hepatitis C virus (HCV) causes both acute and chronic infection, which can potentially develop into cirrhosis and liver cancer. Healthcare systems are struggling to finance costly direct-acting antiviral agents through public funding for uninsured patients, despite the unprecedented high cure rates of these agents. Vulnerable populations are at higher risk of HCV infection. The personal importation scheme is based on the legal right to import any unauthorized generics for personal use. This study was designed to assess the knowledge and perceptions of stakeholders on unauthorized generics. Methods: We conducted an anonymous online survey based on the fictitious situation of a patient diagnosed with HCV who lacked mandatory health insurance and personal financial resources. Results: We obtained a sample of 781 respondents: 445 physicians, 77 pharmacists, 51 patients and 207 non-healthcare professionals. We found that only 36% and 58% of respondents believe that the quality and efficacy, respectively, of unauthorized generics are equivalent to their corresponding brand. An overwhelming majority (98%) favoured quality control upon arrival, and 31% felt they could recognize fraudulent websites. A total of 79% expressed support for financial assistance for vulnerable patients, and support among physicians was 83%. Conclusions: Overall, the limited knowledge of the efficacy and quality of unauthorized generics, despite evidence in peer-reviewed literature, contrasts with the overwhelmingly positive attitudes toward financial assistance for personal import. This finding emphasizes the need for clearer information on imported generics and the potential safety provided by buyers' club schemes to complete the WHO agenda of eradicating viral hepatitis by 2030 within otherwise excluded vulnerable populations. [ABSTRACT FROM AUTHOR]

Thrips transmit one of the most devastating plant viruses worldwide–tomato spotted wilt tospovirus (TSWV). Tomato spotted wilt tospovirus is a type species in the genus Orthotospovirus and family Tospoviridae. Although there are more than 7,000 thrips species, only nine thrips species are known to transmit TSWV. In this study, we investigated the molecular factors that could affect thrips ability to transmit TSWV. We assembled transcriptomes of a vector, Frankliniella fusca [Hinds], and a non-vector, Frankliniella tritici [Fitch], and performed qualitative comparisons of contigs associated with virus reception, virus infection, and innate immunity. Annotations of F. fusca and F. tritici contigs revealed slight differences across biological process and molecular functional groups. Comparison of virus cell surface receptors revealed that homologs of integrin were present in both species. However, homologs of another receptor, heperan sulfate, were present in F. fusca alone. Contigs associated with virus replication were identified in both species, but a contig involved in inhibition of virus replication (radical s-adenosylmethionine) was only present in the non-vector, F. tritici. Additionally, some differences in immune signaling pathways were identified between vector and non-vector thrips. Detailed investigations are necessary to functionally characterize these differences between vector and non-vector thrips and assess their relevance in orthotospovirus transmission. [ABSTRACT FROM AUTHOR]

Background: Worldwide, the number of emerging and re-emerging infectious diseases is increasing, highlighting the importance of global disease pathogen surveillance. Traditional population-based methods may fail to capture important events, particularly in settings with limited access to health care, such as urban informal settlements. In such environments, a mixture of surface water runoff and human feces containing pathogenic microorganisms could be used as a surveillance surrogate. Method: We conducted a temporal metagenomic analysis of urban sewage from Kibera, an urban informal settlement in Nairobi, Kenya, to detect and quantify bacterial and associated antimicrobial resistance (AMR) determinants, viral and parasitic pathogens. Data were examined in conjunction with data from ongoing clinical infectious disease surveillance. Results: A large variation of read abundances related to bacteria, viruses, and parasites of medical importance, as well as bacterial associated antimicrobial resistance genes over time were detected. Significant increased abundances were observed for a number of bacterial pathogens coinciding with higher abundances of AMR genes. Vibrio cholerae as well as rotavirus A, among other virus peaked in several weeks during the study period whereas Cryptosporidium spp. and Giardia spp, varied more over time. Conclusion: The metagenomic surveillance approach for monitoring circulating pathogens in sewage was able to detect putative pathogen and resistance loads in an urban informal settlement. Thus, valuable if generated in real time to serve as a comprehensive infectious disease agent surveillance system with the potential to guide disease prevention and treatment. The approach may lead to a paradigm shift in conducting real-time global genomics-based surveillance in settings with limited access to health care. [ABSTRACT FROM AUTHOR]

Introduction: Patients suffering from Sickle Cell Disease (SCD) are at increased risk for complications due to influenza virus. Annual influenza vaccination is strongly recommended but few clinical studies have assessed its immunogenicity in individuals with SCD. The aim of this study was to explore the biological efficacy of annual influenza vaccination in SCD patients by characterizing both their humoral and cell-mediated immunity against influenza antigen. We also aimed to investigate these immunological responses among SCD individuals according to their treatment (hydroxyurea (HU), chronic blood transfusions (CT), both HU and CT or none of them). Methods: Seventy-two SCD patients (49 receiving HU, 9 on CT, 7 with both and 7 without treatment) and 30 healthy controls were included in the study. All subjects received the tetravalent influenza α-RIX-Tetra® vaccine from the 2016–2017 or 2017–2018 season. Results: Protective anti-influenza HAI titers were obtained for the majority of SCD patients one month after vaccination but seroconversion rates in patient groups were strongly decreased compared to controls. Immune cell counts, particularly cellular memory including memory T and memory B cells, were greatly reduced in SCD individuals. Functional activation assays confirmed a poorer CD8+ T cell memory. We also document an imbalance of cytokines after influenza vaccination in SCD individuals with an INFγ/IL-10 ratio (Th1-type/Treg-type response) significantly lower in the SCD cohort. Conclusion: SCD patients undergoing CT showed altered immune regulation as compared to other treatment subgroups. Altogether, the cytokine imbalance, the high regulatory T cell levels and the low memory lymphocyte subset levels observed in the SCD cohort, namely for those on CT, suggest a poor ability of SCD patients to fight against influenza infection. Nevertheless, our serological data support current clinical practice for annual influenza vaccination, though immunogenicity to other vaccines involving immunological memory might be hampered in SCD patients and should be further investigated. [ABSTRACT FROM AUTHOR]

Background: Persons who inject drugs (PWID) have high HIV incidence and prevalence, and may have limited access to antiretroviral therapy (ART) in some settings. We evaluated HIV drug resistance in PWID in a randomized clinical trial (HPTN 074). The study intervention included ART at any CD4 cell count with enhanced support for ART and substance use treatment. Methods: HPTN 074 enrolled HIV-infected PWID (index participants) with viral loads ≥1,000 copies/mL and their HIV-uninfected injection-network partners in Indonesia, Ukraine, and Vietnam; the study limited enrollment of people who reported being on ART. HIV drug resistance testing and antiretroviral (ARV) drug testing were performed using samples collected from index participants at study enrollment. Results: Fifty-four (12.0%) of 449 participants had HIV drug resistance; 29 (53.7%) of the 54 participants had multi-class resistance. Prevalence of resistance varied by study site and was associated with self-report of prior or current ART, detection of ARV drugs, and a history of incarceration. Resistance was detected in 10 (5.6%) of 177 newly diagnosed participants. Participants with resistance at enrollment were less likely to be virally suppressed after 52 weeks of follow-up, independent of study arm. Conclusions: In HPTN 074, many of the enrolled index participants had HIV drug resistance and more than half of those had multi-class resistance. Some newly-diagnosed participants had resistance, suggesting that they may have been infected with drug-resistant HIV strains. Behavioral and geographic factors were associated with baseline resistance. Baseline resistance was associated with reduced viral suppression during study follow-up. These findings indicate the need for enhanced HIV care in this high-risk population to achieve sustained viral suppression on ART. [ABSTRACT FROM AUTHOR]

Background: Many countries have initiated school-based human papillomavirus (HPV) vaccination programs. The real-life effectiveness of HPV vaccines has become increasingly evident, especially among girls vaccinated before HPV exposure in countries with high vaccine uptake. In 2009, Norway initiated a school-based HPV vaccination program for 12-year-old girls using the quadrivalent HPV vaccine (Gardasil®), which targets HPV6, 11, 16, and 18. Here, we aim to assess type-specific vaginal and oral HPV prevalence in vaccinated compared with unvaccinated girls in the first birth cohort eligible for school-based vaccination (born in 1997). Methods: This observational, cross-sectional study measured the HPV prevalence ratio (PR) between vaccinated and unvaccinated girls in Norway. Facebook advertisement was used to recruit participants and disseminate information about the study. Participants self-sampled vaginal and oral specimens using an Evalyn® Brush and a FLOQSwab™, respectively. Sexual behavior was ascertained through a short questionnaire. Results: Among the 312 participants, 239 (76.6%) had received at least one dose of HPV vaccine prior to sexual debut. 39.1% of vaginal samples were positive for any HPV type, with similar prevalence among vaccinated and unvaccinated girls (38.5% vs 41.1%, PR: 0.93, 95% confidence interval [CI]: 0.62–1.41). For vaccine-targeted types there was some evidence of lower prevalence in the vaccinated (0.4%) compared to the unvaccinated (6.8%) group (PR: 0.06, 95%CI: 0.01–0.52). This difference remained after adjusting for sexual behavior (PR: 0.04, 95%CI: 0.00–0.42). Only four oral samples were positive for any HPV type, and all of these participants had received at least one dose of HPV vaccine at least 1 year before oral sexual debut. Conclusion: There is evidence of a lower prevalence of vaccine-targeted HPV types in the vagina of vaccinated girls from the first birth cohort eligible for school-based HPV vaccination in Norway; this was not the case when considering all HPV types or types not included in the quadrivalent HPV vaccine. [ABSTRACT FROM AUTHOR]

Background: In Sub-Saharan Africa, both HIV/AIDS and anemia have considerable public health problems. Anemia has an adverse effect on treatment outcome and it decreases the quality of life among adult HIV patients. This study was aimed to assess the prevalence of anemia and its associated factors among adult HIV positive patients in Wolaita Sodo University Teaching Referral Hospital. Method: Institution based cross-sectional study was conducted at Wolaita Sodo University Teaching Referral Hospital from 01 October to December 30, 2016. A randomly selected 411 adult people living with the human immunodeficiency virus were included in the study. A pre-tested questionnaire was used to collect data. Variables with P-value ≤0.25 in the bivariable logistic regression model were taken into multivariable logistic regression analysis along with 95% confidence interval and Odds Ratio was used to examine the association between anemia and independent variables. P˗value ≤ 0.05 was taken as statistically significant. Result: Prevalence of anemia in this study was 36.5% with 95% CI (32%-41%). Factors associated with anemia among adult people living with HIV/AIDS were individuals who lived with HIV ≥9years (AOR = 2.6, 95% CI:-1.03–6.59),years lived with HIV 5–8 years (AOR = 2.59, 95% CI:-1.02–6.57),CD4 count <200cells/ul (AOR = 4.2, 95%CI:-2.03–8.67), CD4 count200-350cells/ul(AOR = 1.82,95%CI:-1.01–3.26),infection with intestinal parasites (AOR = 2.04, 95% CI:-1.06–3.95), Participants with BMI <18.5kg/m2 (AOR = 2.96, 95%CI:-1.37–6.390),BMI 18.5-25kg/m2(AOR = 1.98, 95%CI:-1.11–3.56) and being HAART naïve (AOR = 2.23, 95% CI:- 1.16–4.28). Conclusion: Prevalence of anemia among this study participant was high. This may affect the treatment outcome, increases morbidity and mortality of the participants. So periodic screening of anemia, a routine checkup of nutritional status, CD4 count and examination for intestinal parasite are essential. [ABSTRACT FROM AUTHOR]