Since 2016, A(H5Nx) high pathogenic avian influenza (HPAI) virus of clade 2.3.4.4b has become one of the most serious global threats not only to wild and domestic birds, but also to public health. In recent years, important changes in the ecology, epidemiology, and evolution of this virus have been reported, with an unprecedented global diffusion and variety of affected birds and mammalian species. After the two consecutive and devastating epidemic waves in Europe in 2020-2021 and 2021-2022, with the second one recognized as one of the largest epidemics recorded so far, this clade has begun to circulate endemically in European wild bird populations. This study used the complete genomes of 1,956 European HPAI A(H5Nx) viruses to investigate the virus evolution during this varying epidemiological outline. We investigated the spatiotemporal patterns of A(H5Nx) virus diffusion to/from and within Europe during the 2020-2021 and 2021-2022 epidemic waves, providing evidence of ongoing changes in transmission dynamics and disease epidemiology. We demonstrated the high genetic diversity of the circulating viruses, which have undergone frequent reassortment events, providing for the first time a complete overview and a proposed nomenclature of the multiple genotypes circulating in Europe in 2020-2022. We described the emergence of a new genotype with gull adapted genes, which offered the virus the opportunity to occupy new ecological niches, driving the disease endemicity in the European wild bird population. The high propensity of the virus for reassortment, its jumps to a progressively wider number of host species, including mammals, and the rapid acquisition of adaptive mutations make the trend of virus evolution and spread difficult to predict in this unfailing evolving scenario.
- Publikační typ
- časopisecké články MeSH
Herein, we present our findings of an early appearance of the Monkeypox virus in Prague, Czech Republic. A retrospective analysis of biological samples, carried out on the 28th of April, revealed a previously unrecognized case of Monkeypox virus (MPxV) infection. Subsequent data analysis confirmed that the virus strain belongs to the ongoing outbreak. Combined with clinical and epidemiological investigations, we extended the roots of the current outbreak at least back to 16th of April, 2022.
- MeSH
- epidemický výskyt choroby MeSH
- lidé MeSH
- opičí neštovice * epidemiologie MeSH
- retrospektivní studie MeSH
- virus opičích neštovic MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- Geografické názvy
- Česká republika MeSH
We report an outbreak of SARS-CoV-2 lineage alpha in gorillas and felid species in a zoo in Prague, Czech Republic. The course of illness and clinical signs are described, as are the results of characterization of these particular SARS-CoV-2 variants by next-generation sequencing and phylogenetic analysis. The putative transmission routes are also discussed.
- MeSH
- COVID-19 * MeSH
- Felidae * MeSH
- fylogeneze MeSH
- Hominidae * MeSH
- lidé MeSH
- SARS-CoV-2 genetika MeSH
- zvířata MeSH
- Check Tag
- lidé MeSH
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- Geografické názvy
- Česká republika MeSH
Despite their widespread distribution, only a single genotype variant of clade 2.3.4.4b H5N1 influenza viruses has been found so far in Europe. Here, we report the detection of a new highly pathogenic avian influenza H5N1 genotype in geese and ducks from a backyard farm in the Czech Republic. Phylogenetic analysis revealed that the Czech H5N1 virus retained the A/Eurasian_Wigeon/Netherlands/1/2020-like backbone with an altered PB2 segment obtained from co-circulating low-pathogenic avian influenza viruses.
- MeSH
- fylogeneze MeSH
- genotyp MeSH
- husy virologie MeSH
- kachny virologie MeSH
- ptačí chřipka u ptáků * epidemiologie virologie MeSH
- virus chřipky A, podtyp H5N1 * genetika MeSH
- zvířata MeSH
- Check Tag
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- Geografické názvy
- Evropa MeSH
The mutual dependence of human and animal health is central to the One Health initiative as an integrated strategy for infectious disease control and management. A crucial element of the One Health includes preparation and response to influenza A virus (IAV) threats at the human-animal interface. The IAVs are characterized by extensive genetic variability, they circulate among different hosts and can establish host-specific lineages. The four main hosts are: avian, swine, human and equine, with occasional transmission to other mammalian species. The host diversity is mirrored in the range of the RT-qPCR assays for IAV detection. Different assays are recommended by the responsible health authorities for generic IAV detection in birds, swine or humans. In order to unify IAV monitoring in different hosts and apply the One Health approach, we developed a single RT-qPCR assay for universal detection of all IAVs of all subtypes, species origin and global distribution. The assay design was centred on a highly conserved region of the IAV matrix protein (MP)-segment identified by a comprehensive analysis of 99,353 sequences. The reaction parameters were effectively optimised with efficiency of 93-97% and LOD95% of approximately ten IAV templates per reaction. The assay showed high repeatability, reproducibility and robustness. The extensive in silico evaluation demonstrated high inclusivity, i.e. perfect sequence match in the primers and probe binding regions, established as 94.6% for swine, 98.2% for avian and 100% for human H3N2, pandemic H1N1, as well as other IAV strains, resulting in an overall predicted detection rate of 99% on the analysed dataset. The theoretical predictions were confirmed and extensively validated by collaboration between six veterinary or human diagnostic laboratories on a total of 1970 specimens, of which 1455 were clinical and included a diverse panel of IAV strains.
- MeSH
- chřipka lidská diagnóza virologie MeSH
- infekce viry z čeledi Orthomyxoviridae diagnóza virologie MeSH
- lidé MeSH
- nemoci prasat diagnóza virologie MeSH
- One Health MeSH
- polymerázová řetězová reakce s reverzní transkripcí metody MeSH
- prasata MeSH
- ptačí chřipka u ptáků diagnóza virologie MeSH
- ptáci virologie MeSH
- reprodukovatelnost výsledků MeSH
- virus chřipky A, podtyp H1N1 genetika izolace a purifikace MeSH
- virus chřipky A, podtyp H3N2 genetika izolace a purifikace MeSH
- virus chřipky A genetika izolace a purifikace MeSH
- zvířata MeSH
- Check Tag
- lidé MeSH
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- hodnotící studie MeSH
- práce podpořená grantem MeSH
- MeSH
- COVID-19 MeSH
- SARS-CoV-2 * genetika izolace a purifikace MeSH
- sekvenování celého genomu metody statistika a číselné údaje MeSH
- Geografické názvy
- Česká republika MeSH
NRL pro chřipku a nechřipková respirační virová onemocnění, detekovala prvé 3 pozitivní případy v ČR 1. 3. 2020, Tyto 3 pozitivní případy byly odeslány ke konfirmaci do EU referenční laboratoře Charité v Berlíně, přesto ještě před oficiální konfirmací pozitivity, byla parciální sekvenací S genu potvrzena pozitivita přímo v la-boratoři. Shodou okolností právě u prvého záchytu jsme dokázali ve spolupráci s SVU Praha získat první českou celogenomovou sekvenci, která byla již 12. 3. 2020 přijata do databáze GISAID. Kmen se zařadil do skupiny „clade“ G, stejně jako další dva osekvenované materiály. Do této klády patří nejen většina italských záchytů viru, ale také většina záchytů z Evropy. Další 2 celogenomové sekvence byly získány v Charité a lze řící, že vyjma několika krátkých úseků, kde je čtení pro Oxford Nanopore technologii obtížné, jsou všechny 3 sekvence shodné, přestože se jedná o 3 nezávislé vstupy.Současně byla NRL úspěšná v izolaci 3 kmenů viru na VERO buňkách. V současnosti je v NRL prováděna především přímá laboratorní diagnostika nového pandemického viru SARS-CoV-2, doposud vyšetřila více než 4 000 pacientů.
The National Reference Laboratory for Influenza and Non-Influenza Viral Diseases (NRL) detected the first three COVID-19 cases in the Czech Republic on 1 March 2020. Their results were referred for confirmation to the EU reference laboratory Charité in Berlin. Before obtaining the official results, the NRL confirmed the COVID-19 positivity by partial S gene sequencing. Coincidentally, in collaboration with the State Veterinary Institute Prague, the first Czech whole genome sequence was obtained for the first virus detected and was submitted to the GISAID database on 12 March 2020. The strain was assigned to clade G, similarly to the other two strains sequenced. Clade G groups not only most Italian but also most European strains. The other two whole genome sequences were obtained from Charité. It can be stated that except for short nucleotide motifs, which are difficult to read by the Oxford Nanopore technology, all three sequences are identical although originating from three different inputs.The NRL also successfully isolated three strains of the virus on VERO cells. At present, the NRL performs mainly direct diagnosis of the new pandemic virus SARS-CoV-2. Over 4 000 patients have been tested to date by the NRL.
- MeSH
- Betacoronavirus * genetika izolace a purifikace MeSH
- koronavirové infekce diagnóza epidemiologie MeSH
- lidé MeSH
- sekvenování celého genomu * MeSH
- Check Tag
- lidé MeSH
- Geografické názvy
- Česká republika MeSH
Letošní sezóna byla charakterizována spíše mírnější chřipkovou epidemií s dominancí subtypu A/H1N1, nicméně výrazně cirkulovaly nechřipkové respirační viry (především respirační syncytiální virus). Podobně jako v předcho-zích sezónách, většina úmrtí v souvislosti s chřipkou byla evidována u osob starších 60 let.
The 2018/2019 season was characterized by a rather moderate epidemic of infl uenza dominanted by the subtypes A/H1N1, but a signifi cant circulation of non-infl uenza respiratory viruses (especially respiratory synsytial virus) was observed. Similar to previous seasons, most deaths associated with infl uenza occurred among people aged 60 or older.
BACKGROUND: To improve national influenza vaccination recommendations, additional data on influenza A and B virus circulation are needed. Here, we describe the circulation of influenza A and B in the Czech Republic during 16 seasons. METHODS: This was a retrospective analysis of data collected from the 2000-2001 to 2015-2016 influenza seasons by the Czech Republic national influenza surveillance network. Influenza was confirmed and viral isolates subtyped by virological assays followed by antigen detection or by reverse transcriptase-polymerase chain reaction. RESULTS: Of 16,940 samples collected, 5144 (30.4%) were influenza-positive. Influenza A represented 78.6% of positive cases overall and accounted for more than 55.0% of all influenza cases in every season, except for 2005-2006 (6.0%). Both A/H1N1 and A/H3N2 were detected in most seasons, except for 2001-2002 and 2003-2004 (only A/H3N2), and 2007-2008 and 2009-2010 (only A/H1N1). Influenza B represented 21.4% of positive cases overall (range, 0.0-94.0% per season). Both influenza B lineages were detected in three seasons, a single B lineage in 11, and no B strain in two. For the 11 seasons where influenza B accounted for ≥20% of positive cases, the dominant lineage was Yamagata in six and Victoria in four. In the remaining season, the two lineages co-circulated. For two seasons (2005-2006 and 2007-2008), the B lineage in the trivalent influenza vaccine did not match the dominant circulating B lineage. CONCLUSIONS: In the Czech Republic, during the 2000-2001 to 2015-2016 influenza seasons, influenza virus circulation varied considerably. Although influenza A accounted for the most cases in almost all seasons, influenza B made a substantial, sometimes dominant, contribution to influenza disease.
- MeSH
- chřipka lidská epidemiologie prevence a kontrola přenos virologie MeSH
- dítě MeSH
- dospělí MeSH
- kojenec MeSH
- lidé středního věku MeSH
- lidé MeSH
- mladiství MeSH
- mladý dospělý MeSH
- novorozenec MeSH
- předškolní dítě MeSH
- retrospektivní studie MeSH
- roční období MeSH
- senioři nad 80 let MeSH
- senioři MeSH
- surveillance populace MeSH
- vakcinace statistika a číselné údaje MeSH
- vakcíny proti chřipce terapeutické užití MeSH
- virus chřipky A, podtyp H1N1 imunologie izolace a purifikace MeSH
- virus chřipky A, podtyp H3N2 imunologie izolace a purifikace MeSH
- virus chřipky B imunologie izolace a purifikace MeSH
- Check Tag
- dítě MeSH
- dospělí MeSH
- kojenec MeSH
- lidé středního věku MeSH
- lidé MeSH
- mladiství MeSH
- mladý dospělý MeSH
- mužské pohlaví MeSH
- novorozenec MeSH
- předškolní dítě MeSH
- senioři nad 80 let MeSH
- senioři MeSH
- ženské pohlaví MeSH
- Publikační typ
- časopisecké články MeSH
- Geografické názvy
- Česká republika MeSH
The ongoing evolution of microbial pathogens represents a significant issue in diagnostic PCR/qPCR. Many assays are burdened with false negativity due to mispriming and/or probe-binding failures. Therefore, PCR/qPCR assays used in the laboratory should be periodically re-assessed in silico on public sequences to evaluate the ability to detect actually circulating strains and to infer potentially escaping variants. In the work presented we re-assessed a RT-qPCR assay for the universal detection of influenza A (IA) viruses currently recommended by the European Union Reference Laboratory for Avian Influenza. To this end, the primers and probe sequences were challenged against more than 99,000 M-segment sequences in five data pools. To streamline this process, we developed a simple algorithm called the SequenceTracer designed for alignment stratification, compression, and personal sequence subset selection and also demonstrated its utility. The re-assessment confirmed the high inclusivity of the assay for the detection of avian, swine and human pandemic H1N1 IA viruses. On the other hand, the analysis identified human H3N2 strains with a critical probe-interfering mutation circulating since 2010, albeit with a significantly fluctuating proportion. Minor variations located in the forward and reverse primers identified in the avian and swine data were also considered.
