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Objective: Although the tenofovir alafenamide/emtricitabine/bictegravir (TAF/FTC/BIC) regimen is recommended in national and international guidelines for changing treatment in treatment-experienced patients living with HIV (PLwHIV), there are limited real-life data reported in Türkiye. We aimed to evaluate the changes in virological and immunological indicators, renal functions, and lipid profiles in the follow-up of patients who switched to TAF/FTC/BIC. Methods: The study included treatment-experienced PLwHIV aged 18 years or older who were followed at the infectious diseases outpatient clinic between January 2020 and December 2021. Follow-up parameters before and after switching to TAF/FTC/BIC were evaluated retrospectively. Results: A total of 77 PLwHIV were included. Of those, 71 (92.2%) were male, and the median age was 42 years. The 24th and 48th week median HIV RNA values of patients whose viral loads were measured were 35 (27-77) copies/ml and 34 (24-49) copies/ml, respectively, after switching. We did not detected a significant difference in CD4+T lymphocyte count, CD4+ T lymphocyte percentage, and CD4+/CD8+ ratio when compared with pre-treatment values. Virological suppression was not maintained in 24.7% (n=19/77) of PLwHIV. While "incomplete virological response" was not detected in any patients, 2.6% (n=2/77) had virological rebound, 1.3% (n=1/77) were virological non-responders, 10.4% (n=8/77) had low-level viremia, and 20.8% (n=16/77) had virological blip. Glomerular filtration rate (GFR) (101 ml/min./1.73m² vs. 96 ml/min./1.73m², p=0.05) and total cholesterol level (199 mg/dl vs. 185 mg/dl, p=0.05) decreased at 48th week. In switching from tenofovir alafenamide/emtricitabine/elvitegravir/cobicistat (TAF/FTC/EVG/Cob) to TAF/FTC/BIC, significant decreases were detected in GFR (101 ml/min./1.73m² vs. 95 ml/min./1.73m², p=0.016) and total cholesterol levels (205 mg/dl vs. 182 mg/dl, p<0.001). Conclusion: Even if virological suppression is achieved before switching, virological suppression may be impaired in patients after switching to TAF/FTC/BIC. Moreover, renal functions should be closely monitored due to the significant decrease in GFR, especially when switching from TAF/FTC/EVG/Cob to TAF/FTC/BIC. [ABSTRACT FROM AUTHOR]

Louis Pasteur, born December 27, 1822 in Dole, France, showed in his childhood and youth great abilities as an artistic painter; however by an age of 19, his interest changed toward science, and he moved to Paris to study chemistry and physics at École Normale Supérieure. During graduation, he initiated research on chiral crystallography and stereochemistry and got his doctorates in 1847 in both chemistry and physics. In 1848, he started as high school teacher in Dijon, but shortly after he became a deputy professor at the University of Strasbourg in chemistry and got married to the rector's daughter Marie Laurent. They had five children, of which only two survived. The family moved to Lille in 1854, where he worked as professor in chemistry and became the dean at the new Faculty of Science at the University of Lille. He initiated his famous research on fermentation in 1855. Louis Pasteur moved back to École Normale Supérieure in 1857, where a major part of his innovative research on fermentation took place ending up with the development of pasteurization in 1864. Through genius experiments, he disputed the spontaneous genesis theory and founded the basis for the germ theory, later confirmed by his enemy Robert Koch and several other research teams, which he for lifetime competed with on the cure and prevention against infectious disease causes by both bacteria such as cholera, anthrax, and virus‐induced infections as yellow fever and rabies. However, most of his experiments were done on animals since Pasteur and his colleagues at École Normale Superiére were not physicians but scientists. The first successful attenuated vaccine used in humans against rabies was, when the 9‐year‐old Joseph Meister was cured or prevented from rabies in 1885 after 13 vaccine injections done by the young pediatrician Joseph Grancher. This worldwide known intervention is both world famous and ethically criticized and disputed. The Pasteur Institute was inaugurated in 1888—now an international prestigious research institute—which has been expanded since in a network of affiliated Pasteur institutes over the whole world. There were multiple links to Danish scientists of the 19th century and to the Danish brewery industry. Most well known is the strong friendship between Louis Pasteur and the Carlsberg brewery and especially to its founder Jacob Christian Jacobsen, who was a great believer on a scientific approach to a cleaner fermentation process and better beer quality. Louis Pasteur stands as a milestone example of the fruitful outcome of scientific competition and collaboration and should therefore be remembered as an inspiration for present and future scientists. [ABSTRACT FROM AUTHOR]

In the United States (US), biosafety and biosecurity oversight of research on viruses is being reappraised. Safety in virology research is paramount and oversight frameworks should be reviewed periodically. Changes should be made with care, however, to avoid impeding science that is essential for rapidly reducing and responding to pandemic threats as well as addressing more common challenges caused by infectious diseases. Decades of research uniquely positioned the US to be able to respond to the COVID-19 crisis with astounding speed, delivering life-saving vaccines within a year of identifying the virus. We should embolden and empower this strength, which is a vital part of protecting the health, economy, and security of US citizens. Herein, we offer our perspectives on priorities for revised rules governing virology research in the US. [ABSTRACT FROM AUTHOR]

The Correction Notice from the Virology Journal addresses the omission of a funding statement in the original article titled "Molecular detection and genomic characterization of Samak Micromys paramyxovirus-1 and -2 in Micromys minutus, Republic of Korea." The updated funding statement includes support from various organizations in Korea and a Novo Nordisk Foundation PAD award. The correction ensures transparency and accuracy in acknowledging the sources of funding for the research. [Extracted from the article]

Dr. William John Paget, a senior scientist at the Netherlands Institute for Health Services Research, passed away on November 4, 2023. He was known for his vibrant personality and his contributions to surveillance and research on infectious diseases, particularly in the context of European and global public health. Dr. Paget played a key role in establishing the European Influenza Surveillance Scheme (EISS) and expanding it to become the largest and most innovative surveillance network in Europe. He also initiated projects on respiratory syncytial virus (RSV) epidemiology and antimicrobial resistance. Dr. Paget was highly respected in the field and was recognized for his diplomatic skills and ability to bring together experts from different disciplines. He will be remembered as a great researcher and a modest man dedicated to improving public health. [Extracted from the article]

The recent Coronavirus Disease 2019 pandemic has once again reminded us the importance of understanding infectious diseases. One important but understudied area in infectious disease research is the role of nuclear architecture or the physical arrangement of the genome in the nucleus in controlling gene regulation and pathogenicity. Recent advances in research methods, such as Genome-wide chromosome conformation capture using high-throughput sequencing (Hi-C), have allowed for easier analysis of nuclear architecture and chromosomal reorganization in both the infectious disease agents themselves as well as in their host cells. This review will discuss broadly on what is known about nuclear architecture in infectious disease, with an emphasis on chromosomal reorganization, and briefly discuss what steps are required next in the field.

This comprehensive review examines the interplay between environmental virology, public health, and sanitation in the unique context of Kenya. The review sheds light on the specific viral threats faced by the country, including waterborne viruses, zoonotic infections, and emerging viral diseases, and their implications for public health. It explores the prevailing public health challenges in Kenya associated with environmental viromics, such as infectious viral diseases, and the rising burden of other infectious particles. The role of sanitation in mitigating viral infections is highlighted, emphasising the importance of clean water supply, proper waste management, and hygienic practises. The review also presents strategies for strengthening environmental virology research in Kenya, including enhancing laboratory capacities and leveraging technological advancements. Furthermore, the policy implications and recommendations derived from the review emphasise the need for multisectoral collaboration, evidence-based decision-making, and long-term investments in infrastructure and behaviour change interventions. Implementing these strategies can enhance the understanding of environmental virology, improve public health outcomes, and ensure sustainable sanitation practises in Kenya, ultimately contributing to the wellbeing of the population and sustainable development. [ABSTRACT FROM AUTHOR]

The human mouth, or oral cavity, is at the crossroads of our external and internal environments, and it is increasingly evident that local colonization of dental, oral, and craniofacial (DOC) tissues and cells by bacteria and viruses may also have systemic effects across myriad diseases and disorders. Better understanding of this phenomenon will require a holistic understanding of host-microbial interactions in both spatiotemporal and biogeographical contexts while also considering person-, organ-, tissue-, cell-, and molecular-level variation. After the acute phase interaction with microbes, the establishment of site-specific reservoirs constitutes an important relationship to understand within the human body; however, despite a preliminary understanding of how viral reservoirs originate and persist across the human body, the landscape of single-cell and spatial multiomic tools has challenged our current understanding of what cells and niches can support microbial reservoirs. The lack of complete understanding impacts research into these relevant topics and implementing precision care for microbial-induced or microbial-influenced diseases. Here, via the lens of acute and chronic microbial infections of the DOC tissues, the goal of this review is to highlight and link the emerging spatiotemporal biogeography of host-viral interactomics at 3 levels: (1) DOC cell types in distinct tissues, (2) DOC-associated microbes, and (3) niche-specific DOC pathologies. Further, we will focus on the impact of postacute infectious syndromes such as long COVID, neurodegenerative disorders, and other underappreciated postviral conditions. We will provide hypotheses about how DOC tissues may play roles systemically in these conditions. Throughout, we will underscore how COVID-19 has catalyzed a new understanding of these biological questions, discuss future directions to study these phenomena, and highlight the utility of noninvasive oral biofluids in screening, monitoring, and intervening to prevent and/or ameliorate human infectious diseases. [ABSTRACT FROM AUTHOR]

Key Clinical Message: We report a case of febrile illness that was presented with mild symptoms. However, laboratory investigation confirmed a malaria and Rift Valley fever co‐infection. Healthcare providers in settings endemic with several infectious diseases should seek rolling out possibilities of other infections prior to starting treatment for achieving effective case management with less resources and better safety of patients. Here we report a case of febrile illness that confirmed to be a co‐infection of malaria and Rift Valley fever. The patient was initially diagnosed with malaria and started on treatment immediately. However, due to the lack of response to the treatment further laboratory investigations were pursued. [ABSTRACT FROM AUTHOR]

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The burden of meningitis in low-and-middle-income countries remains significant, but the infectious causes remain largely unknown, impeding institution of evidence-based treatment and prevention decisions. We conducted a validation and application study of unbiased metagenomic next-generation sequencing (mNGS) to elucidate etiologies of meningitis in Bangladesh. This RNA mNGS study was performed on cerebrospinal fluid (CSF) specimens from patients admitted in the largest pediatric hospital, a World Health Organization sentinel site, with known neurologic infections (n = 36), with idiopathic meningitis (n = 25), and with no infection (n = 30), and six environmental samples, collected between 2012 and 2018. We used the IDseq bioinformatics pipeline and machine learning to identify potentially pathogenic microbes, which we then confirmed orthogonally and followed up through phone/home visits. In samples with known etiology and without infections, there was 83% concordance between mNGS and conventional testing. In idiopathic cases, mNGS identified a potential bacterial or viral etiology in 40%. There were three instances of neuroinvasive Chikungunya virus (CHIKV), whose genomes were >99% identical to each other and to a Bangladeshi strain only previously recognized to cause febrile illness in 2017. CHIKV-specific qPCR of all remaining stored CSF samples from children who presented with idiopathic meningitis in 2017 (n = 472) revealed 17 additional CHIKV meningitis cases, exposing an unrecognized meningitis outbreak. Orthogonal molecular confirmation, case-based clinical data, and patient follow-up substantiated the findings. Case-control CSF mNGS surveys can complement conventional diagnostic methods to identify etiologies of meningitis, conduct surveillance, and predict outbreaks. The improved patient- and population-level data can inform evidence-based policy decisions.IMPORTANCE Globally, there are an estimated 10.6 million cases of meningitis and 288,000 deaths every year, with the vast majority occurring in low- and middle-income countries. In addition, many survivors suffer from long-term neurological sequelae. Most laboratories assay only for common bacterial etiologies using culture and directed PCR, and the majority of meningitis cases lack microbiological diagnoses, impeding institution of evidence-based treatment and prevention strategies. We report here the results of a validation and application study of using unbiased metagenomic sequencing to determine etiologies of idiopathic (of unknown cause) cases. This included CSF from patients with known neurologic infections, with idiopathic meningitis, and without infection admitted in the largest children's hospital of Bangladesh and environmental samples. Using mNGS and machine learning, we identified and confirmed an etiology (viral or bacterial) in 40% of idiopathic cases. We detected three instances of Chikungunya virus (CHIKV) that were >99% identical to each other and to a strain previously recognized to cause systemic illness only in 2017. CHIKV qPCR of all remaining stored 472 CSF samples from children who presented with idiopathic meningitis in 2017 at the same hospital uncovered an unrecognized CHIKV meningitis outbreak. CSF mNGS can complement conventional diagnostic methods to identify etiologies of meningitis, and the improved patient- and population-level data can inform better policy decisions.

Chlamydia trachomatis (Ct), an intracellular pathogen, is the most common bacterial sexually transmitted infection. In addition to acute cervicitis and urethritis, Ct can lead to serious sequelae of significant public health burden including pelvic inflammatory disease (PID) and infertility. Ct control efforts have not resulted in desired outcomes such as reduced incidence and reinfection, and this highlights the need for the development of an effective Ct vaccine. To this end, NIAID organized a workshop to consider the current status of Ct vaccine research and address critical questions in Ct vaccine design and clinical testing. Topics included the goal(s) of a vaccine and the feasibility of achieving these goals, animal models of infection including mouse and nonhuman primate (NHP) models, and correlates of protection to guide vaccine design. Decades of research have provided both whole cell-based and subunit vaccine candidates for development. At least one is currently in clinical development and efforts now need to be directed toward further development of the most attractive candidates. Overall, the discussions and presentations from the workshop highlighted optimism about the current status of Ct vaccine research and detailed the remaining gaps and questions needed to move vaccines forward.

BackgroundHIV infection is associated with increased susceptibility to common pathogens, which may trigger chronic antigenic stimulation and hyperactivation of B cells, events known to precede the development of AIDS-associated non-Hodgkin lymphoma (AIDS-NHL).MethodsTo explore whether cumulative exposure to infectious agents contributes to AIDS-NHL risk, we tested sera from 199 AIDS-NHL patients (pre-NHL, average lead time 3.9 years) and 199 matched HIV-infected controls from the Multicenter AIDS Cohort Study, for anti-IgG responses to 18 pathogens using multiplex serology. Odds ratios (ORs) and 95% confidence intervals (CIs) were estimated using conditional logistic regression models.ResultsWe found no association between cumulative exposure to infectious agents and AIDS-NHL risk (OR 1.01, 95% CI: 0.91 to 1.12). However, seropositivity for trichodysplasia spinulosa polyomavirus (TSPyV), defined as presence of antibodies to TSPyV capsid protein VP1, was significantly associated with a 1.6-fold increase in AIDS-NHL risk (OR 1.62, 95% CI: 1.02 to 2.57). High Epstein-Barr virus (EBV) anti-VCA p18 antibody levels closer to the time of AIDS-NHL diagnosis (

Background: The aim of this study was to determine whether the occurrence of the SARS-CoV-2 pandemic affected the incidence of influenza in Poland and the efficiency of the SENTINEL influenza surveillance system. Methods: The analysis was based on virologic data from the 2018/2019–2021/2022 epidemic seasons. The data in question were obtained from the SENTINEL influenza surveillance system, which is utilized in Poland. Results: In the 2020/2021 epidemic season, only one positive case was confirmed. In the epidemic season of 2021/2022, the number of positive cases increased. There was a delay in the peak of the season, since the start of pandemic, which was observed in the 14th week of 2022. Previously, it was recorded in the 5–10th week, depending on the season. Before the pandemic, the number of positive samples in relation to the tested ones oscillated between 41–49.4%. After the pandemic, it was 0.3% and below 20%, respectively, for season 2020/2021 and season 2021/2022. Conclusions: The COVID-19 pandemic caused a decline in many other infectious diseases, including influenza, as a result of the numerous lockdowns and from people shifting to remote work. Other safety measures, such as obligatory protective masks and the use of disinfectants, had a significant impact on reducing the number of cases. [ABSTRACT FROM AUTHOR]

Freshwater mussels (Unionida) are among the world's most imperiled taxa, but the relationship between freshwater mussel mortality events and infectious disease is largely unstudied. We surveyed viromes of a widespread and abundant species (mucket, Actinonaias ligamentina; syn: Ortmanniana ligamentina) experiencing a mortality event of unknown etiology in the Huron River, Michigan, in 2019–2020 and compared them to viromes from mucket in a healthy population in the St. Croix River, Wisconsin and a population from the Clinch River, Virginia and Tennessee, where a mortality event was affecting the congeneric pheasantshell (Actinonaias pectorosa; syn: Ortmanniana pectorosa) population. We identified 38 viruses, most of which were associated with mussels collected during the Huron River mortality event. Viral richness and cumulative viral read depths were significantly higher in moribund mussels from the Huron River than in healthy controls from each of the three populations. Our results demonstrate significant increases in the number and intensity of viral infections for freshwater mussels experiencing mortality events, whereas individuals from healthy populations have a substantially reduced virome comprising a limited number of species at low viral read depths. [ABSTRACT FROM AUTHOR]

In its first 2 decades, the NHS witnessed the near eradication of life-threatening community-acquired infections. However, medical advances have created different challenges (such as antimicrobial resistance and healthcare-associated infections) against a background of an increasingly ageing population. The recent COVID-19 pandemic has highlighted a lack of parity with regards to provision of NHS 'infection services' (infectious diseases, microbiology and virology) across the UK, which urgently needs to be addressed. We recommend a fundamental review of NHS infection service provision: divided into four key areas. Firstly, there should be a consideration of a single multidisciplinary specialty of infection medicine removing barriers to training and service delivery. Secondly, streamline infection training via a single pathway through to certificate of completion of training, encompassing all aspects of infection service provision, for example, infection diagnostics, clinical care (including inpatient, outpatient and community based care), and infection prevention and control. There should be flexibility within the training curriculum to facilitate combined training with general internal medicine (GIM) as well as out of programme activities. Innovative ways of providing clinical experience should be considered, acknowledging the roles that medical microbiologists working closely with GIM colleagues in district general hospitals can play in managing patients with infections. Thirdly, formally commission a national network of specialised infectious diseases units with the creation of service standards. This can facilitate future pandemic resilience using a hub-and-spoke model utilising local infection expertise. Lastly, standardise the NHS framework to lead and coordinate development of integrated infection services at the local level. [ABSTRACT FROM AUTHOR]