Virus Family Research Articles

Depth-related microbial communities and functional genes in alpine permafrost

<p>Permafrost microorganisms have received increased attention due to their critical role in biogeochemical cycles and the potential biosafety risks associated with climate warming. However, knowledge regarding the depth-related community structure and function of permafrost microorganisms remains limited. In this study, we employed metagenomic methods to investigate microbial communities, functional genes, and their controlling factors in alpine permafrost of the Shule River headwaters on the northeastern margin of the Qinghai-Tibet Plateau. A total of 287 metagenome-assembled genomes were constructed, representing 20 bacterial phyla and 1 archaeal phylum. Additionally, we identified <styled-content style-type="number">2079</styled-content> viral contigs spanning more than 14 viral families, with approximately 67% constituting previously unknown taxa, forming a unique virome in alpine permafrost compared to other regions. Significant variations in bacterial and viral compositions, along with their metabolic potentials, were observed across vertical profiles from the active layer to the permafrost table layer. Viral diversity showed an initial increase followed by a decrease, reaching the maximum at the depth of 90-140 cm. We identified abundant genomic capabilities related to carbon, nitrogen, and sulfur cycling. Moreover, our analysis revealed 60 auxiliary metabolic genes in viruses and 7,000 putative biosynthetic gene clusters for secondary metabolites from 21 prokaryotic phyla. Soil temperature emerged as the most significant environmental variable influencing the composition of microbial communities and functional genes, as well as the diversity of microbial communities. These results offer valuable insights into the potential functional transformations and biosafety risks mediated by permafrost microorganisms under future warming.</p>

ВИРУСЫ ЛЕТУЧИХ МЫШЕЙ, ОБЛАДАЮЩИХ ЗООНОЗНЫМ ПОТЕНЦИАЛОМ

In recent years, the study of bat viruses has become particularly relevant in light of the coronavirus pandemic and other major outbreaks of viral diseases, such as Ebola fever and the Zika virus. Bats are important reservoirs for many pathogens that can cause diseases in humans and animals. These mam-mals not only serve as primary sources of various infections but also play a key role in their transmission, making them a subject of increased interest for virologists and epidemiologists.This article attempts to systematize information about the most common viruses associated with bats on a global scale. It examines the main viral families circulating among bats, as well as their pathogenic properties and mechanisms of interaction with the host. Additionally, the article presents an overview of current research conducted in Kazakhstan regarding bat viruses. The relevance of these studies is ana-lyzed in the context of public health and the potential for preventing future outbreaks of viral diseases.Thus, this work emphasizes the significance of bats as biological indicators of ecosystem and human health, as well as their role in the epidemiology of infectious diseases.

Infectious Triggers of Cytokine Storm Syndromes: Herpes Virus Family (Non-EBV).

The herpesviruses are the most common infectious agents associated with both primary and secondary cytokine storm syndromes (CSS). While Epstein-Barr Virus (EBV) is most frequently reported in association with CSS, cytomegalovirus (CMV) and many other herpesviruses (e.g., herpes simplex virus, varicella zoster virus, and human herpesviruses 6 and 8) are clearly associated with CSS in children and adults. Immunocompromised hosts, whether due to primary immunodeficiency or secondary immune compromise (e.g., solid organ or stem cell transplantation), appear to be at particularly increased risk of herpesvirus-associated CSS. In this chapter, the association of the non-EBV herpesviruses with CSS will be discussed, including predisposing factors and treatment considerations.

Prevalence of Cardiovascular Involvement in Patients With COVID-19 Disease

Background: Coronaviruses are a huge family of viruses that lead to various diseases from a common cold to more unadorned illnesses for example SARS-CoV and MERS-CoV. Common symptoms of this infection include respiratory symptoms. In addition, this disease can also manifest with an acute cardiovascular (CV) syndrome. The aim of this study was to determine the frequency of CV involvement in patients with COVID-19 disease admitted to Afzalipour Hospital in Kerman. Methods: In this study, all patients who were diagnosed with COVID-19 disease and were hospitalized and monitored due to disease conditions were eligible to enter the study. At the beginning of the patient’s hospitalization, the patients’ vital signs were recorded and the first 12-lead electrocardiography was taken. Then, patients underwent cardiac monitoring and echocardiography at the beginning of hospitalization and afterwards during the course of disease. Preliminary tests including biochemistry, blood cell count, C-reactive protein (CRP) and erythrocyte sedimentation rate (ESR) and troponin were also performed for patients. Results: The mean age of patients with COVID-19 was 55.63 years and 20.2% of them had a history of heart disease. More than half of these patients were men. Ejection fraction was normal in 87.8% of patients. There was a significant relationship between diastolic dysfunction grade and the history of heart disease (P=0.02). Conclusion: Since the incidence of underlying diseases such as diabetes, hypertension and cardiac disorders can raise the risk of corona viruses’ disease and also increase the mortality rate of this disease in these people, it is suggested that more attention be paid to the observance of health protocols for people with underlying diseases, and that people with underlying diseases be given priority in vaccinating against this disease.

Generation of Viral Particles with Brain Cell-Specific Tropism by Pseudotyping HIV-1 with the Zika Virus E Protein.

Flaviviruses are a family of RNA viruses that includes many known pathogens, such as Zika virus (ZIKV), West Nile virus (WNV), dengue virus (DENV), and yellow fever virus (YFV). A pseudotype is an artificial virus particle created in vitro by incorporating the flavivirus envelope proteins into the structure of, for example, a retrovirus such as human immunodeficiency virus type-1 (HIV-1). They can be a useful tool in virology for understanding the biology of flaviviruses, evaluating immune responses, developing antiviral strategies but can also be used as vectors for gene transfer experiments. This protocol describes the generation of a ZIKV/HIV-1 pseudotype developed as a new tool for infecting cells derived from a highly malignant brain tumor: glioblastoma multiforme grade 4.

A tale of caution: How endogenous viral elements affect virus discovery in transcriptomic data.

Large-scale metagenomic and -transcriptomic studies have revolutionized our understanding of viral diversity and abundance. In contrast, endogenous viral elements (EVEs), remnants of viral sequences integrated into host genomes, have received limited attention in the context of virus discovery, especially in RNA-Seq data. EVEs resemble their original viruses, a challenge that makes distinguishing between active infections and integrated remnants difficult, affecting virus classification and biases downstream analyses. Here, we systematically assess the effects of EVEs on a prototypical virus discovery pipeline, evaluate their impact on data integrity and classification accuracy, and provide some recommendations for better practices. We examined EVEs and exogenous viral sequences linked to Orthomyxoviridae, a diverse family of negative-sense segmented RNA viruses, in 13 genomic and 538 transcriptomic datasets of Culicinae mosquitoes. Our analysis revealed a substantial number of viral sequences in transcriptomic datasets. However, a significant portion appeared not to be exogenous viruses but transcripts derived from EVEs. Distinguishing between transcribed EVEs and exogenous virus sequences was especially difficult in samples with low viral abundance. For example, three transcribed EVEs showed full-length segments, devoid of frameshift and nonsense mutations, exhibiting sufficient mean read depths that qualify them as exogenous virus hits. Mapping reads on a host genome containing EVEs before assembly somewhat alleviated the EVE burden, but it led to a drastic reduction of viral hits and reduced quality of assemblies, especially in regions of the viral genome relatively similar to EVEs. Our study highlights that our knowledge of the genetic diversity of viruses can be altered by the underestimated presence of EVEs in transcriptomic datasets, leading to false positives and altered or missing sequence information. Thus, recognizing and addressing the influence of EVEs in virus discovery pipelines will be key in enhancing our ability to capture the full spectrum of viral diversity.

Effects of Lamiaceae family plants and their bioactive ingredients on coronavirus-induced lung inflammation.

Coronaviruses (CoVs) are a family of viruses that cause infection in respiratory and intestinal systems. Different types of CoVs, those responsible for the SARS-CoV and the new global pandemic of coronavirus disease 2019 in people, have been found. Some plants were used as food additives: spices and dietary and/or medicinal purposes in folk medicine. We aimed to provide evidence about possible effects of two Lamiaceae family plants on control or treatment of CoVs-induced inflammation. The keywords including coronaviruses, Thymus vulgaris, Zataria multiflora, thymol, carvacrol, antivirus, and anti-inflammatory and antioxidant effects were searched in various databases such as PubMed, Web of Sciences (ISI), and Google Scholar until September 2022. The medicinal herbs and their main ingredients, thymol and carvacrol, showed antiviral properties and reduced inflammatory mediators, including IL-1β; IL-6, and TNF-α, at both gene and protein levels but increased the levels of IFN-γ in the serum as anti-inflammatory cytokine. These medicinal herbs and their constituents also reduce oxidative stress and enhance antioxidant capacity. The results of molecular docking analyses also indicated that polyphenol components such as thymol, carvone, and carvacrol could inhibit the entry of the viruses into the host cells in molecular docking analyses. The antiviral, anti-inflammatory, and antioxidant effects of these plants may be due to actions of their phenolic compounds that modulate immune response and may be useful in the control and treatment of CoV-induced lung disorder.

Differences in the Clinical Manifestations and Host Immune Responses to SARS-CoV-2 Variants in Children Compared to Adults.

The COVID-19 pandemic challenged the medical field to rapidly identify and implement new approaches to the diagnosis, treatment and prevention of SARS-CoV-2 infections. The scientific community also needed to rapidly initiate basic, translational, clinical and epidemiological studies to understand the pathophysiology of this new family of viruses, which continues to evolve with the emergence of new genetic variants. One of the earliest clinical observations that provided a framework for the research was the finding that, in contrast to most other respiratory viruses, children developed less severe acute and post-acute disease compared to adults. Although the clinical manifestations of SARS-CoV-2 infection changed with each new wave of the pandemic, which was dominated by evolving viral variants, the differences in severity between children and adults persisted. Comparative immunologic studies have shown that children mount a more vigorous local innate response characterized by the activation of interferon pathways and recruitment of innate cells to the mucosa, which may mitigate against the hyperinflammatory adaptive response and systemic cytokine release that likely contributed to more severe outcomes including acute respiratory distress syndrome in adults. In this review, the clinical manifestations and immunologic responses in children during the different waves of COVID-19 are discussed.

An Update on SARS-CoV-2 Clinical Trial Results-What We Can Learn for the Next Pandemic.

The coronavirus disease 2019 (COVID-19) pandemic has claimed over 7 million lives worldwide, providing a stark reminder of the importance of pandemic preparedness. Due to the lack of approved antiviral drugs effective against coronaviruses at the start of the pandemic, the world largely relied on repurposed efforts. Here, we summarise results from randomised controlled trials to date, as well as selected in vitro data of directly acting antivirals, host-targeting antivirals, and immunomodulatory drugs. Overall, repurposing efforts evaluating directly acting antivirals targeting other viral families were largely unsuccessful, whereas several immunomodulatory drugs led to clinical improvement in hospitalised patients with severe disease. In addition, accelerated drug discovery efforts during the pandemic progressed to multiple novel directly acting antivirals with clinical efficacy, including small molecule inhibitors and monoclonal antibodies. We argue that large-scale investment is required to prepare for future pandemics; both to develop an arsenal of broad-spectrum antivirals beyond coronaviruses and build worldwide clinical trial networks that can be rapidly utilised.

Prevalence of Torque Teno Virus (TTV) in Blood Donor from Baghdad-Iraq

Background: In 1997, Torque Teno virus (TTV) discovered for the first time in Japanese patients who suffer from hepatitis. Then, it is detected in healthy individuals without causing harmful effects. Also, it is a part of our microbiome, with a high rate in all populations. This virus belong to a large viral family called Anelloviridae. Today, there are many suggestions to use TTV as a novel biomarker for medical and environmental purposes.
 Objective: To determine the rate of TTV infection in Iraqi blood donors. And evaluate any association with demographic and risk factors.
 Methods: This cross-sectional study conducted on serum samples from 359 participants who attended the blood donation unit of Al-Imammain Al-Kadhimain Medical City Hospital and National Blood Transfusion Center in Baghdad. The study sample consists of 351 males and only 8 females; their mean age is (36.04 ± 9.35 SD). For a period from November 2022 to January 2023. A nested polymerase chain reaction (PCR) was used to detect TTV untranslated region.
 Results: The TTV virus was detected in 93.9% (337 out of 359) of blood donors. However, no significant association was found between demographic data (sex, age) and risk factors such as history of (medical surgery, tattooing, cupping practice, marital status, multiple sexual partners, animal husbandry , travel history), under line medical condition (diabetes mellitus and hypertension), viral hepatitis co-infection and occupation with TTV infection rate.
 Conclusion: This study showed a high prevalence of TTV among healthy blood donors with no significant association with demographic data and risk factors. These results support that TTV as a part of the human virobiome and normally found in the majority of populations.

Investigating the Effect of Social Support, Healthy Behavior, and Religious Coping on Free COVID-19 Pandemic through Immunity in West Sumatera, Indonesia

The coronaviruses are a large family of viruses that cause disease in humans and animals. Data from West Sumatra captures that until December 31, 2020, there were 23,441 confirmed cases of COVID-19 and 21,601 people recovered. Does the recovery from COVID-19 have anything to do with social support, health behaviors that are always recommended by Regional Leaders in West Sumatra, Religious coping for the people of West Sumatra which affects the free pandemic of COVID-19? To answer this phenomenon, it is necessary to investigate the effect of social support, healthy behavior, religious coping on COVID-19 Pandemic free through immunity in West Sumatra, Indonesia.as a population, with the Slovin formula sample Becomes 174 respondents. The recovery of COVID-19, whether it has to do with social support, religious coping in which West Sumatra, and health behaviors that are always recommended by the Regional Leadership in the West Sumatera, give rise to immunity so that it influences the pandemic COVID-19. The research model used is a mixed-method, by combining quantitative with SEM software AMOS-24 and qualitative with interviews with respondents and the community as well as the COVID-19 West Sumatera Cluster Team. The result indicates that changes in immunity are influenced by religious coping, healthy behavior and social support is 95.60%, the remaining 3.40% is influenced by other variables not included in this study. changes in the Free COVID-19 pandemics are influenced by 100% religious coping, healthy behavior, social support and immunity.

Pediatric central nervous system infections in the Amazon: clinical and laboratory profiles.

Central nervous system (CNS) infections are important causes of mortality and morbidity in children, and they are related to severe problems such as hearing loss, neurological sequelae, and death. The objective was to describe clinical and laboratory exam profiles of children who were diagnosed with CNS infections. We conducted a cross-sectional study based on medical records, which included pediatric patients aged from 3 months to 15 years, with a clinical suspicion of CNS infection between January 2014 to December 2019. The pathogens were confirmed in cerebrospinal fluid (CSF) samples using Gram staining, cell culture, molecular diagnostics (PCR and qPCR), and serology. Out of the 689 enrolled patients, 108 (15.6%) had laboratory-confirmed infections in CSF. The most common bacterial pathogens isolated from the culture were Neisseria meningitidis serogroup C in 19, Streptococcus pneumoniae in 11, and Haemophilus influenzae in seven samples. The viruses identified were Enterovirus, Cytomegalovirus, Varicella-zoster virus, Epstein-Barr virus, and arbovirus. No patient was found to be positive for Herpes simplex virus 1 and 2. Patients with viral infections showed altered levels of consciousness (p = 0.001) when compared to bacterial infections. This study shows the presence of important vaccine-preventable pathogens, and different families of viruses causing CNS infections in the pediatric patients of Manaus.

A meta‐analysis exploring associations between habitat degradation and Neotropical bat virus prevalence and seroprevalence

Habitat degradation can increase zoonotic disease risks by altering infection dynamics in wildlife and increasing wildlife–human interactions. Bats are an important taxonomic group to consider these effects, because they harbour many relevant zoonotic viruses and have species‐ and context‐dependent responses to degradation that could affect zoonotic virus dynamics. Yet our understanding of the associations between habitat degradation and bat virus prevalence and seroprevalence are limited to a small number of studies, which often differ in the bats or viruses sampled, the study region, and methodology. To develop a broad understanding of the associations between bat viruses and habitat degradation, we conducted an initial phylogenetic meta‐analysis that combines published prevalence and seroprevalence (‘(sero)prevalence') with remote‐sensing habitat degradation data. Our dataset includes 588 unique records of (sero)prevalence across 16 studies, 64 bat species, and five virus families. We quantified the overall strength and direction of the relationship between habitat degradation and bat virus outcomes and tested how this relationship is moderated by the time between habitat degradation and bat sampling and by ecological traits of bat hosts while controlling for phylogenetic non‐independence among bat species. We found no effect of degradation on prevalence overall, although a weak effect may exist when forest loss occurs the year prior to bat sampling. In contrast, we detected a negative but weak association between degradation and seroprevalence overall that was strengthened when forest loss occurred the year prior to bat sampling. No bat traits that we investigated interacted with habitat degradation to impact virus outcomes, suggesting observed trends are independent of these traits. Biases in our initial dataset highlight opportunities for future work; prevalence was highly zero‐inflated, and seroprevalence was dominated by Desmodus rotundus and rabies virus. These findings and subsequent analyses will improve our understanding of how global change affects host–pathogen dynamics.

ICTV Virus Taxonomy Profile: Tulasviridae 2023.

Tulasviridae is a family of ambisense RNA viruses with genomes of about 12.2 kb that have been found in fungi. The tulasvirid genome is nonsegmented and contains three open reading frames (ORFs) that encode a nucleoprotein (NP), a large (L) protein containing an RNA-directed RNA polymerase (RdRP) domain, and a protein of unknown function (X). This is a summary of the International Committee on Taxonomy of Viruses (ICTV) Report on the family Tulasviridae, which is available at ictv.global/report/tulasviridae.

ICTV Virus Taxonomy Profile: Cruliviridae 2023.

Cruliviridae is a family of negative-sense RNA viruses with genomes of 10.8-11.5 kb that have been found in crustaceans. The crulivirid genome consists of three RNA segments with ORFs that encode a nucleoprotein (NP), a glycoprotein (GP), a large (L) protein containing an RNA-directed RNA polymerase (RdRP) domain, and in some family members, a zinc-finger (Z) protein of unknown function. This is a summary of the International Committee on Taxonomy of Viruses (ICTV) Report on the family Cruliviridae, which is available at ictv.global/report/cruliviridae.

ICTV Virus Taxonomy Profile: Wupedeviridae 2023.

Wupedeviridae is a family of negative-sense RNA viruses with genomes of about 20.5 kb that have been found in myriapods. The wupedevirid genome consists of three monocistronic RNA segments with open reading frames (ORFs) that encode a nucleoprotein (NP), a glycoprotein (GP), and a large (L) protein containing an RNA-directed RNA polymerase (RdRP) domain. This is a summary of the International Committee on Taxonomy of Viruses (ICTV) Report on the family Wupedeviridae, which is available at ictv.global/report/wupedeviridae.

Limited high-throughput screening compatibility of the phenuivirus cap-binding domain

Bunyaviruses constitute a large and diverse group of viruses encompassing many emerging pathogens, such as Rift Valley fever virus (family Phenuiviridae), with public and veterinary health relevance but with very limited medical countermeasures are available. For the development of antiviral strategies, the identification and validation of virus-specific targets would be of high value. The cap-snatching mechanism is an essential process in the life cycle of bunyaviruses to produce capped mRNAs, which are then recognized and translated into viral proteins by the host cell translation machinery. Cap-snatching involves cap-binding as well as endonuclease functions and both activities have been demonstrated to be druggable in related influenza viruses. Here, we explore the suitability of the phenuivirus cap-binding function as a target in medium- and high-throughput drug discovery approaches. We developed a range of in vitro assays aiming to detect the interaction between the cap-binding domain (CBD) and the analogue of its natural cap-ligand m7GTP. However, constricted by its shallow binding pocket and low affinity for m7GTP, we conclude that the CBD has limited small molecule targeting potential using classical in vitro drug discovery approaches.

Research progress of Monkeypox and its current prevention and treatment options

Monkeypox (MPX), a smallpox-like zoonotic infectious disease caused by the monkeypox virus (MPXV), was first detected in laboratory animals in 1958. Since the eradication of the smallpox virus in the 80s of the 20th century, MPXV has become one of the members of the pox virus family with the greatest public health impact, mainly in the central and western regions of Africa. However, since May 7, 2022, human cases of MPXV infection have been reported in several countries outside endemic areas in Africa. As of July 15, 2022, based on the latest data from the US Centers for Disease Control and Prevention, there have been at least 1,814 suspected or confirmed cases in the US, and a total of 12,556 confirmed cases have been reported in 68 countries around the world. The World Health Organization (WHO) has said that the spread of MPX epidemics in more than 70 countries is an "extraordinary" situation, listing it as a global emergency. This paper mainly reviews the physicochemical characteristics, gene characteristics, pathogenic mechanism, transmission mechanism, and clinical features of MPXV etiology. It also discusses and summarizes the current prevention and treatment options, in order to provide reference for the current exploration of monkeypox prevention and treatment.

ICTV Virus Taxonomy Profile: Mypoviridae 2023.

Mypoviridae is a family of negative-sense RNA viruses with genomes of about 16.0 kb that have been found in myriapods. The mypovirid genome consists of three monocistronic RNA segments that encode a nucleoprotein (NP), a glycoprotein (GP), and a large (L) protein containing an RNA-directed RNA polymerase (RdRP) domain. This is a summary of the International Committee on Taxonomy of Viruses (ICTV) Report on the family Mypoviridae, which is available at: ictv.global/report/mypoviridae.

Circulation of picobirnavirus in Neotropical free-ranging mammals.

Picobirnavirus (PBV) is a family of non-enveloped double-stranded RNA viruses with bisegmented genomes. Segment 1 encodes the capsid protein and segment 2 encodes RNA-dependent RNA polymerase. They exhibit high genomic heterogeneity and infect a wide range of vertebrate hosts, including humans. The objective of this study was to expand our knowledge of the circulation of PBV in free-living animals from two regions (Brazil and Argentina) of the Atlantic Forest. Fecal samples were analyzed from free-living animals: tapir, brocket deer, peccary, and different species of rodents and marsupials. A total of 133 samples were collected and analyzed by RT-PCR, of which 44 (33.08%) were PBV-positive. Nine amplicons were sequenced, five species from Argentina and four from Brazil, and phylogenetic analysis was performed. The nucleotide and amino acid identities of the PBV strains detected in animals from Argentina and Brazil were between 66.3% and 82.5% and between 55.3% and 74.2%, respectively. The analysed strains presented conserved nucleotide blocks without distinction of the host species. The phylogenetic tree showed that PBV strains from Atlantic Forest animals belonging to genogroup I were grouped into different clusters, without defining groups according to host species (human or animal) or the geographical area of detection. This is the first study on PBV in free-living animals in the Atlantic Forest. Our analysis suggested that PBV strains can infect different animal species, leading to PBV transmission between animals and humans. This reinforces the hypothesis of previous crossover points in the ecology and evolution of heterologous PBV strains.