Genomic and clinical epidemiology of SARS-CoV-2 in coastal Kenya: insights into variant circulation, reinfection, and multiple lineage importations during a post-pandemic wave.

Background: Between November 2023 and March 2024, coastal Kenya experienced another wave of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections detected through our continued genomic surveillance. Herein, we report the clinical and genomic epidemiology of SARS-CoV-2 infections from 179 individuals (a total of 185 positive samples) residing in the Kilifi Health and Demographic Surveillance System (KHDSS) area (~ 900 km).

Methods: We analyzed genetic, clinical, and epidemiological data from SARS-CoV-2 positive cases across pediatric inpatient, health facility outpatient, and homestead community surveillance platforms.

Genomic epidemiology of clade Ia monkeypox viruses circulating in the Central African Republic in 2022-24: a retrospective cross-sectional study.

Background: The spread of monkeypox virus (Orthopoxvirus monkeypox) clade Ib from the Democratic Republic of the Congo to neighbouring countries has raised global concerns, leading to WHO declaring mpox a public health emergency on Aug 14, 2024. We applied genomic epidemiology to investigate the causes of recurrent mpox outbreaks in the Central African Republic. We aimed to determine whether frequent zoonotic spillovers or increased human-to-human transmissions are driving mpox epidemiology.

Extensive cross-species transmission of pathogens and antibiotic resistance genes in mammals neglected by public health surveillance.

Non-traditional farmed and wild mammals are often neglected in pathogen surveillance. Through metagenomic and metatranscriptomic sequencing of fecal and tissue samples from 973 asymptomatic mammals, we identified 128 viruses (30 novel), including a new coronavirus genus, 10,255 bacterial species (over 7,000 undescribed), 201 fungi, and 7 parasites. Farmed and wild mammals shared 13.

Resolution of experimental malaria-associated acute respiratory distress syndrome is Alox12 independent and shows residual inflammation.

Background: Malaria-associated acute respiratory distress syndrome (MA-ARDS) is a lung complication affecting 5-25% of adults with severe malaria and has a mortality rate of ~ 40% despite mechanical ventilation. Effective recovery requires the resolution of inflammation, an active process involving pathogen clearance, suppression of inflammation, and tissue repair. While antimalarial drugs eliminate the parasite, they do not adequately promote resolution.

Novel Viral Sequences in a Patient with Cryptogenic Liver Cirrhosis Revealed by Serum Virome Sequencing.

Clinical studies indicate the etiology of liver disease to be unknown in 5% to 30% of patients. A long-standing hypothesis is the existence of unknown viruses beyond hepatitis A through E virus. We conducted serum virome sequencing in nine patients with cryptogenic liver disease and identified eight contigs that could not be annotated.

The recency and geographical origins of the bat viruses ancestral to SARS-CoV and SARS-CoV-2.

The emergence of SARS-CoV in 2002 and SARS-CoV-2 in 2019 led to increased sampling of sarbecoviruses circulating in horseshoe bats. Employing phylogenetic inference while accounting for recombination of bat sarbecoviruses, we find that the closest-inferred bat virus ancestors of SARS-CoV and SARS-CoV-2 existed less than a decade prior to their emergence in humans. Phylogeographic analyses show bat sarbecoviruses traveled at rates approximating their horseshoe bat hosts and circulated in Asia for millennia.

Impact of Environmental Factors on the Distribution Patterns of Nephropathia Epidemica Cases in Western Europe.

Background: Environmental factors, such as fluctuations of climatic conditions and land cover, play a pivotal role in driving infectious disease epidemics, particularly those originating from wildlife reservoirs. , hosted by bank voles in Europe, is the causative agent of a form of hemorrhagic fever and renal syndrome called nephropathia epidemica. Despite two decades of consistent presence in western Europe, nephropathia epidemica outbreaks still pose challenges due to localized periodic occurrences and a lack of understanding of its environmental drivers.

Prevention and control of avian influenza virus: Recent advances in diagnostic technologies and surveillance strategies.

The natural host for avian influenza virus (AIV) is waterfowl. However, certain subtypes have breached species barriers, causing epizootics in many avian and mammalian species with occasional zoonotic infections in humans. The ongoing spread of highly pathogenic avian influenza (HPAI) A(H5N1) poses a significant and growing public health threat.

Transmission dynamics of the 2022 mpox epidemic in New York City.

The 2022 global mpox epidemic was caused by transmission of MPXV clade IIb, lineage B.1 through sexual contact networks, with New York City (NYC) experiencing the first and largest outbreak in the United States. By performing phylogeographic analysis of MPXV genomes sampled from 757 individuals in NYC between April 2022 and April 2023, and 3,287 MPXV genomes sampled around the world, we identify over 200 introductions of MPXV into NYC with at least 84 leading to onward transmission.

Recently reported SARS-CoV-2 genomes suggested to be intermediate between the two early main lineages are instead likely derived.

Understanding the genomic diversity of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) at the outset of the coronavirus disease 2019 pandemic can provide insight into the circumstances leading to its emergence. Early SARS-CoV-2 genomic diversity has been classified into two distinct viral lineages, denoted "A" and "B," which we hypothesized were separately introduced into humans. Recently published data contain two genomes with a haplotype suggested to be an evolutionary intermediate to these two lineages, known as "T/T.

The Effect of HBV Therapy on Glycemic Control in HBV-Infected Patients With Diabetes: A 90-day Multicenter Study.

Patients with diabetes are at increased risk of HBV infection; however, the effects of HBV infection and anti-HBV therapy on the management of type 1 diabetes (T1D), type 2 diabetes (T2D), and latent autoimmune diabetes in adults (LADA) remain unclear. From 2016 to 2023, we recruited a multicenter cohort of 355 HBV-infected inpatients, including 136 with T1D, 140 with T2D, and 79 with LADA. The control group included 525 HBV-uninfected inpatients, comparing 171 with T1D, 204 with T2D and 150 with LADA.

Emergence of Omicron FN.1 a descendent of BQ.1.1 in Botswana.

Botswana, like the rest of the world, has been significantly impacted by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). In December 2022, we detected a monophyletic cluster of genomes comprising a sublineage of the Omicron variant of concern (VOC) designated as B.1.

A spatially-heterogeneous impact of fencing on the African swine fever wavefront in the Korean wild boar population.

In October 2019, South Korea's first case of African swine fever (ASF) was reported in wild boar in the north of the country. Despite the implementation of a 2300 km-long fencing strategy, the ASF wavefront continued to invade southward. Our study aimed to investigate the ASF wavefront dynamics in different regions of South Korea, as well as to assess the effectiveness of the fencing measures on ASF dispersal and wavefront velocity.

Modeling the velocity of evolving lineages and predicting dispersal patterns.

Accurate estimation of the dispersal velocity or speed of evolving organisms is no mean feat. In fact, existing probabilistic models in phylogeography or spatial population genetics generally do not provide an adequate framework to define velocity in a relevant manner. For instance, the very concept of instantaneous speed simply does not exist under one of the most popular approaches that models the evolution of spatial coordinates as Brownian trajectories running along a phylogeny.

Integrating indicator-based and event-based surveillance data for risk mapping of West Nile virus, Europe, 2006 to 2021.

BackgroundWest Nile virus (WNV) has an enzootic cycle between birds and mosquitoes, humans being incidental dead-end hosts. Circulation of WNV is an increasing public health threat in Europe. While detection of WNV is notifiable in humans and animals in the European Union, surveillance based on human case numbers presents some limitations, including reporting delays.

Modeling the velocity of evolving lineages and predicting dispersal patterns.

Accurate estimation of the dispersal velocity or speed of evolving organisms is no mean feat. In fact, existing probabilistic models in phylogeography or spatial population genetics generally do not provide an adequate framework to define velocity in a relevant manner. For instance, the very concept of instantaneous speed simply does not exist under one of the most popular approaches that models the evolution of spatial coordinates as Brownian trajectories running along a phylogeny (Lemey et al.

Zoonotic infections by avian influenza virus: changing global epidemiology, investigation, and control.

Avian influenza virus continues to pose zoonotic, epizootic, and pandemic threats worldwide, as exemplified by the 2020-23 epizootics of re-emerging H5 genotype avian influenza viruses among birds and mammals and the fatal jump to humans of emerging A(H3N8) in early 2023. Future influenza pandemic threats are driven by extensive mutations and reassortments of avian influenza viruses rooted in frequent interspecies transmission and genetic mixing and underscore the urgent need for more effective actions. We examine the changing global epidemiology of human infections caused by avian influenza viruses over the past decade, including dramatic increases in both the number of reported infections in humans and the spectrum of avian influenza virus subtypes that have jumped to humans.

Impact of BK Polyomavirus NCCR variations in post kidney transplant outcomes.

The human BK Polyomavirus (BKPyV) is a DNA virus that is prevalent in 80 % of the population. Infection with this virus may begin in childhood, followed by asymptomatic persistence in the urinary tract. However, in immunocompromised individuals, especially kidney transplant recipients (KTRs), heightened replication of BKPyV can lead to severe complications.