Virus Strains Research Articles

Retrospective research: identifying and conducting phylogenetic analyses on four Orf virus strains isolated in Yunnan province between 2021 and 2023—revealing their significance and characteristic features

Contagious Eczema (CE), caused by ORFV, impacts sheep and goats globally, with severe symptoms and economic losses. The ORFV situation in Yunnan, China, was unclear before 2021–2023 study. Eleven scab samples from goats on small farms in three Yunnan municipalities were collected. Four ORFV strains were isolated and characterized using scanning electron microscopy, cytopathic effect observation, and PCR. Phylogenetic analyses of ORFV011 and ORFV059 genes showed significant results. For ORFV011, the nucleotide similarity of the four strains to D1701 strain was 98.4–99%. For ORFV059, it was 97.2–97.9% with OV-SA00 strain. These findings suggest gene rearrangements and interactions among strains during Yunnan’s ORFV outbreak, forming a unique evolutionary lineage. Our study is the first comprehensive one on Yunnan’s ORFV prevalence with in-depth phylogenetic analysis. It has important implications. In vaccine development, understanding genetic variances helps create better vaccines. For disease control, customized strategies like targeted quarantine and disinfection can be designed based on strain characteristics. From a public health aspect, as CE is zoonotic, closely monitoring ORFV in goats aids in predicting and preventing human infections, thus being significant for protecting goats against CE in Yunnan.

Chikungunya Outbreak Risks after the 2014 Outbreak, Dominican Republic.

The 2014 chikungunya outbreak in the Dominican Republic resulted in intense local transmission, with high postoutbreak seroprevalence. The resulting population immunity will likely minimize risk for another large outbreak through 2035, but changes in population behavior or environmental conditions or emergence of different virus strains could lead to increased transmission.

Molecular evidence of novel Begomoviruses and associated Betasatellite complexes linked to Papaya Leaf Curl Disease (PLCD) in Indian Provinces

Papaya leaf curl disease (PLCD) is caused by distinct begomoviruses affecting papaya globally. This study aims to identify and dissect the genetic complexities of begomoviruses-betasatellites associated with PLCD. Surveys in various Indian provinces to collect symptomatic papaya leaf samples. Molecular characterization of 15 DNA-A positives isolates revealed that PSB 8 and PSB 14 from Lucknow shared 89.69% and 87.25% nucleotide sequence identity with other reported begomoviruses and 85.36% with each other. Based on ICTV's species demarcation threshold, these isolates are proposed as novel begomoviruses, named papaya leaf curl Lucknow virus-1 (PaLCLV-1) and papaya leaf curl Lucknow virus-2 (PaLCLV-2). This study also reports a novel strain (PSB 63) of duranta leaf curl virus (DLCV) on papaya, with a 93.48% sequence identity with known DLCV. The samples did not amplify for DNA-B but did for betasatellites. Nine of the 15 DNA-A positive samples were associated with betasatellites, revealing a novel betasatellite (PSBB 34) from Gujarat, sharing 88.46% similarity with ludwigia leaf distortion betasatellite (LuLDB), named papaya leaf curl Lucknow betasatellite (PaLCLB). Another new strain, tomato leaf curl betasatellite (ToLCLB), shared 91.96% identity with other betasatellites. These begomoviruses are monopartite and likely originated in the Old World. This study is the first to show an association between LuLDB and PaLCV (PSB 34). Recombination analysis revealed that major viral genome regions were obtained from previously reported begomoviruses. The study identified eight papaya-infecting begomoviruses and seven associated betasatellites as prominent in the sampled regions.

Developing a human monoclonal antibody combination CRM25 to prevent rabies after exposure

Immunization against rabies post-exposure prophylaxis (PEP) requires passive immunization with either monoclonal antibody (mAb) or blood-derived rabies immunoglobin (RIG). Currently, replacing traditional RIG with emerging mAb or mAb combinations is highly recommended due to the limited supply and potential safety risks of RIG. Here, we developed a mAb combination named CRM25 by combining two human mAbs, RM02 and RM05, at a 1:1 mass ratio. RM02 and RM05 were non-competing and non-overlapping mAbs targeting epitopes I and III, respectively. K226 and G229 were found to be the critical amino acid sites for RM02 neutralization, but the mutant I338T displayed decreased susceptibility to RM05 neutralization. Notably, CRM25 was capable of cross-neutralizing rabies virus (RABV) strains containing K226M or I338T mutations. CRM25 additionally showed an inhibitory effect on the infection of all tested common RABVs and non-RABV phylogroup I lyssaviruses. CRM25 not only exhibited neutralizing activity but also exhibited antiviral effects via Fc-mediated effector functions. Importantly, CRM25 was comparable to human RIG in terms of its capacity to protect Syrian golden hamsters from lethal RABV challenges. These findings promote more thorough research on CRM25′s antiviral properties in cells and in vivo to enhance its clinical applicability and suggest that it may be a viable candidate medication for rabies PEP.

A retrospective genomic characterisation of the 2022 mpox outbreak in Belgium, and in vitro assessment of three antiviral compounds

Since the beginning of May 2022, cases of mpox have been reported in several European and American countries where the disease is nonendemic. We performed a retrospective genomic characterisation of the 2022 mpox outbreak in Belgium, and assessed the invitro sensitivity of three antiviral compounds to a monkeypox virus (MPXV) strain from the 2022 outbreak. We sequenced the complete genomes of MPXV isolated from skin-, throat-, anorectal- and genital swab samples using the Oxford Nanopore Technologies (ONT) GridION. We subsequently analysed high-quality complete MPXV genomes and conducted a genomic analysis of MPXV complete genomes from this study with all other complete MPXV genomes available on GISAID up to October 28th, 2022. The invitro activity of tecovirimat, brincidofovir, and cidofovir was also tested in human and monkey cell lines. We produced 248 complete MPXV genomes. Phylogenetic analysis of the complete MPXV genomes revealed that they all belong to MPXV Clade IIb B.1. Surprisingly, through phylogeographic analysis we identified a minimum number of 79 introduction events into Belgium, along with sustained local transmission. We also demonstrated the superior invitro efficacy and selectivity of tecovirimat to the 2022 MPXV clinical strain. The number of sequences provides sufficient information about the MPXV lineages that were circulating in Belgium. The 2022 mpox outbreak, in Belgium, was mainly characterised by many introduction events that were promptly contained and resulted in limited human-to-human transmission of MPXV. The invitro efficacy of antivirals against a 2022 MPXV Belgian strain highlights the potent activity and specificity of tecovirimat and its ability to prevent the formation of the extracellular enveloped viruses. None.

Phylogenetic and phylodynamic analysis of respiratory syncytial virus strains circulating in children less than five years of age in Karachi-Pakistan

BackgroundRespiratory syncytial virus (RSV) is one of the leading causes of infant morbidity and mortality worldwide, especially in Pakistan. To date, few studies have explored RSV epidemiology in different areas of Pakistan. However, none have performed comprehensive phylogenetic and phylodynamic analyses of RSV strains. This study presents a comprehensive genetic and phylodynamic analysis of RSV strains in children under five years in Karachi, Pakistan. MethodsThis study used retrospectively collected nasopharyngeal (swab) samples from 155 children with qPCR-confirmed RSV infection. The samples were used to perform RSV genotyping using PCR employing RSV glycoprotein gene-specific primers. The RSVA and RSVB genotyping was performed using BLAST and Maximum-likelihood (ML) phylogenetic methods. Similarly, the relationship with other RSV strains was analyzed using ML phylogenetic cluster analysis. The RSVA and RSVB mean genetic diversity and coefficient of differentiation were calculated using MEGA7 software. Furthermore, the time to the most common recent ancestor (tMRCA) and effective population size of RSV genotypes A and B were estimated using a Bayesian MCMC analysis. Finally, site selection pressure and glycosylation analyses were performed using FUBAR and NetNGlyc/NetOGlyc tools. ResultsOut of 155, 98 and 57 sequences were RSVA and RSVB, respectively. The tMRCA was estimated to be around 2002 and 2005 for RSVA and RSVB, respectively. RSVA sequences formed two NA1 genotype clusters, comprising 95 and three sequences, respectively. RSVB formed three clusters, where 24 and two sequences clustered with BA9 and BA12 genotypes, respectively, while 31 sequences formed a unique cluster. The RSVA and RSVB glycoprotein gene sequences exhibited N- and O- glycosylation and selection pressure at several sites. RSV B exhibited slightly higher (0.042) nucleotide diversity per site (π) as compared to RSVA (0.019). ConclusionsOur results suggest that RSVA and RSVB strains in Pakistan exhibit distinct genotypic clusters and differ in their estimated tMRCA. Additionally, both genotypes showed glycosylation and selection pressure at specific sites, with RSVB exhibiting higher nucleotide divergence per site (π), indicating its potential to undergo further evolutionary changes and adaptation. Overall, this study provides unique insights into RSV molecular epidemiology. The study may also help improve our understanding of RSV evolutionary changes and the emergence of new genotypes in different regions worldwide and within Pakistan.

Novel Mastadenovirus Infection as Cause of Pneumonia in Imported Black-and-White Colobuses (Colobus guereza), Thailand.

We identified a novel mastadenovirus, herein referred to as colobus adenovirus (CoAdV), as the likely cause of fatal respiratory and enteric diseases in multiple black-and-white colobuses (Colobus guereza) imported into Thailand in 2022. Among 9 affected colobuses, 4 died. Viral antigen was abundant in respiratory and enteric tissues, where prominent lesions and clinical signs were observed. We successfully cultivated CoAdV in Vero cells and characterized the complete viral genome, which indicated the virus is genetically distinct from other simian adenoviruses. We also conducted a retrospective study of archival samples from 7 other unrelated colobuses that had respiratory distress or diarrhea and found similar viral strains in 4 of those colobuses. Although we could not determine the potential harm to humans or other nonhuman primates from current information, the zoonotic and spillover potential of this virus to other related hosts should not be neglected. Veterinarians should consider CoAdV when pneumonia is diagnosed in colobuses.

Genetic Characterization of the Thymidine Kinase of Koi Herpesvirus 3 in Sulaymaniyah Province, Iraq

Koi herpesvirus 3 (KHV-3) is nominated as an emerging, highly devastating, and contagious viral disease with severe economic losses in the carp aquaculture industries worldwide. Carp rearing under intensive culture conditions is constantly vulnerable to infection by various pathogens in the water. Water temperature has a major influence on the onset and severity of the disease. Since common carp have gained importance in the Iraqi fish industry, the investigation and control of associated diseases, including KHV, are warranted. We confirmed the first detection of the KHV from the collected specimens from the suspected cages in the Sulaymaniyah region. Also, an analysis of the thymidine kinase (TK) gene sequence of the KHV showed that the virus strain had a point mutation (proline, P193) instead of threonine, T193. The isolated KHV strains were subdivided into three clades with three distinct genotypes: Asian (Iranian, Indonesian, Japanese, and Chinese), European (UK), and North American (USA and Mexico) genotypes. The virus sequences were more closely related to the Iranian and Indonesian genotypes. This report describes the first isolation and genetic characterization of koi herpesvirus (KHV) in the Sulaymaniyah province, which is important for efficacious management and vaccination programs in the future to control KHV infection in carp cages in Northern Iraq.

Genetic, phylogenetic, and serological analysis of a Getah virus strain isolated from Culex tritaeniorhynchus mosquitoes in Nagasaki, Japan in 2022.

Getah virus (GETV), belonging to the genus Alphavirus within the family Togaviridae, is a mosquito-borne virus that causes fever, rash, and edema in horses and fatalities and pregnancy disorders in pigs. It has caused occasional outbreaks in horse populations in Japan, China, and India, and endemic areas are gradually expanding, particularly in Asia and Oceania. In this study, we isolated a new GETV strain from Culex tritaeniorhynchus mosquitoes collected from Nagasaki Prefecture, Japan in 2022. Phylogenetic analysis revealed that this new strain, 22IH8, is more closely related to previous Chinese strains than to the strains prevalent in Japan in the 2010s. Furthermore, some amino acid substitutions in the viral proteins of strain 22IH8 were found to be common with those in previous Chinese strains. These results suggest that 22IH8 strain may have recently invaded the Japanese archipelago from mainland Asia. The antiserum against the current vaccine strain, MI-110, showed high neutralization activity against the 22IH8 strain indicating the efficiency of the current vaccine for horses in Japan.

Are Domestic Dogs (Canis familiaris) the Family Scapegoats? A Systematic Review of Canine Distemper Virus in African Wildlife, 1978-2021.

Free-living wildlife across Africa is found across expansive rangelands, frequently interacting with pastoral communities, their livestock, and domestic dogs (Canis familiaris). African wildlife populations are threatened by development, poaching and disease. Infectious diseases have caused significant declines, sabotaging conservation efforts. Canine distemper virus (CDV) infections have increased in incidence in wildlife over the past four decades. Sympatric domestic dogs have been presumed to be the reservoirs of the virus for wildlife. A systematic review using Preferred Reporting Items for Systematic Reviews and Meta-Analyses 2020 guidelines was carried out to investigate CDV infections in wildlife in Africa, to 1) analyze the conservation concerns associated with the disease, 2) identify the dynamics of the virus across different ecoregions, and 3) ascertain the source of the virus for free-living wildlife. The database searches identified 65 articles relevant to the study questions and an additional 43 valuable for wider discussion of the topic area. Canine distemper outbreaks were reported to occur in wildlife in six African countries, with mortality rates between 30% and 94% across all species affected. Eleven wildlife species were identified as susceptible, 64% of which (7/11) are classified as threatened by the International Union for Conservation of Nature. Disease dynamics varied between ecoregions because of differences in land use; virus strains; climate change and concurrent infections; ecotones; domestic and wildlife population densities; wildlife monitoring capacity; and wildlife movement. Nine countries reported outbreaks in domestic dog populations in or near wildlife habitats, but none reported confirmed transmission to wildlife. Of 23 reports investigating the role of domestic dogs as CDV reservoirs, 14 (61%) concluded that domestic dogs acted as either reservoirs or sources of CDV for wildlife, four (17%) did not identify dogs as reservoirs, and five (22%) were not sure of the role played by domestic dogs. This review highlights the importance of integrating active CDV surveillance in wildlife conservation programs.

COVID-AMD database for coronavirus-infected animal models with comparative analysis tools

Respiratory infections caused by coronaviruses have posed serious and unpredictably public health threats; reliable animal models continue to be essential for advancing our understanding of the virus’s transmission, pathophysiology, and immunological mechanisms. In response to the critical need for centralized resources in coronavirus research, the COVID-AMD database (Coronavirus Disease Animal Model Database, https://www.uc-med.net/CoV-AMD) has been developed as an integrated platform. Data was gathered from public literature databases, refined and integrated using ETL (Extract, Transform, Load) methodology. After data conversion and cleaning, COVID-AMD was implemented using MySQL relational database with jQuery and JBoss. COVID-AMD database consolidates comprehensive data on animal models infected with various CoVs, including MERS-CoV, SARS-CoV, and SARS-CoV-2, featuring methodologies for establishing infection models, clinical features, and phenotypic data. It catalogs 869 animal models across 29 species and 312 virus strains, covering five diseases and ten infection routes. With global and advanced search capabilities, it facilitated data preprocessing, integration, analysis, and visualization, and provided tools for comparative analysis, model recommendation and omics analysis based on model and phenotype data. The open access to this rich repository aims to enable rapid identification of animal models for CoVs, thereby accelerating the development and clinical trial progression of prospective therapeutics and vaccines.

The antiviral activity of myricetin against pseudorabies virus through regulation of the type I interferon signaling pathway.

PRV, belonging to the Herpesviridae family, is an easily overlooked zoonotic pathogen that can threaten human health. The immunoprotective efficacy of conventional vaccines is significantly reduced due to the continuous mutation of the PRV genome, which constantly generates new viral strains. Therefore, there is a need to develop potent therapeutic drugs. PRV is capable of evading the host's natural immunity by suppressing the host's type I interferon signaling pathway, and the search for drugs that activate natural immunity can induce the body to produce type I IFN interferon and exert antiviral effects. Accordingly, the present study sought to identify active compounds from flavonoids that modulate the type I IFN interferon signaling pathway and thus inhibit the proliferation of PRV, which provides a new idea for the development of anti-PRV drugs from flavonoids that modulate the type I IFN interferon signaling pathway to enhance the body's antiviral immunity.

Molecular diagnostics using the QIAstat-Dx syndromic device for covering avian influenza pandemic preparedness

IntroductionA key factor in influenza pandemic preparedness is the ability to detect zoonotic influenza virus strains as they emerge in humans through spillover events, ideally before human-to-human transmission occurs. DesignIn this study, the utility of the QIAstat-Dx syndromic device for influenza surveillance was evaluated. Bioinformatic analysis was performed on all WHO-recommended influenza Candidate Vaccine Viruses (CVVs), including the common strains recommended for the 2023–2024 influenza vaccine composition in the northern hemisphere, and 16 different H5 highly pathogenic avian influenza virus (HPAIV) and two H9N2 low pathogenic avian influenza virus (LPAIV) strains. For laboratory validation, engineered gene fragments and real HPAIV and LPAIV samples were tested using the QIAstat-Dx Respiratory SARS-CoV-2 Panel. ResultsDuring the bioinformatic screening, common influenza strains were positive including influenza A subtypes, and all H5 HPAIV and LPAIV H9N2 were detected as Influenza A positive without subtype discrimination. In all cases, laboratory validation confirmed all bioinformatic results. ConclusionQIAstat-Dx can detect all tested potentially zoonotic influenza A virus strains, and discriminate them from human sesonal influenza A viruses, ensuring a correct diagnosis. Any tool available for surveillance and pandemic preparedness is essential for a rapid response to reduce healthcare costs and severity of future influenza pandemics.

Molecular characterization of human respiratory syncytial virus strains circulating among hospitalized children in Jordan

BackgroundHuman Respiratory Syncytial Virus (HRSV) is a primary cause of severe pediatric respiratory infections, particularly in infants and young children, often resulting in hospitalization. The virus possesses a high degree of mutagenic potential, contributing to significant antigenic diversity, which complicates immune responses and poses challenges for vaccine development and disease management. This study was conducted in Jordan from 2022 to 2023 to epidemiologically determine the prevalence and molecular characteristics of RSV.MethodsA total of 288 nasopharyngeal (NP) swabs were collected from hospitalized children at Prince Hamza Hospital, Amman, Jordan. All samples were screened for common viral and bacterial respiratory pathogens using PCR. A partial segment of the G gene of RSV was amplified for molecular characterization and phylogenetic tree analysis.ResultsViral and/or bacterial infection was identified in 71.9% (207/288) of the tested specimens. Among these, 35 samples (12.2%, 35/288) tested positive for RSV. Specific subgroup PCR analysis identified (25, 71.4%) RSV-A, (4, 11.4%) RSV-B, and (6, 17.1%) could not be identified using our set of primers. Phylogenetic tree analysis revealed that RSV-A ON1 and RSV-B BA9 genotype strains predominate in Jordan. We observed multiple substitutions in our studied sample which would drive variation in the level of antigenicity and pathogenicity of RSV. Glycosylation sites identified were consistent with previously reported studies.ConclusionThis study provides updated epidemiological data on the strains circulating in Amman, Jordan and their molecular characteristics. Continuous RSV surveillance informs vaccine development, guides public health interventions, and enables timely administration of prophylactic treatments, reducing the burden of RSV-related illness.

COORDINATION COMPOUNDS AS ANTIVIRALS AGAINST NEGLECTED TROPICAL DISEASES.

Neglected tropical viral diseases are a burden to social and economic welfare being responsible for higher pathogen-related mortality rates and chronic debilitating patient conditions. Climatic changes have widened up the infectibility ratio of such diseases, with autochthonous transmission in formerly temperate-to-cold environments. The slow-paced development of potential vaccines followed by the inexistence of antiviral drugs for such diseases considerably worsens the situation. Coordination compounds are a class of molecules that have been extensively explored as antiviral drugs for viruses such as poliovirus, HIV and, more recently, SARS-CoV-2, figuring as potential molecules to be explored and capitalized as antivirals against neglected viral strains. In this review the current efforts from the inorganic medicinal chemistry to address viral neglected tropical diseases, with emphasis to coordination compounds, is presented. Since many of neglected viruses are also arthropod-borne viruses, relying on a vector for transmission, coordination entities able to mitigate vectors are also presented as a parallel strategy to prevent and control such diseases.

Consortium of ‘consistent amino acid substitutions’ on influenza A (H1N1) viral proteins emerged at specific stages of viral infection: a big data analysis

Influenza A (H1N1) virus has been one of the most common threats to humankind since 1918. The viral genome is frequently substituted, leading to new strains and recurrent pandemics. Despite knowing the effects of single amino acid substitutions on individual viral proteins, the effects of collective substitutions on viral infection remain elusive. Here, we addressed whether the ‘consistent amino acid substitutions’ occur in a consortium on functional domains and protein-protein interaction (PPI) sites, impacting overall viral infection and host immune responses. By definition, ‘consistent substitutions’ occur on ‘all’ the Influenza A (H1N1) viral strains isolated in a particular year. To address this question, big protein data (563370 sequences and 9824 PPI) were analysed using multiple sequence alignment, text mining, protein structure analyses etc. A total of one hundred and five ‘consistent substitutions’ were mapped on the ten viral proteins of influenza A(H1N1) pdm09 strain. Fifty of those emerged on viral protein functional domains and PPIs, engaged in the specific stages of the viral infection, namely, i) cell surface entry and exit, ii) nuclear import, vRNP assembly, and nuclear export, and iii) antagonizing immune responses. For the first time, the study showed that a consortium of ‘consistent substitutions’ emerged on protein functional domains and PPIs, impacting specific stages of viral infection rather than a single protein and presumably navigating viral escape from human immune response.

Development of a genotype-matched Newcastle disease DNA vaccine candidate adjuvanted with IL-28b for the control of targeted velogenic strains of Newcastle disease virus in Africa

Newcastle disease virus (NDV) is an extremely contagious and deadly virus that affects numerous bird species, posing serious threats to poultry production on a global scale. In addition to implementing biosecurity practices in farming systems, vaccination remains the most effective means of controlling Newcastle disease (ND). However, while existing commercial vaccines provide some level of protection, the effectiveness of these vaccines can be questionable, particularly in field settings where the complexity of vaccination program implementation poses significant challenges, especially against virulent genotypes of NDV. A genotype-matched NDV DNA vaccine could potentially offer a more effective vaccination approach than currently available live attenuated vaccines. By being specifically tailored to match circulating strains, such a vaccine might improve efficacy and reduce the risk of vaccine failure due to genotype mismatch. To develop an alternative vaccine approach, two ND DNA vaccines were constructed in this study. Each vaccine developed in this study contains the fusion (F) and haemagglutinin-neuraminidase (HN) genes of a virulent NDV genotype VII isolate from Tanzania. Interferon lambda-3 (IFNλ3; IL-28b), which has demonstrated capacity to significantly enhance specific adaptive immune responses and decreased levels of inflammatory cytokines, as well as improved protective responses at a high viral challenge dose, was included in one of the developed vaccines. These plasmids were designated pTwist-F-HN-VII-IL28b and pTwist-F-HN-VII. The two plasmids differed in that pTwist-F-HN-VII-IL28b contained the cytokine adjuvant IL-28b. Transfection of cells and subsequent immunofluorescence assays indicated that both plasmids expressed high levels of NDV F-HN proteins. In vivo immunization demonstrated that chicks intramuscularly immunized with pTwist-F-HN-VII-IL28b exhibited significant immune responses compared to chicks immunized with pTwist-F-HN-VII or the commonly used LaSota vaccine (LaSota), which was used as a control. The protective efficacy of pTwist-F-HN-VII-IL28b was 80% after challenge with the highly virulent NDV strain ON148423, compared to 60% for chicks vaccinated using LaSota, and pTwist-F-HN-VII. The findings of this study indicate that IL-28b can be employed as a molecular adjuvant for NDV vaccines. This study represents a key milestone in Newcastle disease vaccine research, particularly in the development of a genotype-matched DNA vaccine candidate. Additionally, this study demonstrated that the combination of F, HN, and IL-28b elicits an efficacious immune response against virulent NDV strains.

Highly Conjugated Ergosterols with Anti-Influenza Virus Activity from the Marine-Derived Fungus Eutypella sp. F0219.

one rare 15-nor-cadinane sesquiterpenoid (1), one new chromene amide derivative (2), and one new highly conjugated ergosterol steroid(3), along with three known compounds (4-6) were isolated from the marine-derived fungus Eutypella sp. F0219. Their chemical structures including absolute configurations were established by HR-ESIMS, extensive 1D and 2D NMR investigations, and electronic circular dichroism (ECD) calculations. All compounds were evaluated for their anti-influenza A virus and anti-influenza B virus activities against the A/PR/8/34 (H1N1), ZX1109 (H1N1, oseltamivir resistant virus), HK68 (H3N2), and B/Florida/78/2015 strains. Compounds 3 and 4 showed significant antiviral activities against those four virus strains with EC50 values ranging from 2.07 to 11.3 μM. Most notably, compound 3 exhibited potent anti-influenza B virus activity against B/Florida/78/2015 strain with EC50 value of 2.27±1.76 μM, versus the postive control (oseltamivir, EC50 = 7.14±1.94 μM).

The Growing Phenomenon of ‘Frozen’ Virus Genome Sequences and Their Likely Origin in Research Facility Escapes

‘Frozen’ virus genome sequences are sampled from outbreaks and have unusually low sequence divergence when compared to genome sequences from historical strains. A growing number of ‘frozen’ virus genome sequences are being reported as virus genome sequencing becomes more common. Examples of ‘frozen’ sequences include the 1977 H1N1 ‘Russian’ flu; Venezuelan Equine Encephalitis Virus from Venezuela and Colombia in 1995; E71 sequences from a Hand, Foot and Mouth outbreak in 2007–2009 in China; and a polio strain isolated in 2014 from Anhui, China. The origin of these ‘frozen’ sequences has been attributed to escapes from research facilities and often appears to be associated with vaccine work. Consequently, a new paradigm for pathogen emergence appears in operation, that involves laboratory research or vaccine production which utilizes ‘live’ virus isolates of historical strains. The accidental release and re-emergence of such strains are straightforward to detect from their genome sequences and should spur the routine sequencing and publication of all known pathogenic viral strains undergoing experimentation, or being used for vaccine manufacture, in order to facilitate tracing. However, it is noted that novel pathogenic viruses accidentally released into the population from research facilities are harder to detect if their sequence has first not been made public, which should prompt the routine sequencing and reporting of all novel pathogenic viruses before experimentation.

Comparative analysis of European subtype tick-borne encephalitis virus strains isolated from patients from Eastern Siberia and Eastern and Northern Europe

Background. Isolation of strains from tick-borne encephalitis (TBE) patients proved that the European subtype tick-borne encephalitis virus (TBEV-Eur) in Siberia is involved in regional human infectious pathology and causes a clinical picture similar to Western TBE. However, a comparative analysis of the genomes of TBEV-Eur strains isolated from TBE patients in Eastern Siberia and Europe has not been carried out.The aim. Genome comparative analysis and search for virulence determinants in TBEV-Eur strains isolated from patients in Eastern Siberia and Northern and Eastern Europe.Materials and methods. In current work, TBEV-Eur strain 1G-98 from the collection of Scientific Сentre for Family Health and Human Reproduction Problems (GenBank Acc. No. KY069119) was used. The analysis also included all complete genome sequences of TBEV-Eur strains from patients submitted in GenBank database at the time the study began. Complete genome sequencing of strain 1G-98 was performed using the Sanger method. The virulence of the strain was assessed by intracerebral and subcutaneous infection of laboratory mice.Results. It has been shown that, according to the coding region of the genomes, the level of differences between TBEV-Eur strains from Siberia does not exceed the previously established maximum for this subtype of 3.1 %. The strain 1G-98, isolated from the blood of TBE patient from the Irkutsk region demonstrated high cerebral and peripheral activity. In this strain, D67G mutation in E protein DII domain was revealed, which could potentially be associated with virulence, and a long deletion in the variable part of the 3’-noncoding genome region, comparable in length to the highly virulent strain Hypr from Europe was found.Conclusions. For the first time, a comparative analysis of the genomes of TBEV-Eur strains from TBE patients from the Asian part of Russia and Europe was carried out showing their genetic similarity, and potential virulence determinants were identified. Key words: tick-borne encephalitis virus, European subtype, genome, amino acid sequence, virulence determinants