Viral Colonization Research Articles (Page 1)

Endogenous viral elements (EVEs) serve as molecular fossils that record the ancient co-evolutionary arms race between viruses and their hosts. In this study, by analyzing 105 host crustacean genomes, we identified 252 infectious hypodermal and haematopoietic necrosis virus-derived EVEs (IHHNV-EVEs), which include 183 ancient and 6 recently inserted EVEs. These IHHNV-EVEs are widely distributed among Decapoda, Thoracica, and Isopoda, with some of them exhibiting a syntenic distribution relative toneighboringhost sequences, suggesting that the IHHNV or its ancestor are potential pathogens of these species with a long-time dynamic interaction during the evolutionary history. An expansion of IHHNV-EVEs was observed indecapodagenomes, reflecting a reinforced arm race betweendecapodaand IHHNV. Notably, we found that nearly all recent IHHNV-EVEs were laboratory contaminants, except for a single authentic integration in Penaeus monodon that persists intact across 16 samples from the 2 populations. These temporal dynamics-ancient genomic stabilization versus modern colonization activity-highlight that EVEs serve as dual archives: historical records of past conflicts and active participants in current evolutionary battles. Our findings redefine viral genomic colonization as a continuum, where ancient EVE fixation coexists with persistent integration processes, providing new insights into host-virus co-evolutionary trajectories.

Little is known regarding the timing of initial establishment of bovine respiratory disease complex (BRDC)-associated bacterial and viral pathogens. The objective was to evaluate the presence of BRDC-associated bacteria and viruses in the upper respiratory tract of newborn calves within the first 24h of life. Commercial beef cows (n = 26) were allocated to indi­vidual pens before calving. A left nasal swab (LNS), right na­sal swab (RNS) and vaginal swab were collected from each cow immediately following parturition (0h). Calf (n = 26) LNS and RNS sampling occurred at 0h, 6h, 12h and 24h post-calv­ing. Samples were submitted to a diagnostic lab for bacterial culture (n = 26 pairs) and real-time PCR (rtPCR; n = 10 pairs) to isolate and identify bacteria and to detect bacterial and viral nucleic acid. While we were unable to isolate bacteria of interest using culture, rtPCR yielded some success. At birth, Histophilus somni (Hs) was detected in 4/30 dam swabs and 1/20 calf swabs, Mannheimia haemolytica (Mh) in 1/30 dam swabs and 1/20 calf swabs, Mycoplasma bovis (Mb) in 4/30 dam swabs and 1/20 calf swabs, Pasteurella multocida (Pm) in 2/30 dam swabs, bovine herpes virus type-1 (BHV1) in 1/30 dam swabs, and bovine respiratory syncytial virus (BRSV) in 1/30 dam swabs. In 6h calf swabs, Hs was detected in 3/20, Mb in 1/20, and BRSV in 1/20. Associations of bacteria and viruses be­tween dam and offspring remain unclear as establishment of the neonatal microbiome appears complex and more sensitive methods may be needed.

Immunoglobulin A controls intestinal virus colonization to preserve immune homeostasis.

Effects of Portulaca oleracea L. Polysaccharide on piglets infected with porcine rotavirus.

Gammaherpesviruses are DNA tumor viruses that establish lifelong latent infections in lymphocytes. For viruses such as Epstein-Barr virus and murine gammaherpesvirus 68, this is accomplished through a viral gene-expression program that promotes cellular proliferation and differentiation, especially of germinal center B cells. Intrinsic host mechanisms that control virus-driven cellular expansion are incompletely defined. Using a small-animal model of gammaherpesvirus pathogenesis, we demonstrate in vivo that the tumor suppressor p53 is activated specifically in B cells latently infected by murine gammaherpesvirus 68. In the absence of p53, the early expansion of murine gammaherpesvirus 68 latency greatly increases, especially in germinal center B cells, a cell type whose proliferation is conversely restricted by p53. We identify the B cell-specific latency gene M2, a viral promoter of germinal center B cell differentiation, as a viral protein sufficient to elicit a p53-dependent anti-proliferative response caused by Src-family kinase activation. We further demonstrate that Epstein-Barr virus-encoded latent membrane protein 1 similarly triggers a p53 response in primary B cells. Our data highlight a model in which gammaherpesvirus latency gene-expression programs that promote B cell proliferation and differentiation to facilitate viral colonization of the host trigger aberrant cellular proliferation that is controlled by p53.

Porcine reproductive and respiratory syndrome virus (PRRSV) is a globally endemic, costly swine arterivirus with wide genetic and antigenic variations, leading to the frequent appearance of novel virulent strains that hampers PRRSV control. Recently, NADC30‐like (lineage 1C, L1C) and NADC34‐like (lineage 1A, L1A) PRRSV strains were reported to be prevalent in mainland South Korea and became the main epidemic strains persistently attributed to PRRSV outbreaks nationwide, raising great concern in the domestic pork industry. Although the genotypic and pathotypic variability of NADC30‐ and NADC34‐like viruses has been explored in the United States and China, their genomic and biological characteristics have been scarcely studied in South Korea. Here, NADC34‐like GNU‐2353 and NADC30‐like GNU‐2377 strains were independently identified from vaccinated swine herds experiencing high piglet mortality. Whole‐genome sequencing and phylogenetic analysis revealed that GNU‐2353 and GNU‐2377 clustered into sublineages L1A (NADC34‐like) and L1C (NADC30‐like), respectively, sharing high genomic homology with their corresponding lineage‐representative strains and harboring the same molecular signatures of continuous 100 and discontinuous 131 amino acid deletions in the nsp2‐coding region, respectively. Recombination detection indicated that GNU‐2353 and GNU‐2377 were recombinants and evolved through natural interlineage recombination between NADC34‐like (L1A, major parent) or NADC30‐like (L1C, major parent) and RespPRRS modified live virus (MLV)–like (lineage 5, minor parent) strains, respectively. Both viruses displayed homogenous growth kinetics but replicated faster than the prototype VR‐2332 in a porcine alveolar macrophage cell line (PAM‐KNU). The transcriptional profiles of immune response genes in infected PAM‐KNU cells varied between the isolates and VR‐2332; particularly, interleukin‐10 expression was dramatically upregulated in cells infected with GNU‐2353 and GNU‐2377. Piglets with GNU‐2353 and GNU‐2377 infection had high fever; weight loss; increased viremia and nasal shedding; viral distribution in various tissues; thymic atrophy; and apparent macroscopic and microscopic lung lesions, including interstitial pneumonia and viral colonization, compared with control piglets, suggesting that both isolates were virulent to pigs. Remarkably, GNU‐2353 caused higher fever, mortality rate (40%) with cyanosis, viremia, and viral shedding within 2 weeks and significantly higher viral loads in several organs than GNU‐2377 infection. Thus, NADC34‐like GNU‐2353 was more pathogenic than NADC30‐like GNU‐2377. Our findings provide insights into the current epizootic circumstance of NADC30‐ and NADC34‐like PRRSV in South Korea and can aid in tailoring improved control strategies.

Abstract BackgroundHIV escape syndrome is characterized by high viral load in the central nervous system despite having a low serum viral load and typically detected after the initiation of antiretroviral therapy during the course of HIV infection. The aim of this report was to reveal different aspects of the neurological involvement of HIV‐escape syndrome and to define the discrete phenotypes of HIV‐escape syndrome characterized by predominant inflammation or HIV‐associated neurocognitive disorder.Case PresentationTwo cases are presented, both were followed collaboratively by neurology and infectious diseases clinics, where the ones in which neurologic complaints associated with HIV‐positivity aggravated by development of HIV‐escape syndrome. The first case, investigated for progressive vision loss, represented the inflammatory course of HIV‐escape with vasculitic involvement on imaging, positive serum anti‐NMDA‐R antibody, and good response to immunotherapy. On the other hand, the second case, who presented with progressive confusion and difficulty in walking, exemplifies the HIV‐associated neurocognitive disorder with parenchymal atrophy, no evidence of inflammation, and benefit only from antiretroviral treatment modifications.ConclusionWith regard to the discussions detailed herein, identifying HIV‐escape syndrome as a balance of viral colonization and antiviral defense dynamics rather than a homogeneous clinical entity will broaden the clinical approaches needed. It should be particularly borne in mind that the initial neurological status may be exacerbated if HIV‐escape syndrome develops.

Lower Respiratory Tract Pathogen Colonization Detected By Metagenomic Next-Generation Sequencing of Bronchoalveolar Lavage Fluid before Allogeneic Hematopoietic Stem Cell Transplantation and Its Predicting Value for Post-Transplant Infection

Purpose To evaluate the clinical characteristics and viral Colonization of corneas donated by volunteers with coronavirus disease 2019 (COVID-19) before and after corneal transplantation. Methods We retrospectively compared the characteristics and clinical outcomes of patients who received corneas from donors with and without a history of COVID-19 after corneal transplantation. Reverse transcription-polymerase chain reaction (RT-PCR) was performed to evaluate the expression of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA on ocular surfaces in corneal preservation solutions as well as the recipients’ tears. Immunofluorescence was also performed to evaluate the expression of viral spike proteins in the corneas. Intraocular pressure (IOP) measurement, optical coherence tomography (OCT), and slit-lamp inspection at each follow-up examination were performed to assess the surgical efficacy. Results The RT-PCR results of eye surface swabs before corneal extraction, the corneal preservation solutions before transplantation as well as the recipients’ tears were negative, thereby indicating the suitability for transplantation. No significant differences in IOP measurements, OCT findings, or in the incidence of post transplantation complications were observed between donors with and without COVID-19. Conclusions Corneal transplantation using corneas from COVID-19 infected donors does not alter clinical outcomes when compared to controls receiving corneas from non-infected donors.

The concept of the aquapelago was introduced into Island Studies in 2012 to identify the close integration of aquatic and terrestrial realms that can arise from human livelihood activities conducted within them. While many aspects of aquapelagos have subsequently been described and analysed, little attention has been extended to their interface with aerial and, particularly, avian domains. This article attempts to redress this through a consideration of human livelihood activities involving seabirds in St Kilda, an isolated group of islands to the west of Scotland’s Outer Hebrides. Using the concept of the aquapelago as a starting point, the article considers various aspects of human-avian relations occurring on St Kilda, and UNESCO’s subsequent designation of the islands as a World Heritage site and intersperses this with the author’s personal experiences of and affective engagements with the islands. In particular, the latter part of the article develops the author’s field notes from a visit in Summer 2022 into a consideration of the limits of isolation occasioned by the presence of the H5N1 strain of HPAIV (Highly Pathogenic Avian Influenza Virus) on St Kilda at that time. The viral colonisation of the bird colonies undermined any sense of St Kilda and similar remote locations being safely isolated refugia and, indeed, signalled a particularly precarious moment of Anthropocene connectivity between mainlands and islands.

ABSTRACT Background Healthcare settings may amplify transmission of respiratory pathogens, however empirical evidence is lacking. We aimed to describe the spectrum and distribution of respiratory pathogens among healthcare workers in eastern China. Methods Healthcare workers were recruited from October 2020 to November 2021 in Jiangsu province. Participants were interviewed regarding demographic and hospital-based protective measures. Thirty-seven common respiratory pathogens were tested using real-time PCR/RT-PCR (Probe qPCR). The role of demographic and hospital-based protective measures on pathogens colonization using multivariable logistic regression models. Results Among 316 enrolled healthcare workers, a total of 21 pathogens were detected. In total, 212 (67.1%) healthcare workers had at least one respiratory pathogen; 195 (61.7%) and 70 (22.2%) with a bacterial and viral pathogen. The most commonly detected pathogen was streptococcus pneumoniae (47.5%) followed by Haemophilus influenzae (21.2%). One hundred and five (33.2%) healthcare workers with copathogens had at least two respiratory pathogens. Both bacterial and viral colonization were more common in 2020 compared to 2021. A decreased risk of colonization was seen in participants with infection prevention and control training and suitable hand hygiene. Conclusions Colonization of respiratory pathogens in healthcare workers from eastern China was high. Differential risk was impacted only by hospital-based protective measures and not demographic factors.

Swimming-induced pulmonary edema (SIPE) is an incompletely understood condition that is often seen in U.S. special operations candidates participating in maritime qualification training courses. We present a case of two monozygotic twins with the simultaneous onset of acute respiratory distress during a crucible event of a maritime assessment and selection course. Subsequent pulmonary ultrasonography in both candidates showed wedge-shaped hyperechoic lines (B-lines) extending from the pleural interface into the interstitium. Chest radiography of both candidates revealed bilateral asymmetric hazy opacities consistent with SIPE. Both candidates recovered with supportive measures but were medically removed from training. Given the near-identical exposures of the candidates to the same ambient and water temperatures, duration of water submersion, magnitude of physical stressors, and viral colonization, this case study suggests that there may be underlying genetic factors, in addition to environmental factors, that predispose individuals to developing SIPE. Further benchtop and clinical research must be performed to identify potential genetic polymorphisms that contribute to the development of SIPE and to investigate safe interventions that address the underlying etiologies of SIPE pathophysiology.

BackgroundThe presence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in myocardial autopsy tissues has been observed in certain individuals with coronavirus disease 2019 (COVID-19). However, the duration of cardiac involvement remains uncertain among recovered COVID-19 patients. Our study aims to evaluate the long-term persistence of SARS-CoV-2 within cardiac tissue.MethodsWe prospectively and consecutively evaluated the patients undergoing mitral valve replacement (MVR) and left atrial (LA) volume reduction surgery from May 25 to June 10, 2023 at our center, who had been approximately 6 months of recovery after Omicron wave. Patients tested positive for SARS-CoV-2 upon admission were excluded. The surgical LA tissue was collected in RNA preservation solution and stored at −80 ℃ immediately. Then SARS-CoV-2, interleukin-6 (IL-6) and interleukin-1β (IL-1β) RNA expression in LA tissues were assessed through thrice-repeated reverse transcription-quantitative polymerase chain reaction (RT-qPCR) analyses. Categorical variables were assessed using the Chi-square or Fisher’s exact tests, and continuous variables was analyzed using the Mann-Whitney U test.ResultsNine of 41 patients were enrolled, all of whom tested negative for SARS-CoV-2 upon admission (two antigen and PCR tests). In four of nine patients, SARS-CoV-2 RNA was detected in their LA tissue, indicating viral colonization. Among the four positive cases, the IL-6 and IL-1β relative expression levels in the LA tissue of one patient were increased approximately 55- and 110-fold, respectively, compared to those of SARS-CoV-2 (−) patients. Increased expression of IL-6 and IL-1β were observed in the myocardium of this patient. Another patient demonstrated a remarkable 7-fold increase in both IL-6 and IL-1β expression, surpassing that of SARS-CoV-2 (−) patients. Additionally, no other cardiac inflammation-related diseases or conditions were presented in these two patients. The IL-6 and IL-1β expression levels of the remaining two patients were not significantly different from those of SARS-CoV-2 (−) patients. The relative expression levels of IL-6 and IL-1β in cardiac tissues of all SARS-CoV-2 (−) patients were relatively low. Interestingly, despite abnormally elevated levels of IL-6 and IL-1β within their cardiac tissue, two patients did not show a significant increase in serum IL-6 and IL-1β levels when compared to other patients.ConclusionsOur research suggests that certain COVID-19-recovered patients have persistent colonization of SARS-CoV-2 in their cardiac tissue, accompanied by a local increase in inflammatory factors.

Immunocompromised children are particularly vulnerable to infections, including those originating from the oral cavity, due to their weakened immune systems. Oral hygiene plays a pivotal role in preventing secondary infections, which can arise from bacterial, fungal, and viral colonization in the mouth. Poor oral hygiene allows pathogenic microorganisms to flourish, increasing the risk of systemic infections such as bacteremia, sepsis, and pneumonia. The mechanisms linking oral health to systemic infections are multifaceted, involving disrupted microbial balance, impaired immune responses, and weakened mucosal barriers. Opportunistic pathogens such as Streptococcus mutans, Porphyromonas gingivalis, and Candida species often proliferate in the oral cavities of these children, leading to conditions like dental caries, periodontitis, and oral candidiasis. Preventive oral hygiene strategies for immunocompromised children include daily toothbrushing with fluoride toothpaste, flossing, and the use of antimicrobial mouth rinses such as chlorhexidine. Chlorhexidine has been shown to significantly reduce the incidence of oral mucositis and related secondary infections. Saliva substitutes and sodium bicarbonate mouthwashes help mitigate the effects of xerostomia, a common side effect of treatments like chemotherapy, which exacerbates the risk of oral infections. In high-risk cases, antibiotic prophylaxis before invasive dental procedures reduces the likelihood of bacteremia, with studies reporting up to 72% reduction in post-procedural infections. Professional dental care, including regular cleanings and the application of fluoride varnishes and sealants, also plays a critical role in preventing infections. Together, these preventive measures reduce the microbial load, support oral tissue integrity, and protect immunocompromised children from potentially lifethreatening secondary infections. Emphasizing the integration of oral hygiene into the overall care plan for immunocompromised children is crucial for reducing morbidity and improving their quality of life.

Chronic sinusitis, a persistent and long-lasting condition, has a significant effect on an individual’s quality of life. This review offers an in-depth analysis of the complex relationship between epithelial failure, mucosal inflammation, and microbial dynamics, explaining their combined role in the pathophysiology of chronic sinusitis. We address the important role of the epithelial barrier and the effects of its disturbance on immune responses. This review focuses on the mucosal inflammation found in chronic sinusitis cases, highlighting the cytokines and cells that contribute to the ongoing inflammatory response. We provide an in-depth overview of the sinus microbiome’s role in both health and disease states, looking at the effects of bacterial, viral, and fungal colonization on sinus inflammation and their relationship with the epithelial barrier. We also discuss the role of mucociliary clearance and the consequences of its disruption on ongoing inflammation. Each of these factors has a relationship with the others, and together they contribute to chronic inflammation. Current treatment methods are somewhat effective but have limitations. These treatments include methods to improve epithelial function, reduce inflammation, use antibiotics and antifungals, introduce probiotics, and improve mucociliary function. As we learn more, we look at potential new treatments and the need for a complete approach that covers all areas. In short, understanding these areas is key to improving patient care and encouraging more research.

Infant gut DNA bacteriophage strain persistence during the first 3 years of life

The porcine reproductive and respiratory syndrome virus (PRRSV) has caused significant economic losses to the swine industry. The U.S., China, and Peru have reported NADC30-like or NADC34-like PRRSV-infected piglets, which have been identified as the cause of a significant number of abortions in clinics. Although the pathogenicity of NADC30-like PRRSV and NADC34-like PRRSV in piglets exhibits significant variability globally, studies on their pathogenicity in China are limited. In this study, the animal experiments showed that within 8-14 days post-infection, both piglets infected with NADC30-like PRRSV GXGG-8011 and those infected with NADC34-like PRRSV LNSY-GY exhibited significant weight loss compared to the control piglets. Additionally, the viremia of the LNSY-GY persisted for 28 days, while the viremia of piglets infected with the GXGG-8011 lasted for 17 days. Similarly, the duration of viral shedding through the fecal-oral route after the LNSY-GY infection was longer than that observed after the GXGG-8011 infection. Furthermore, post-infection, both the LNSY-GY and GXGG-8011 led to pronounced histopathological lesions in the lungs of piglets, including interstitial pneumonia and notable viral colonization. However, the antibody production in the LNSY-GY-infected group occurred earlier than that in the GXGG-8011-infected group. Our research findings indicate that LNSY-GY is a mildly pathogenic strain in piglets, whereas we speculate that the GXGG-8011 might be a highly pathogenic strain.

Viral diversity has been discovered across scales from host individuals to populations. However, the drivers of viral community assembly are still largely unknown. Within-host viral communities are formed through co-infections, where the interval between the arrival times of viruses may vary. Priority effects describe the timing and order in which species arrive in an environment, and how early colonizers impact subsequent community assembly. To study the effect of the first-arriving virus on subsequent infection patterns of five focal viruses, we set up a field experiment using naïve Plantago lanceolata plants as sentinels during a seasonal virus epidemic. Using joint species distribution modelling, we find both positive and negative effects of early season viral infection on late season viral colonization patterns. The direction of the effect depends on both the host genotype and which virus colonized the host early in the season. It is well established that co-occurring viruses may change the virulence and transmission of viral infections. However, our results show that priority effects may also play an important, previously unquantified role in viral community assembly. The assessment of these temporal dynamics within a community ecological framework will improve our ability to understand and predict viral diversity in natural systems.

MB-1 is an attenuated infectious bursal disease virus vaccine. Previously, we observed a temporal delay of vaccine virus replication in the bursae of chicks due to maternally derived antibodies (MDAs). The mechanism that allowed its survival despite MDA neutralization remained unclear. We hypothesized that after vaccination at 1 day of age (DOA), the MB-1 virus penetrates and resides in local macrophages that are then distributed to lymphoid organs. Furthermore, MB-1's ability to survive within macrophages ensures its survival during effective MDA protection. PCR analysis of lymphoid organs from chicks with MDA, vaccinated on 1 DOA, demonstrated that the MB-1 virus was identified at low levels solely in the spleen pre-14 days of age. Fourteen days after vaccination, the virus was identified using PCR in the bursa, with viral levels increasing with time. The possible delay in viral colonization of the bursa was attributed to the presence of anti-IBDV capsid VP2 maternal IgA and IgY in the bursa interstitium. These indicate that during the period of high MDA levels, a small but viable MB-1 viral reservoir was maintained in the spleen, which might have served to colonize the bursa after MDA levels declined. Thereafter, individual immunization of chicks against Gumboro disease was achieved.

Abstract The recent COVID‐19 pandemic and the accelerating rise of deaths associated with antibiotic‐resistant bacterial strains have highlighted the global health and economic threats caused by the super spreading of pathogens. A major route of transmission for pathogens is via surfaces contaminated by touch or droplets generated via sneezing and coughing. Current surface disinfection strategies are having diminishing efficacy, due to the increasing number of superbugs and the short‐lasting effect of disinfectants resulting in recontamination. New strategies for inhibiting surface‐mediated pathogen transmission are the focus of significant multi‐disciplinary efforts. Among those, the development of superhydrophobic surfaces (SHS) is increasingly regarded as a powerful alternative, or additive, to antimicrobial strategies. SHS provide a neutral/inert interface that can prevent viral and bacterial surface colonization. Here, the use of such water‐repellent coatings are critically reviewed to impede the surface‐mediated transmission of pathogens, addressing the challenges and future directions for their translation into real‐world settings.