Denevérek által hordozott vírusok evolúciós kapcsolatainak vizsgálata európai denevérfajokban

A denevérek rendje (Chiroptera) jelenleg több mint 1250 fajt számlál, amely a bolygón élő emlősök körübelül 20%-át jelenti. Rendkívül széles földrajzi elterjedésüknek köszönhetően az Antarktisz kivételével minden kontinensről ismertek, olyan különleges biológiai adaptációkkal rendelkeznek, mint például az echolokáció vagy a repülés. Filogenetikai vizsgálataikból igen alapos irodalmi háttér áll rendelkezésre, amely jelenlegi ismereteink szerint a korai Eocénba teszi első megjelenésüket (50-52 millió évvel ezelőtt). Tekintettel viszonylag hosszú evolúciós múltjukra és a szárazföldi emlősök között egyedülálló repülési képességükre, rendkívül jelentős fajgazdagságra és földrajzi elterjedésre tettek szert. Egyelőre tudományos szempontból kevéssé magyarázott az a képességük, miszerint tünetmentes hordozói számos magas patogenitású kórokozónak. Hosszú evolúciós múltjuk és rendkívül változatos diverzifikációjuk számos koevolúciós folyamatot is eredményezett a velük kapcsolatban álló élőlényekkel, köztük ektoparazitákkal vagy vírusokkal is. A virális zoonózisok állatokról emberre terjedő vírusokat jelentenek. A zoonózisok jelentős hányada vadállatokról kerül a humán populációra. Érdekes módon az ilyen fertőzési események gyakrabban történnek meg vadállatok-emberek, mint háziállatok-emberek között. Az elmúlt évtizedben a denevérek egyre gyakrabban jelentették egy-egy humán populációban kitört járvány forrásait. Markáns példa a 2002-2003-as SARS (Severe Acute Respiratory Syndrome) coronavírus világjárvány, vagy a jelenleg is tartó MERS (Middle Eastern Respiratory Syndrome) coronavírus járvány az Arab-félszigeten. A 2014-es nyugat-afrikai ebolavirus járvány legvalószínűbb forrásaként is a denevéreket tartják számon. A WHO által számontartott, emberiségre legveszélyesebb kórokozók közül is több denevérekhez köthető (Nipahvirus, Hendravirus, Filovírusok stb). A globalizációs folyamatok (kereskedelem, turizmus stb.) és az emberiség folyamatos térnyerése egyre több denevér-ember kontakt eseményre ad lehetőséget, amely tekintettel az ismertetett tényekre komoly közegészségügyi kockázatot jelent a felbukkanó virális zoonózisok tekintetében. Az elmúlt évtizedekben felbukkant két magas patogenitású coronavirus (SARS, MERS) megjelenése az emberi populációban is ezeknek a folyamatoknak volt köszönhető

The importance of equally accessible genomic surveillance in the age of pandemics

Genomic epidemiology is now a core component in investigating the spread of a disease during an outbreak and for future preparedness to tackle emerging zoonoses. During the last decades, several viral diseases arose and emphasized the importance of molecular epidemiology in tracking the dispersal route, supporting proper mitigation measures, and appropriate vaccine development. In this perspective article, we summarized what has been done so far in the genomic epidemiology field and what should be considered in the future. We traced back the methods and protocols employed over time for zoonotic disease response. Either to small outbreaks such as the severe acute respiratory syndrome (SARS) outbreak identified first in 2002 in Guangdong, China, or to a global pandemic like the one that we are experiencing now since 2019 when the severe acute respiratory syndrome 2 (SARS-CoV-2) virus emerged in Wuhan, China, following several pneumonia cases, and subsequently spread worldwide. We explored both the benefits and shortages encountered when relying on genomic epidemiology, and we clearly present the disadvantages of inequity in accessing these tools around the world, especially in countries with less developed economies. For effectively addressing future pandemics, it is crucial to work for better sequencing equity around the globe. © 2023, The Author(s)

Retrospective Detection and Complete Genomic Sequencing of Canine morbillivirus in Eurasian Otter (Lutra lutra) Using Nanopore Technology

The Eurasian otter (Lutra lutra) is a piscivorous apex predator in aquatic habitats, and a flagship species of conservation biology throughout Europe. Despite the wide distribution and ecological relevance of the species, there is a considerable lack of knowledge regarding its virological and veterinary health context, especially in Central Europe. Canine morbillivirus (Canine distemper virus (CDV)) is a highly contagious viral agent of the family Paramyxoviridae with high epizootic potential and veterinary health impact. CDV is present worldwide among a wide range of animals; wild carnivores are at particular risk. As part of a retrospective study, lung-tissue samples (n = 339) from Eurasian otters were collected between 2000 and 2021 throughout Hungary. The samples were screened for CDV using a real-time RT-PCR method. Two specimens proved positive for CDV RNA. In one sample, the complete viral genome was sequenced using a novel, pan-genotype CDV-specific amplicon-based sequencing method with Oxford Nanopore sequencing technology. Both viral sequences were grouped to a European lineage based on the hemagglutinin-gene phylogenetic classification. In this article, we present the feasibility of road-killed animal samples for understanding the long-term dynamics of CDV among wildlife and provide novel virological sequence data to better understand CDV circulation and evolution

Complete genomic sequencing of canine distemper virus with nanopore technology during an epizootic event

Canine distemper virus (CDV) endangers a wide range of wild animal populations, can cross species barriers and therefore representing a significant conservational and animal health risk around the globe. During spring to autumn 2021, according to our current estimates a minimum of 50 red foxes (Vulpes vulpes) died of CDV in Hungary, with CDV lesions. Oral, nasal and rectal swab samples were RT-PCR screened for Canine Distemper Virus from red fox carcasses. To investigate in more detail the origins of these CDV strains, 19 complete genomes were sequenced with a pan-genotype CDV-specific amplicon-based sequencing method developed by our laboratory and optimized for the Oxford Nanopore Technologies platform. Phylogenetic analysis of the complete genomic sequences and separately the hemagglutinin gene sequences revealed the role of the Europe lineage of CDV as a causative agent for the current epizootic. Here we highlight the growing importance of fast developing rapid sequencing technologies to aid rapid response activities during epidemics or epizootic events. We also emphasize the urgent need for improved surveillance of CDV, considering the epizootic capability of enzootic strains as reported in the current study. For such future efforts, we provide a novel NGS protocol to facilitate future genomic surveillance studies

Single-particle detection of native SARS-CoV-2 virions by microfluidic resistive pulse sensing

Microfluidic resistive pulse sensing (MRPS) was used to determine the size –distribution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) based on detecting nearly 30,000 single virions. However, the ultrastructure of SARS-CoV-2 is thoroughly described, but ensemble properties of SARS-CoV-2, e.g., its particle size distribution, are sparsely reported. According to the MRPS results, the size distribution of SARS-CoV-2 follows a log-normal function with a mean value of 85.1 nm, which corresponds to an approximate diameter of the viral envelope. This result also confirms the low number (< 50) of spike proteins on the surface of the virions

A Single Early Introduction Governed Viral Diversity in the Second Wave of SARS-CoV-2 Epidemic in Hungary

Retrospective evaluation of past waves of the SARS-CoV-2 epidemic is key for designing optimal interventions against future waves and novel pandemics. Here we report on analysing genome sequences of SARS-CoV-2 from the first two waves of the epidemic in 2020 in Hungary, mirroring a suppression and a mitigation strategy, respectively. Our analysis reveals that the two waves markedly differed in viral diversity and transmission patterns. Specifically, unlike in several European areas or in the USA, we have found no evidence for early introduction and cryptic transmission of the virus in the first wave of the pandemic in Hungary. Despite the introduction of multiple viral lineages, extensive community spread was prevented by a timely national lockdown in March 2020. In sharp contrast, the majority of the cases in the much larger second wave can be linked to a single transmission lineage of the pan-European B.1.160 variant. This lineage was introduced unexpectedly early, followed by a two-month-long cryptic transmission before a soar of detected cases in September 2020. Epidemic analysis has revealed that the dominance of this lineage in the second wave was not associated with an intrinsic transmission advantage. This finding is further supported by the rapid replacement of B.1.160 by the alpha variant (B.1.1.7) that launched the third wave of the epidemic in February 2021. Overall, these results illustrate how the founder effect in combination with cryptic transmission, instead of repeated international introductions or higher transmissibility, can govern viral diversity

Nursing homes and the elderly regarding the COVID-19 pandemic: situation report from Hungary

The global impact of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic is significant in terms of public health effects and its long-term socio-economic implications. Among all social groups, the elderly is by far the most affected age group regarding morbidity and mortality. In multiple countries spanning several continents, there are an increasing number of reports referencing the novel coronavirus disease-2019 (COVID-19) spread among nursing homes. These areas are now recognized as potent hotspots regarding the pandemic, which one considers with special regard. Herein, we present currently available data of fatal COVID-19 cases throughout Hungary, along with the analysis of the co-morbidity network. We also report on viral genomic data originating from a nursing home resident. The genomic data was used for viral haplotype network analysis. We emphasize the urgent need for public health authorities to focus on nursing homes and residential service units worldwide, especially in the care of the elderly and infirmed. Our results further emphasize the recent statement released by the World Health Organization (WHO) regarding the vulnerability among seniors and especially the high risk of COVID-19 emergence throughout nursing and social homes

In-depth Temporal Transcriptome Profiling of Monkeypox and Host Cells using Nanopore Sequencing

The recent human Monkeypox outbreak underlined the importance of studying basic biology of orthopoxviruses. However, the transcriptome of its causative agent has not been investigated before neither with short-, nor with long-read sequencing approaches. This Oxford Nanopore long-read RNA-Sequencing dataset fills this gap. It will enable the in-depth characterization of the transcriptomic architecture of the monkeypox virus, and may even make possible to annotate novel host transcripts. Moreover, our direct cDNA and native RNA sequencing reads will allow the estimation of gene expression changes of both the virus and the host cells during the infection. Overall, our study will lead to a deeper understanding of the alterations caused by the viral infection on a transcriptome level