Concomitant Tickborne Encephalitis and Human Granulocytic Ehrlichiosis

We report a patient with febrile illness and epidemiologic and clinical findings consistent with human granulocytic ehrlichiosis and tickborne encephalitis, in whom infection with Anaplasma phagocytophilum was demonstrated by polymerase chain reaction and seroconversion. Tickborne encephalitis virus infection was established by serum immunoglobulin (Ig) M and IgG antibodies

Okužba s citomegalovirusom v nosečnosti

Citomegalovirus (CMV) je najpogostejši virusni vzrok okužbe ploda v maternici. Virus je nevrotropen, zato povzroča predvsem nevrološke zaplete. Je najpogostejši negenetski vzrok senzorinevralne naglušnosti, nevroloških nepravilnosti in umske zaostalosti, hkrati je vzrok tudi za nedonošenost, smrt ploda v maternici in umrljivost novorojenčkov. Okužbo s CMV potrjujemo z dokazom za CMV specifičnih protiteles IgM in IgG. Prisotnost virusa dokazujemo s PCR. Za časovno opredelitev okužbe s CMV določamo avidnost protiteles IgG. Prirojena okužba je posledica viremije ob primarni ali sekundarni okužbi nosečnice. Ob znotrajmaternični okužbi so lahko prisotni značilni ultrazvočni znaki. Prenatalna diagnoza prirojene okužbe s CMV se postavi z amniocentezo. Simptome ob rojstvu ima do 15 % otrok mater s potrjeno okužbo v nosečnosti. Pri novorojenčkih s simptomi pride v 40–60 % do trajnih posledic, od katerih je najpogostejša senzorinevralna naglušnost. Svetovanje nosečnici s primarno okužbo s CMV je težavno, saj po doslej razpoložljivih podatkih in izsledkih raziskav izida za plod še ne znamo natančno napovedati. Ocene resnosti okužbe in možnih posledic temeljijo predvsem na časovni opredelitvi okužbe nosečnice, prisotnosti in vrsti nepravilnosti pri plodu in laboratorijskih parametrih. Rutinsko zdravljenje nosečnic s potrjeno okužbo s CMV z virostatikom valaciklovirjem ali s hiperimunimi globulini se zaradi pomanjkanja zadostnih dokazov o učinkovitosti ne priporoča. Vse nosečnice bi morale biti seznanjene o nevarnostih okužbe s CMV in preventivnih ukrepih za zaščito pred okužbo s CMV v nosečnosti. Pregledni članek povzema znana dejstva glede presejanja, diagnosticiranja in zdravljenja okužbe s CMV v nosečnosti z navajanjem najnovejših spoznanj in dokazov ter predstavlja prilagoditev tujih priporočil za dobro klinično prakso v Sloveniji

Viral Load as Predictor of Crimean-Congo Hemorrhagic Fever Outcome

We used quantitative real-time reverse transcription–PCR to measure viral load in serum from 24 patients in Kosovo who had acute Crimean-Congo hemorrhagic fever. Viral load correlated with clinical disease and antibodies and could be used as a predictor of disease outcome

The complete genome sequence of a Crimean-Congo Hemorrhagic Fever virus isolated from an endemic region in Kosovo

The Balkan region and Kosovo in particular, is a well-known Crimean-Congo hemorrhagic fever (CCHF) endemic region, with frequent epidemic outbreaks and sporadic cases occurring with a hospitalized case fatality of approximately 30%. Recent analysis of complete genome sequences of diverse CCHF virus strains showed that the genome plasticity of the virus is surprisingly high for an arthropod-borne virus. High levels of nucleotide and amino acid differences, frequent RNA segment reassortment and even RNA recombination have been recently described. This diversity illustrates the need to determine the complete genome sequence of CCHF virus representatives of all geographically distinct endemic areas, particularly in light of the high pathogenicity of the virus and its listing as a potential bioterrorism threat. Here we describe the first complete CCHF virus genome sequence of a virus (strain Kosova Hoti) isolated from a hemorrhagic fever case in the Balkans. This virus strain was isolated from a fatal CCHF case, and passaged only twice on Vero E6 cells prior to sequence analysis. The virus total genome was found to be 19.2 kb in length, consisting of a 1672 nucleotide (nt) S segment, a 5364 nt M segment and a 12150 nt L segment. Phylogenetic analysis of CCHF virus complete genomes placed the Kosova Hoti strain in the Europe/Turkey group, with highest similarity seen with Russian isolates. The virus M segments are the most diverse with up to 31 and 27% differences seen at the nt and amino acid levels, and even 1.9% amino acid difference found between the Kosova Hoti and another strain from Kosovo (9553-01). This suggests that distinct virus strains can coexist in highly endemic areas

Cervids as Babesiae Hosts, Slovenia

We describe cervids as potential reservoir hosts of Babesia EU1 and B. divergens. Both babesial parasites were found in roe deer. Sequence analysis of 18S rRNA showed 99.7% identity of roe deer Babesia EU1 with the human EU1 strain. B. divergens detected in cervids was 99.6% identical to bovine B. divergens

Enterovirus D68 circulation between 2014 and 2022 in Slovenian children

IntroductionEnterovirus D68 (EV-D68) belongs to the Picornaviridae family, genus Enterovirus. It is mostly known as a respiratory virus causing upper and lower respiratory tract infections, but it is also rarely associated with a variety of central nervous system complications, with acute flaccid myelitis being reported most frequently. This study assesses the incidence, seasonality, clinical presentation, and molecular epidemiology of the EV-D68 strain in EV-positive children hospitalized between 2014 and 2022 at the largest pediatric medical center in Slovenia.MethodsEV-D68 was detected using specific qRT-PCR, whereas partial VP1 sequences were obtained with Sanger sequencing, and further analyzed using the software CLC Main Workbench version 7 and MEGA version X.ResultsEV-D68 was detected in 154 out of 1,145 (13.4%) EV-positive children. In the two epidemic years, 2014 and 2016, EV-D68 was most frequently detected in the summer and early autumn, peaking in September. The median age of EV-D68–infected children was 3 years (IQR 1–3 years), with a female: male ratio of 1:1.17. Rhinorrhea was present in 74.0% of children, respiratory distress in 82.5%, and hypoxemia requiring supplemental oxygen in 44.1%. Out of 154 patients, 80.0% were hospitalized, with a median stay of 2 days (IQR 1–3 days). Lower respiratory tract infection was observed in 89.0% of EV-D68–positive patients, with bronchitis and bronchiolitis being most frequently diagnosed. No central nervous system manifestations of EV-D68 infection were observed in the study cohort. Phylogenetic analysis of partial VP1 sequences of EV-D68 revealed close similarity to the EV-D68 variants that were circulating in other European countries in these years.DiscussionSlovenia faced two EV-D68 epidemics in 2014 and 2016; however, after 2016 only nine more cases were detected until the end of the study period. Based on the results of this study, EV-D68 was a frequent cause of lower respiratory tract infection among EV-positive patients. However, none of the patients we studied needed ICU treatment, and none developed acute flaccid paralysis. Our results indicate that EV-D68 is not present constantly, so additional monitoring studies should be conducted in the future to better understand the implications of this EV type in human disease

Enrichment of SARS-CoV-2 sequence from nasopharyngeal swabs whilst identifying the nasal microbiome

Simultaneously characterising the genomic information of coronaviruses and the underlying nasal microbiome from a single clinical sample would help characterise infection and disease. Metatranscriptomic approaches can be used to sequence SARS-CoV-2 (and other coronaviruses) and identify mRNAs associated with active transcription in the nasal microbiome. However, given the large sequence background, unenriched metatranscriptomic approaches often do not sequence SARS-CoV-2 to sufficient read and coverage depth to obtain a consensus genome, especially with moderate and low viral loads from clinical samples. In this study, various enrichment methods were assessed to detect SARS-CoV-2, identify lineages and define the nasal microbiome. The methods were underpinned by Oxford Nanopore long-read sequencing and variations of sequence independent single primer amplification (SISPA). The utility of the method(s) was also validated on samples from patients infected seasonal coronaviruses. The feasibility of profiling the nasal microbiome using these enrichment methods was explored. The findings shed light on the performance of different enrichment strategies and their applicability in characterising the composition of the nasal microbiome

Zika: an old virus with a new face

Zika virus is a mosquito-borne flavivirus that represents a public health emergency at the ongoing epidemic. This obscure virus was limited to sporadic cases in Africa and Asia, until the emergence of Zika virus in Brazil in 2015, when it rapidly spread throughout the Americas. Most Zika virus infections are subclinical or characterized by mild febrile illness. However, neurological complications, including Guillain-Barré syndrome in adults, and congenital anomalies, including microcephaly in babies born to infected mothers, raised a grave concern. Currently, there is no specific antiviral treatment or vaccine available for Zika virus infection. Thus, international public health response is primarily focused on preventing infection, particularly in pregnant women, and on providing up-to-date recommendations to reduce the risk of non-vector transmission of Zika virus

Sivi puh (Myoxus glis) kao domadar medicinski važnih mikroorganizama

The fat dormouse (Myoxus glis) was examined as a potential host of hantaviruses and rickettsiae. 98 animals were collected from three different regions in Slovenia (Godovic, Metlika, Sneznik). Serological methods were used for, the detection of specific viral and/or rickesttsial antibodies in animal sera samples. With the PCR method and restriction enzyme digestion, viral and rickettsial genomes were examined. Myoxus glis was confirmed as a host of Hantaan virus. The prevalence of hantaviral infection among the population of Myoxus glis was 13.3 %. It was established that animal age plays a role in the probability of infection with hantaviruses, but not sex. Rickettsial infection was not confirmed in Myoxus glis with any of the methods used.The fat dormouse (Myoxus glis) was examined as a potential host of hantaviruses and rickettsiae. 98 animals were collected from three different regions in Slovenia (Godovic, Metlika, Sneznik). Serological methods were used for, the detection of specific viral and/or rickesttsial antibodies in animal sera samples. With the PCR method and restriction enzyme digestion, viral and rickettsial genomes were examined. Myoxus glis was confirmed as a host of Hantaan virus. The prevalence of hantaviral infection among the population of Myoxus glis was 13.3 %. It was established that animal age plays a role in the probability of infection with hantaviruses, but not sex. Rickettsial infection was not confirmed in Myoxus glis with any of the methods used