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Amplicon sequencing is an effective and increasingly applied method for studying viral communities in the environment. Here, we present vAMPirus, a user‐friendly, comprehensive, and versatile DNA and RNA virus amplicon sequence analysis program, designed to support investigators in exploring virus amplicon sequencing data and running informed, reproducible analyses. vAMPirus intakes raw virus amplicon libraries and, by default, performs nucleotide‐ and amino acid‐based analyses to produce results such as sequence abundance information, taxonomic classifications, phylogenies and community diversity metrics. The vAMPirus analytical framework leverages 16 different opensource tools and provides optional approaches that can increase the ratio of biological signal‐to‐noise and thereby reveal patterns that would have otherwise been masked. Here, we validate the vAMPirus analytical framework and illustrate its implementation as a general virus amplicon sequencing workflow by recapitulating findings from two previously published double‐stranded DNA virus datasets. As a case study, we also apply the program to explore the diversity and distribution of a coral reef‐associated RNA virus. vAMPirus is streamlined within Nextflow, offering straightforward scalability, standardization and communication of virus lineage‐specific analyses. The vAMPirus framework is designed to be adaptable; community‐driven analytical standards will continue to be incorporated as the field advances. vAMPirus supports researchers in revealing patterns of virus diversity and population dynamics in nature, while promoting study reproducibility and comparability. [ABSTRACT FROM AUTHOR]

Background and Purpose: There is a need for effective anti‐COVID‐19 treatments, mainly for individuals at risk of severe disease such as the elderly and the immunosuppressed. Drug repositioning has proved effective in identifying drugs that can find a new application for the control of coronavirus disease, in particular COVID‐19. The purpose of the present study was to find synergistic antiviral combinations for COVID‐19 based on lethal mutagenesis. Experimental Approach: The effect of combinations of remdesivir and ribavirin on the infectivity of SARS‐CoV‐2 in cell culture has been tested. Viral populations were monitored by ultra‐deep sequencing, and the decrease of infectivity as a result of the treatment was measured. Key Results: Remdesivir and ribavirin exerted a synergistic inhibitory activity against SARS‐CoV‐2, quantified both by CompuSyn (Chou‐Talalay method) and Synergy Finder (ZIP‐score model). In serial passage experiments, virus extinction was readily achieved with remdesivir‐ribavirin combinations at concentrations well below their cytotoxic 50 value, but not with the drugs used individually. Deep sequencing of treated viral populations showed that remdesivir, ribavirin, and their combinations evoked significant increases of the number of viral mutations and haplotypes, as well as modification of diversity indices that characterize viral quasi‐species. Conclusion and Implications: SARS‐CoV‐2 extinction can be achieved by synergistic combination treatments based on lethal mutagenesis. In addition, the results offer prospects of triple drug treatments for effective SARS‐CoV‐2 suppression. [ABSTRACT FROM AUTHOR]

Fig mosaic disease (FMD) poses a significant threat to fig (Ficus carica) trees globally. Fig mosaic virus (Emaravirus fici, Family Fimoviridae) is one of the main causes involved in FMD. E. fici has been reported in many countries, including Iran. This research investigated the genetic diversity and distribution of this virus in Kermanshah Province, the third fig‐producing region in Iran. In 2021 and 2022, 128 samples, mainly displaying FMD symptoms, were collected from fig trees across nine counties. Using DAS‐ELISA with polyclonal antibodies, 86 samples tested positive for fig mosaic virus. The 2‐year‐old healthy fig saplings grafted with scions from infected trees exhibited mosaic symptoms and tested positive for the virus in DAS‐ELISA. Reverse transcription‐polymerase chain reaction (RT‐PCR) by RdRp‐specific primers (E5‐s and E5‐a) also amplified a DNA fragment with the expected size of about 302 bp from the ELISA‐positive samples. Five of the 12 symptomless samples showed positive results in both DAS‐ELISA and RT‐PCR. This indicates that the absence of symptoms in propagation sources does not imply that they are virus‐free. Nucleotide sequences of RT‐PCR products confirmed the fig mosaic virus infection. BLAST analysis of 20 samples (GenBank accession numbers OQ552535 to OQ552554) revealed that 19 sequences show high nucleotide identity (93.4%–96.8%) with an isolate from Lorestan Province, Iran (GenBank accession number KT732024). Notably, isolate FM203 showed distinct genetic divergence (86.6%–90.2% nucleotide identity) and shared similarities with some other Iranian isolates, including those from Kermanshah and Mazandaran provinces. Phylogenetic analysis grouped most isolates with the Lorestan isolate, while FM203 was placed in a separate cluster. This study highlighted the widespread presence of fig mosaic virus in Kermanshah Province, emphasizing varying infection rates across different counties, with Dalahoo County (Rijab) showing the highest prevalence. [ABSTRACT FROM AUTHOR]

A virus discovery investigation using high‐throughput sequencing in sugarcane samples from Ethiopia revealed the presence of sugarcane mild mosaic virus (SCMMV, genus Ampelovirus) and sugarcane umbra‐like virus (SULV, genus Umbravirus). The genome sequences of two isolates of SCMMV and one SULV were determined. The sequences of the two SCMMV isolates were 13,005 nucleotides in length and showed ~73.5% nucleotide identity along the genome and ~90.2, 96.8, and 90.4% amino acid sequence identity among each other in the RdRp, CP, and HSP70h, respectively. Isolate SCMMV ET2 showed a close relationship to group A isolates from Colombia, the USA, and the Philippines, with amino acid sequence identity of the predicted virus proteins in the range of 94–98.9%. Conversely, SCMMV ET1 shared a closer relationship with group B isolates from Colombia, Ivory Coast, and Argentina, exhibiting a 93–99% amino acid sequence identity. The complete genome sequence of SULV, comprising 3041 nucleotides, exhibited the highest identity with its counterpart from South Africa (MN868593). These findings contribute to expanding our understanding of the viral diversity within the sugarcane crop in Ethiopia. [ABSTRACT FROM AUTHOR]

Dengue, a mosquito‐borne viral disease, poses a significant public health challenge in Pakistan, with a significant outbreak in 2023, prompting our investigation into the serotype and genomic diversity of the dengue virus (DENV). NS‐1 positive blood samples from 153 patients were referred to the National Institute of Health, Pakistan, between July and October 2023. Among these, 98 (64.1%) tested positive using multiplex real‐time PCR, with higher prevalence among males (65.8%) and individuals aged 31‐40. Serotyping revealed DENV‐1 as the predominant serotype (84.7%), followed by DENV‐2 (15.3%). Whole‐genome sequencing of 18 samples (DENV‐1 = 17, DENV‐2 = 01) showed that DENV‐1 (genotype III) samples were closely related (>99%) to Pakistan outbreak samples (2022), and approx. > 98% with USA (2022), Singapore and China (2016), Bangladesh (2017), and Pakistan (2019). The DENV‐2 sequence (cosmopolitan genotype; clade IVA) shared genetic similarity with Pakistan outbreak sequences (2022), approx. > 99% with China and Singapore (2018−2019) and showed divergence from Pakistan sequences (2008−2013). No coinfection with dengue serotypes or other viruses were observed. Comparisons with previous DENV‐1 sequences highlighted genetic variations affecting viral replication efficiency (NS2B:K55R) and infectivity (E:M272T). These findings contribute to dengue epidemiology understanding and underscore the importance of ongoing genomic surveillance for future outbreak responses in Pakistan. [ABSTRACT FROM AUTHOR]

Dried blood spots (DBS) have emerged as a promising alternative to traditional venous blood for hepatitis C virus (HCV) testing. However, their capacity to accurately reflect the genetic diversity of HCV remains poorly understood. We employed deep sequencing and advanced phylogenetic analyses on paired plasma and DBS samples from two common subtypes to evaluate the suitability of DBS for genomic surveillance. Results demonstrated that DBS captured equivalent viral diversity compared to plasma with no phylogenetic discordance observed. The ability of DBS to accurately reflect the profile of viral genetic diversity suggests it may be a promising avenue for future surveillance efforts to curb HCV outbreaks. [ABSTRACT FROM AUTHOR]

Invasions of arthropod vectors and viruses are the main factors associated with emerging plant viral diseases. The presence of the Banana bunchy top virus (BBTV, genus Babuvirus), an aphid‐transmitted virus responsible for the banana bunchy top disease (BBTD), was first confirmed in 2008 in the South region of Cameroon. This study reports on surveys over 14 years to determine the status of BBTV spread and virus diversity in Cameroon. A total of 544 fields extending through 81 districts in 7 regions were surveyed in 5 phases: (1) 2009–10, (2) 2012, (3) 2013–14, (4) 2016–17, and (5) 2022. BBTV was detected in 36 sites, all located in the Ambam district in the South region, with an incidence in the virus‐affected fields ranging from 5% to 40%, with an average incidence of 14.8%. The findings indicate BBTV expansion from the location of first detection in 2008 to about 4–25 km in all directions, with the virus spread range of about 700 km2, as of the last survey in 2022. Phylogenetic analysis using complete nucleotide sequences of the BBTV‐R and BBTV‐S gene aligned Cameroon isolates with the sub‐Saharan Africa subgroup of the Pacific‐Indian Oceans (PIO) group of BBTV isolates, suggesting a likely virus invasion from neighbouring central African countries where BBTV presence had been reported in the 1980s. Knowledge of BBTV distribution provided through the detection and delimiting surveys has contributed to the efficient targeting of interventions to limit the expansion of an emerging virus threat to banana production in Cameroon. [ABSTRACT FROM AUTHOR]

Insect‐specific viruses (ISVs) can affect insect health and fitness, but can also interact with other insect‐associated microorganisms. Despite this, ISVs are often studied in isolation from each other, in laboratory populations. Consequently, their diversity, prevalence and associations with other viruses in field populations are less known, yet these parameters are important to understanding virus epidemiology. To help address this knowledge gap, we assessed the diversity, prevalence and coinfections of three ISVs (horizontally transmitted cripavirus, biparentally transmitted sigmavirus and maternally transmitted iflavirus) in 29 field populations of Queensland fruit fly, Australia's most significant horticultural pest, in the context of their different transmission modes. We detected new virus variant diversity. In contrast to the very high virus prevalence in laboratory populations, 46.8% of 293 field flies carried one virus and 4.8% had two viruses. Cripavirus and sigmavirus occurred in all regions, while iflavirus was restricted to subtropical and tropical regions. Cripavirus was most prevalent (37.5%), followed by sigmavirus (13.7%) and iflavirus (4.4%). Cripavirus coinfected some flies with either one of the two vertically transmitted viruses. However, sigmavirus did not coinfect individuals with iflavirus. Three different modelling approaches detected negative association patterns between sigmavirus and iflavirus, consistent with the absence of such coinfections in laboratory populations. This may be linked with their maternal transmission and the ineffective paternal transmission of sigmavirus. Furthermore, we found that, unlike sigmavirus and iflavirus, cripavirus load was higher in laboratory than field flies. Laboratory and mass‐rearing conditions may increase ISV prevalence and load due to increased transmission opportunities. We conclude that a combination of field and laboratory studies is needed to uncover ISV interactions and further our understanding of ISV epidemiology. [ABSTRACT FROM AUTHOR]

Viral infections on cucurbit fields can cause major economic losses. Monitoring of the main producing areas is essential to identify both prevalent and emerging viruses. For two consecutive years (2019–2020), the presence and molecular diversity of nine aphid‐ and whitefly‐transmitted viruses in the main cucurbit‐producing areas of the Spanish Mediterranean basin and other important regions were studied. In analyses of symptomatic plants, watermelon mosaic virus (WMV), cucurbit aphid‐borne yellows virus (CABYV) and cucumber mosaic virus (CMV) were found to be prevalent in all the monitored areas, regardless of the crop and the farming conditions. Moroccan watermelon mosaic virus (MWMV) and tomato leaf curl New Delhi virus (ToLCNDV) were also found at lower rates, mainly in mixed infections with WMV. Phylogenetic analyses were conducted to determine the molecular variability of the different isolates. Whereas the sequences of CABYV, MWMV and ToLCNDV isolates all clustered within their corresponding Mediterranean clade, new viral variants of WMV and CMV were found. Seven new WMV profiles and a reassorting CMV isolate (IB‐IB‐IA) were observed. Moreover, the complete genome of the newly described WMV isolates was sequenced. Further studies should be done to determine if these new variants spread to new areas and if they can overcome the previously described resistances. [ABSTRACT FROM AUTHOR]

Tick‐associated viruses remain a substantial zoonotic risk worldwide, so knowledge of the diversity of tick viruses has potential health consequences. Despite their importance, large amounts of sequences in public data sets from tick meta‐genomic and ‐transcriptomic projects remain unannotated, sequence data that could contain undocumented viruses. Through data mining and bioinformatic analysis of more than 37,800 public meta‐genomic and ‐transcriptomic data sets, we found 83 unannotated contigs exhibiting high identity with known tick viruses. These putative viral contigs were classified into three RNA viral families (Alphatetraviridae, Orthomyxoviridae and Chuviridae) and one DNA viral family (Asfarviridae). After manual checking of quality and dissimilarity towards other sequences in the data set, these 83 contigs were reduced to five contigs in the Alphatetraviridae from four putative viruses, four in the Orthomyxoviridae from two putative viruses and one in the Chuviridae which clustered with known tick‐associated viruses, forming a separate clade within the viral families. We further attempted to assess which previously known tick viruses likely represent zoonotic risks and thus deserve further investigation. We ranked the human infection potential of 133 known tick‐associated viruses using a genome composition‐based machine learning model. We found five high‐risk tick‐associated viruses (Langat virus, Lonestar tick chuvirus 1, Grotenhout virus, Taggert virus and Johnston Atoll virus) that have not been known to infect human and two viral families (Nairoviridae and Phenuiviridae) that contain a large proportion of potential zoonotic tick‐associated viruses. This adds to the knowledge of tick virus diversity and highlights the importance of surveillance of newly emerging tick‐associated diseases. [ABSTRACT FROM AUTHOR]

Following the discovery of Acanthamoeba polyphaga mimivirus, diverse giant viruses have been isolated. However, only a small fraction of these isolates have been completely sequenced, limiting our understanding of the genomic diversity of giant viruses. MinION is a portable and low‐cost long‐read sequencer that can be readily used in a laboratory. Although MinION provides highly error‐prone reads that require correction through additional short‐read sequencing, recent studies assembled high‐quality microbial genomes only using MinION sequencing. Here, we evaluated the accuracy of MinION‐only genome assemblies for giant viruses by re‐sequencing a prototype marseillevirus. Assembled genomes presented over 99.98% identity to the reference genome with a few gaps, demonstrating a high accuracy of the MinION‐only assembly. As a proof of concept, we de novo assembled five newly isolated viruses. Average nucleotide identities to their closest known relatives suggest that the isolates represent new species of marseillevirus, pithovirus and mimivirus. The assembly of subsampled reads demonstrated that their taxonomy and genomic composition could be analysed at the 50× sequencing coverage. We also identified a pithovirus gene whose homologues were detected only in metagenome‐derived relatives. Collectively, we propose that MinION‐only assembly is an effective approach to rapidly perform a genome‐wide analysis of isolated giant viruses. [ABSTRACT FROM AUTHOR]

The impact and frequency of infectious disease outbreaks demonstrate the need for timely genomic surveillance to inform public health responses. In the largest known outbreak of mpox, genomic surveillance efforts have primarily focused on high‐incidence nations in Europe and the Americas, with a paucity of data from South‐East Asia and the Western Pacific. Here we analyzed 102 monkeypox virus (MPXV) genomes sampled from 56 individuals in Melbourne, Australia. All genomes fell within the 2022 MPXV outbreak lineage (B.1), with likely onward local transmission detected. We observed within‐host diversity and instances of co‐infection, and highlight further examples of structural variation and apolipoprotein B editing complex‐driven micro‐evolution in the current MPXV outbreak. Updating our understanding of MPXV emergence and diversification will inform public health measures and enable monitoring of the virus' evolutionary trajectory throughout the mpox outbreak. [ABSTRACT FROM AUTHOR]

Hepatitis E virus (HEV) is an emerging causative agent of acute hepatitis. To clarify the epidemiology of HEV and characterize the genetic diversity of the virus in Japan, nationwide enhanced surveillance and molecular characterization studies of HEV in Japan were undertaken from 2014 to 2021. In total, 2770 hepatitis E cases were reported, of which 88% were domestic cases, while only 4.1% represented cases following infection abroad. In addition, 57% of domestic infections occurred in males aged in their 40s–70s. For domestic cases, infection via pork meat consumption continued to be the most reported route. Analysis of the 324 sequences detected between 2016 and 2021 showed that the majority of domestic HEV strains belong to Genotype 3a (G3a) and G3b. In contrast, six of eight cases of G1 HEV reflected infection abroad. Our results suggest that HEV is circulating widely in Japan, with genotypes G3a and G3b being most prevalent. Continued surveillance is necessary to monitor future trends and changes in the epidemiology of HEV in Japan. [ABSTRACT FROM AUTHOR]

In May 2022, several countries reported mpox cases from patients without history of traveling to endemic areas. France was one of the most affected European countries by this outbreak. In this study, the clinical characteristics of mpox cases in France were described, and the genetic diversity of the virus was studied. Patients diagnosed with mpox infection (quantitative polymerase chain reaction ct < 28) between May 21, and July 4, 2022 and between 16th August and 10th September 2022 were included to this study. Twelve amplicons corresponding to the most polymorphic regions of the mpox genome and covering ~30 000 nucleotides were generated and sequenced using the S5 XL Ion Torrent technology to evaluate the genetic diversity of mpox sequences. One hundred and forty‐eight patients were diagnosed with mpox‐infection. 95% were men, 5% transgender (M‐to‐F), 50% were taking human immunodeficiency virus (HIV) pre‐exposure prophylaxis, and 25% were HIV seropositive. One hundred and sixty‐two samples (some patients had two samples) were sequenced and compared to GenBank sequences. Overall, low genetic diversity of mpox sequences was found compared with pre‐epidemic Western‐African sequences, with 32 distinct mutational patterns. This study provides a first glance at the mutational landscape of early mpox 2022 circulating strains in Paris (France). [ABSTRACT FROM AUTHOR]

Pakistan is an endemic country for Crimean−Congo hemorrhagic fever (CCHF) and its Balochistan province is considered a hotspot region for circulation of the virus whereas sporadic cases have been reported from other parts of the country. Our study aims to investigate the genomic diversity of the CCHF virus circulating in Punjab and Khyber Pakhtunkhwa provinces of Pakistan. Between April to September 2022, 46 samples from suspected CCHF patients were tested, with 6 (13%) showing positive RT‐PCR results. Among the positive cases, all were male, aged 14−48 years among which 4 were butchers. Three CCHF patients succumbed to the disease. The complete S‐M‐L‐gene fragments of 4 positive samples were sequenced. The S and L segments belonged to the Asia‐1 clade and clustered with regional strains from Iran, India, and Afghanistan. One M segment sequence grouped into Africa‐2 along with those reported from India during 2016−2019. We report the detection of a reassorted virus (NIH‐PAK‐CCHF‐03|2022) having Asia‐1‐Africa‐2‐Asia‐1 (S‐M‐L) segment pattern for the first time from Pakistan. Mutational analysis showed M segments harboring eight mutations (T55A, S80P, T110I, T185A, T189A, A212T, and N239I/T) in the mucin‐like domain, five mutations (D250N, T333S, I375V, M401I, A433T), four mutations (N545D, Y657F, K688R, and I824V) in GP38‐domain, and three mutations (T1418N, A1431V, and G1449S) in Gc‐domain. These findings highlight the significance of whole‐genome sequencing of indigenous strains for a better understanding of the CCHFV evolution in Pakistan. [ABSTRACT FROM AUTHOR]

An instance of host range evolution relevant to plant virus disease control is resistance breaking. Resistance breaking can be hindered by across‐host fitness trade‐offs generated by negative effects of resistance‐breaking mutations on the virus fitness in susceptible hosts. Different mutations in pepper mild mottle virus (PMMoV) coat protein result in the breaking in pepper plants of the resistance determined by the L3 resistance allele. Of these, mutation M138N is widespread in PMMoV populations, despite associated fitness penalties in within‐host multiplication and survival. The stability of mutation M138N was analysed by serial passaging in L3 resistant plants. Appearance on passaging of necrotic local lesions (NLL), indicating an effective L3 resistance, showed reversion to nonresistance‐breaking phenotypes was common. Most revertant genotypes had the mutation N138K, which affects the properties of the virus particle, introducing a penalty of reversion. Hence, the costs of reversion may determine the evolution of resistance‐breaking in addition to resistance‐breaking costs. The genetic diversity of the virus population in NLL was much higher than in systemically infected tissues, and included mutations reported to break L3 resistance other than M138N. Infectivity assays on pepper genotypes with different L alleles showed high phenotypic diversity in respect to L alleles in NLL, including phenotypes not reported in nature. Thus, high diversity at NLL may potentiate the appearance of genotypes that enable the colonization of new host genotypes or species. Collectively, the results of this study contribute to better understanding the evolutionary dynamics of resistance breaking and host‐range expansions. [ABSTRACT FROM AUTHOR]

Since its discovery in 2012, the role of the trichovirus named grapevine Pinot gris virus (GPGV) as the causative agent of grapevine leaf mottling and deformation (GMLD) syndrome, a grapevine disease for which symptoms had been observed in north Italy and western Slovenia a few years earlier, has been a matter of discussion. In the following 10 years of investigations, evidence has emerged of a role for the genetic diversity of the virus and for the varietal diversity of the host, as well as their interaction during antiviral defence (i.e. RNA silencing) and virus‐mediated defence suppression. In a context of wider research efforts, several relevant aspects of GPGV evolution and GMLD epidemiology were also clarified. Nevertheless, a complete understanding of the molecular events and the environmental conditions that could affect viral infection severity and symptom display remains a challenging puzzle. In the meantime, we are witnessing a large spread of the virus, which has almost completely permeated the regions where it first appeared, while spreading through most areas of grapevine cultivation. A deeper knowledge of the molecular context of the disease is key to establishing whether the impressive potential of GPGV to spread makes it a candidate as the next emerging threat for the grapevine industry. [ABSTRACT FROM AUTHOR]

Ribes are essential berry crops in the temperate zones in Eurasia and New Zealand, and viral infections are common constraints in their cultivation. Gooseberry vein banding associated virus (GVBaV) is vectored by aphids and has been reported from a few European countries and North America. Knowledge on how GVBaV interacts with its vectors on Ribes is still limited. The occurrence of GVBaV in cultivated and wild Ribes in various habitats was studied, focusing on germplasm collections, wild localities, home gardens and green spaces where chemical plant protection is not applied. GVBaV was confirmed for the first time in Latvia in all studied Ribes groups except Ribes×nidigrolaria, and in all habitats surveyed; however, its occurrence did not exceed 8%. Ribes alpinum and R. aureum were found as new naturally infected hosts. GVBaV was detectable in single aphid specimens by PCR and confirmed in Aphis schneideri, Cryptomyzus galeopsidis, Cryptomyzus ribis, Hyperomyzus lactucae and Nasonovia ribisnigri. Phylogenetic analyses did not reveal supported clustering related to host or geographic origin, except for GVBaV isolates in A. schneideri obtained from cultivated gooseberry. This is the first study contributing to the understanding of virus genetic diversity in its vector species in relation to the host plants. A. schneideri that feeds only on Ribes is probably a major contributor to GVBaV spread in comparison with other aphid species migrating to secondary hosts. [ABSTRACT FROM AUTHOR]

Wild plant species play an important role in plant virus epidemiology, mainly by harbouring viruses pathogenic to cultivated plant species. The genus Solanum includes important crop species as well as some highly abundant and widely distributed wild plant species. The aim of the present study was to profile the viromes of 11 wild Solanum spp. found in five provinces of South Africa. Metatranscriptomic analysis of pooled RNA samples from each of the Solanum spp. detected viruses belonging to 13–19 families. Reverse transcription PCR confirmed the detection of potato virus Y (PVY), potato leaf roll virus (PLRV), tomato torrado virus (ToTV) and tomato chlorosis virus (ToCV) for the first time in some of the Solanum spp. studied. Phylogenetic analyses indicated that the PVY and PLRV strains from the wild Solanum spp. were divergent from those reported in cultivated crops, while there was limited divergence among ToTV and ToCV isolates. Viruses detected for the first time in South Africa included tobacco mild green mosaic virus, tomato matilda virus, a pepper enamovirus from Rwanda and a cytorhabdovirus from potato in Kenya. Potentially novel viruses were also detected in S. lichtensteinii, S. mauritianum and S. viarum. This study demonstrates the role of Solanum spp. in harbouring viruses pathogenic to solanaceous crops, and in the emergence of new virus strains. It may therefore inform strategies for virus disease management by control of wild solanums that harbour viruses pathogenic to important Solanum crops. [ABSTRACT FROM AUTHOR]

There is growing recognition of the diversity of viruses that can infect the cells of the central nervous system (CNS). While the majority of CNS infections are successfully cleared by the immune response, some viral infections persist in the CNS. As opposed to resolved infections, persistent viruses can contribute to ongoing tissue damage and neuroinflammatory processes. In this manuscript, we provide an overview of the current understanding of factors that lead to viral persistence in the CNS including how viruses enter the brain, how these pathogens evade antiviral immune system responses, and how viruses survive and transmit within the CNS. Further, as the CNS may serve as a unique viral reservoir, we examine the ways in which persistent viruses in the CNS are being targeted therapeutically. [ABSTRACT FROM AUTHOR]

Background: We aimed to describe the prevalence of human respiratory syncytial virus (HRSV) and evaluate associations between HRSV subgroups and/or genotypes and epidemiologic characteristics and clinical outcomes in patients hospitalized with severe respiratory illness (SRI). Methods: Between January 2012 and December 2015, we enrolled patients of all ages admitted to two South African hospitals with SRI in prospective hospital‐based syndromic surveillance. We collected respiratory specimens and clinical and epidemiological data. Unconditional random effect multivariable logistic regression was used to assess factors associated with HRSV infection. Results: HRSV was detected in 11.2% (772/6908) of enrolled patients of which 47.0% (363/772) were under the age of 6 months. There were no differences in clinical outcomes of HRSV subgroup A‐infected patients compared with HRSV subgroup B‐infected patients but among patients aged <5 years, children with HRSV subgroup A were more likely be coinfected with Streptococcus pneumoniae (23/208, 11.0% vs. 2/90, 2.0%; adjusted odds ratio 5.7). No significant associations of HRSV A genotypes NA1 and ON1 with specific clinical outcomes were observed. Conclusions: While HRSV subgroup and genotype dominance shifted between seasons, we showed similar genotype diversity as noted worldwide. We found no association between clinical outcomes and HRSV subgroups or genotypes. [ABSTRACT FROM AUTHOR]

The severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) originated in Wuhan, China in early December 2019 has rapidly widespread worldwide. Over the course of the pandemic, due to the advance of whole‐genome sequencing technologies, an unprecedented number of genomes have been generated, providing both invaluable insights into the ongoing evolution and epidemiology of the virus and allowing the identification of hundreds of circulating genetic variants during the pandemic. In recent months variants of SARS‐CoV‐2 that have an increased number of mutations on the Spike protein have brought concern all over the world. These have been called "variants of concerns" (VOCs), and/or "variants of interests" (VOIs) as it has been suggested that their genome mutations might impact transmission, immune control, and virulence. Tracking the spread of emerging SARS‐CoV‐2 variants is crucial to inform public health efforts and control the ongoing pandemic. In this review, a concise characterization of the SARS‐CoV‐2 mutational patterns of the main VOCs and VOIs circulating and cocirculating worldwide has been presented to determine the magnitude of the SARS‐CoV‐2 threat to better understand the virus genetic diversity and its potential impact on vaccination strategy. Highlights: Over the course of the pandemic an unprecedented number of SARS‐CoV‐2 genomes have been generated.Genomic monitoring allowed the identification of "variants of concerns" (VOCs), and/or "variants of interests" (VOIs) wordlwide.Tracking the spread of emerging SARS‐CoV‐2 variants is crucial to control the ongoing pandemic. [ABSTRACT FROM AUTHOR]

Summary: Viruses can play critical roles in symbioses by initiating horizontal gene transfer, affecting host phenotypes, or expanding their host's ecological niche. However, knowledge of viral diversity and distribution in symbiotic organisms remains elusive. Here we use deep‐sequenced metagenomic DNA (PacBio Sequel II; two individuals), paired with a population genomics approach (Pool‐seq; 11 populations, 550 individuals) to understand viral distributions in the lichen Umbilicaria phaea. We assess (i) viral diversity in lichen thalli, (ii) putative viral hosts (fungi, algae, bacteria) and (iii) viral distributions along two replicated elevation gradients. We identified five novel viruses, showing 28%–40% amino acid identity to known viruses. They tentatively belong to the families Caulimoviridae, Myoviridae, Podoviridae and Siphoviridae. Our analysis suggests that the Caulimovirus is associated with green algal photobionts (Trebouxia) of the lichen, and the remaining viruses with bacterial hosts. We did not detect viral sequences in the mycobiont. Caulimovirus abundance decreased with increasing elevation, a pattern reflected by a specific algal lineage hosting this virus. Bacteriophages showed population‐specific patterns. Our work provides the first comprehensive insights into viruses associated with a lichen holobiont and suggests an interplay of viral hosts and environment in structuring viral distributions. [ABSTRACT FROM AUTHOR]

Yam (Dioscorea spp.) is a major staple food whose production is hampered by viral diseases. However, the prevalence, diversity, transmission, and impact of yam‐infecting viruses remain poorly documented. This study reports on the symptomatology, prevalence, and molecular diversity of eight viruses in 38 D. rotundata accessions from a germplasm collection and 206 F1 hybrid progenies maintained in Côte d'Ivoire. Mean severity scores as assessed from leaf symptoms ranged from 2 to 4 in the germplasm collection and from 1 to 3 in F1 hybrids, respectively. Dioscorea mosaic‐associated virus (DMaV), potexviruses, and yam mosaic virus (YMV) were detected by PCR‐based diagnosis tools in single and mixed infections in both the D. rotundata collection and F1 progenies, whereas badnaviruses were detected only in the germplasm collection. In contrast, cucumber mosaic virus (CMV), yam macluraviruses, yam asymptomatic virus 1 (YaV1), and yam mild mosaic virus (YMMV) could not be detected. No correlation could be established between severity scores and indexing results. Phylogenetic analysis performed on partial viral sequences amplified from infected samples unveiled the presence of two putative novel viral species belonging to genera Badnavirus and Potexvirus and provided evidence for plant‐to‐plant transmission of YMV, DMaV, and yam potexviruses. [ABSTRACT FROM AUTHOR]

More systematic analysis of hepatitis B virus (HBV) genome diversity, linked with tenofovir disoproxil fumarate (TDF) treatment and HBeAg seroconversion, are needed. GS‐US‐174–0115 was a double‐blind, placebo‐controlled, Phase 3, 192‐week clinical trial that evaluated TDF in adolescents with chronic hepatitis B (CHB). HBV full‐genome deep sequencing was performed using Illumina MiSeq at baseline (BL; n = 85), Week 8 (W8; n = 80), Week 72 (W72; PBO only, n = 42), and treatment‐free follow‐up (TDF only, n = 25). The viral diversity was calculated using Shannon entropy and population nucleotide diversity with a 2% variant cutoff. Our data showed (i) a higher viral diversity in the X region at baseline than the core/polymerase/surface regions, (ii) higher core/surface viral diversity at baseline for patients with seroconversion, (iii) an expected reduction in viral diversity after 8 weeks of TDF treatment, and (iv) a drop in viral diversity at W72 for patients receiving placebo with a seroconversion (n = 7). The higher viral diversity in X was associated with higher baseline alanine aminotransferase (ALT) levels (p <.001). Patients with greater reduction of diversity at W8 of TDF treatment had higher baseline ALT levels. For placebo patients who seroconverted, the drop in viral diversity at W72 (p =.04) coincided with reduction of serum HBV DNA (average change from baseline = −4.10 log10 copies/ml) and unique combinations of variants were enriched in a patient's viral population post seroconversion. The basal core promoter (BCP) variants, A1762T and G1764A, and the pC variant, G1896A, were most often enriched at or after seroconversion. [ABSTRACT FROM AUTHOR]

Four gastroenteritis viruses were responsible for 54% of the acute gastroenteritis (AGE) cases in children hospitalized between May 2017 and December 2019 in Pune city of Maharashtra state, Western India. The majority (79%) of the children were <2 years of age. The prevalence of Rotavirus A (RVA) was 30.5% followed by 14.3% for norovirus, 8.4% for adenovirus, and 5.5% for astrovirus. The severity of the disease was highest in patients with coinfections compared with the patients with a single infection or negative for all (p = 0.024). Genotyping analysis showed that the majority of the RVA‐positive samples (66%) could be typed as G3P[8], 63.6% of the norovirus as GII.4 Sydney [P16], 44% of the adenovirus as type 41%, and 56.2% of the astrovirus as astrovirus type 1. The almost equivalent prevalence of rotavirus and nonrotaviruses and acute gastroenteritis (AGE) cases without known etiology in around 46% of the cases was noted in the present study. Our data highlight that after the recent inclusion of rotavirus vaccines as a part of the National Immunization schedule in India, conducting extensive AGE surveillance in children should include nonrotaviruses such as norovirus. Highlights: Four gastroenteritis viruses were responsible for 54% of the acute gastroenteritis (AGE) cases in children, Western India.Significant decline in Rotavirus A (RVA) AGE cases in children age <5 years.Dominance of RVA G3P[8] and decline of G1P[8] & G2P[4] genotype strains.Highly transmissible GII.P16‐GII.4 genotype strains in 63.6% of norovirus infections.Clinical severity of the disease showed, no correlation with regard to different RVA genotypes or norovirus strains. [ABSTRACT FROM AUTHOR]

Summary: Deep‐sea hydrothermal vents are inhabited by complex communities of microbes and their viruses. Despite the importance of viruses in controlling the diversity, adaptation and evolution of their microbial hosts, to date, only eight bacterial and two archaeal viruses isolated from abyssal ecosystems have been described. Thus, our efforts focused on gaining new insights into viruses associated with deep‐sea autotrophic archaea. Here, we provide the first evidence of an infection of hyperthermophilic methanogenic archaea by a head‐tailed virus, Methanocaldococcus fervens tailed virus 1 (MFTV1). MFTV1 has an isometric head of 50 nm in diameter and a 150 nm‐long non‐contractile tail. Virions are released continuously without causing a sudden drop in host growth. MFTV1 infects Methanocaldococcus species and is the first hyperthermophilic head‐tailed virus described thus far. The viral genome is a double‐stranded linear DNA of 31 kb. Interestingly, our results suggest potential strategies adopted by the plasmid pMEFER01, carried by M. fervens, to spread horizontally in hyperthermophilic methanogens. The data presented here open a new window of understanding on how the abyssal mobilome interacts with hyperthermophilic marine archaea. [ABSTRACT FROM AUTHOR]

Summary: Our current knowledge of the virosphere in deep‐sea sediments remains rudimentary. Here we investigated viral diversity at both gene and genomic levels in deep‐sea sediments of Southwest Indian Ocean. Analysis of 19 676 106 non‐redundant genes from the metagenomic DNA sequences revealed a large number of unclassified viral groups in these samples. A total of 1106 high‐confidence viral contigs were obtained after two runs of assemblies, and 217 of these contigs with sizes up to ~120 kb were shown to represent complete viral genomes. These contigs are clustered with no known viral genomes, and over 2/3 of the ORFs on the viral contigs encode no known functions. Furthermore, most of the complete viral contigs show limited similarity to known viral genomes in genome organization. Most of the classified viral contigs are derived from dsDNA viruses belonging to the order Caudovirales, including primarily members of the families Myoviridae, Podoviridae and Siphoviridae. Most of these viruses infect Proteobacteria and, less frequently, Planctomycetes, Firmicutes, Chloroflexi, etc. Auxiliary metabolic genes (AMGs), present in abundance on the viral contigs, appear to function in modulating the host ability to sense environmental gradients and community changes, and to uptake and metabolize nutrients. [ABSTRACT FROM AUTHOR]

Direct‐acting antivirals (DAAs) have proven highly effective against chronic hepatitis C virus (HCV) infection. However, some patients experience treatment failure, associated with resistance‐associated substitutions (RASs). Our aim was to investigate the complete viral coding sequence in hepatitis C patients treated with DAAs to identify RASs and the effects of treatment on the viral population. We selected 22 HCV patients with sustained virologic response (SVR) to match 21 treatment‐failure patients in relation to HCV genotype, DAA regimen, liver cirrhosis and previous treatment experience. Viral‐titre data were compared between the two patient groups, and HCV full‐length open reading frame deep‐sequencing was performed. The proportion of HCV NS5A‐RASs at baseline was higher in treatment‐failure (82%) than matched SVR patients (25%) (p =.0063). Also, treatment failure was associated with slower declines in viraemia titres. Viral population diversity did not differ at baseline between SVR and treatment‐failure patients, but failure was associated with decreased diversity probably caused by selection for RAS. The NS5B‐substitution 150V was associated with sofosbuvir treatment failure in genotype 3a. Further, mutations identified in NS2, NS3‐helicase and NS5A‐domain‐III were associated with DAA treatment failure in genotype 1a patients. Six retreated HCV patients (35%) experienced 2nd treatment failure; RASs were present in 67% compared to 11% with SVR. In conclusion, baseline RASs to NS5A inhibitors, but not virus population diversity, and lower viral titre decline predicted HCV treatment failure. Mutations outside of the DAA targets can be associated with DAA treatment failure. Successful DAA retreatment in patients with treatment failure was hampered by previously selected RASs. [ABSTRACT FROM AUTHOR]

Background: Simian immunodeficiency virus (SIV) naturally infects African non‐human primates (NHPs) and poses a threat of transmission to humans through hunting and consumption of monkeys as bushmeat. This study investigated the as of yet unknown molecular diversity of SIV in free‐ranging Chlorocebus species (African green monkeys—AGMs) and Papio anubis (olive baboons) within Mombasa, Kisumu and Naivasha urban centres in Kenya. Methods: We collected blood samples from 124 AGMs and 65 olive baboons in situ, and detected SIV by high‐resolution melting analysis and sequencing of PCR products. Results: Simian immunodeficiency virus prevalence was 32% in AGMs and 3% in baboons. High‐resolution melting (HRM) analysis demonstrated distinct melt profiles illustrating virus diversity confirmed by phylogenetic analysis. Conclusions: There is persistent evolutionary diversification of SIVagm strains in its natural host, AGMs and cross‐species infection to olive baboons is occurring. Further study is required to establish pathogenesis of the diverse SIVagm variants and baboon immunological responses. [ABSTRACT FROM AUTHOR]

In 2017, Tamil Nadu, a southern state, had the second highest number of dengue cases from India. In the present study, the serotype‐specific differences in the clinical manifestations and laboratory parameters among hospitalized children with dengue were investigated and molecular characterization of the circulating dengue virus (DENV) serotypes during 2017 in Tamil Nadu was performed. Eighty children with dengue‐like symptoms consecutively admitted to a tertiary care hospital and positive for DENV NS1 antigen were investigated for DENV serotype utilizing a real‐time reverse transcriptase based polymerase chain reaction assay. Complete envelope (E) gene sequencing of the DENV strains was performed. Seventy samples were positive for serotyping (25 DENV‐1, 17 DENV‐2, six DENV‐3, and 22 DENV‐4). DENV‐4 infections were associated with elevated levels of liver enzymes; Alanine aminotransferase (P =.021) and aspartate aminotransferase (P =.001). However, none of the serotype was associated with any specific clinical features and severe dengue. Asian and American/African genotypes of DENV‐1 were cocirculating. The circulating genotype was cosmopolitan for DENV‐2 with multiple lineages, genotype III for DENV‐3 and genotype I for DENV‐4. Unique mutations were present in the 2017 DENV‐4 isolates. The present study suggests the association of DENV‐4 with elevated liver enzymes in children hospitalized for dengue. Further, the study reports the genetic diversity of DENV circulating in Tamil Nadu during 2017. The study calls for continuous monitoring of the circulating serotypes and genotypes at regional level in India which might result in a region wise database useful in predicting future outbreaks. Research Highlights: In Tamil Nadu, India, Asian and American/African genotypes of DENV‐1, cosmopolitan genotype of DENV‐2, genotype III of DENV‐3 and genotype I of DENV‐4 strains were circulating during 2017.DENV‐4 was associated with elevated levels of liver enzymes in children hospitalized for dengue.DENV serotypes were not associated with disease severity in children hospitalized for dengue.The study calls for continuous monitoring of the circulating serotypes and genotypes at regional level in India. [ABSTRACT FROM AUTHOR]

There has been little surveillance of influenza A viruses (IAVs) circulating in swine at live animal markets, particularly in the United States. To address this gap, we conducted active surveillance of IAVs in pigs, the air, and the environment during a summer and winter season in a live animal market in St. Paul, Minnesota, that had been epidemiologically associated with swine‐origin influenza cases in humans previously. High rates of IAV were detected by PCR in swine lungs and oral fluids during both summer and winter seasons. Rates of IAV detection by PCR in the air were similar during summer and winter, although rates of successful virus isolation in the air were lower during summer than in winter (26% and 67%, respectively). H3N2 was the most prevalent subtype in both seasons, followed by H1N2. Genetically diverse viruses with multiple gene constellations were isolated from both winter and summer, with a total of 19 distinct genotypes identified. Comparative phylogenetic analysis of all eight segments of 40 virus isolates from summer and 122 isolates from winter revealed that the summer and winter isolates were genetically distinct, indicating IAVs are not maintained in the market, but rather are re‐introduced, likely from commercial swine. These findings highlight the extent of IAV genetic diversity circulating in swine in live animal markets, even during summer months, and the ongoing risk to humans. [ABSTRACT FROM AUTHOR]

The structure and connectivity of wildlife host populations may influence zoonotic disease dynamics, evolution and therefore spillover risk to people. Fruit bats in the genus Pteropus, or flying foxes, are the primary natural reservoir for henipaviruses—a group of emerging paramyxoviruses that threaten livestock and public health. In Bangladesh, Pteropus medius is the reservoir for Nipah virus—and viral spillover has led to human fatalities nearly every year since 2001. Here, we use mitochondrial DNA and nuclear microsatellite markers to measure the population structure, demographic history and phylogeography of P. medius in Bangladesh. We combine this with a phylogeographic analysis of all known Nipah virus sequences and strains currently available to better inform the dynamics, distribution and evolutionary history of Nipah virus. We show that P. medius is primarily panmictic, but combined analysis of microsatellite and morphological data shows evidence for differentiation of two populations in eastern Bangladesh, corresponding to a divergent strain of Nipah virus also found in bats from eastern Bangladesh. Our demographic analyses indicate that a large, expanding population of flying foxes has existed in Bangladesh since the Late Pleistocene, coinciding with human population expansion in South Asia, suggesting repeated historical spillover of Nipah virus likely occurred. We present the first evidence of mitochondrial introgression, or hybridization, between P. medius and flying fox species found in South‐East Asia (P. vampyrus and P. hypomelanus), which may help to explain the distribution of Nipah virus strains across the region. see also the Perspective by Carver et al [ABSTRACT FROM AUTHOR]

To understand the genetic diversity and patterns of circulation of rhinoviruses (RV) and enteroviruses (EV) in Singapore, we retrospectively screened 2950 nasal swab samples collected from adults presenting to primary care services with signs of febrile illness in Singapore during 2007‐2013 using sequencing and phylogenetic methods. Through sequencing and phylogenetic analysis, our results show the year‐round circulation of the three rhinovirus species, A, B, and C. A diverse set of RV/EV serotypes were detected in Singapore with a predominance of RV‐A in all years, whereas serotypes EV‐C A21 and EV‐D68 were only sporadically detected. This study highlights the previously unrecognized diversity and burden in the adult population in Singapore. [ABSTRACT FROM AUTHOR]

Objective: To investigate the link between fluctuations in the prevalence of dengue virus (DENV) serotypes and the number of dengue cases in the metropolitan area of Bucaramanga, Santander State, Colombia, in the 2007-2010 and 2014-2017 periods.Method: Viruses were isolated from febrile patient samples by direct application to C6/36-HT cells and typed using monoclonal antibodies. We performed autocorrelation and cross-correlation analyses to determine whether fluctuations in the prevalence of DENV serotypes and dengue cases were correlated. Full envelope (E) gene sequences were employed to examine the genetic diversity of serotypes circulating by using a phylogenetic approach.Results: All four dengue virus serotypes were detected. DENV-1 was the dominant serotype in both periods followed by DENV-3 or DENV-2 depending on the period; DENV-4 was the least prevalent virus in both periods. Cross-correlation analyses suggest a temporal relation between the fluctuations in the prevalence of DENV serotypes, which were almost simultaneous (lag = 0) or related to recent past fluctuations (lag > 1.0) in the number of dengue cases. Data suggest that a sustained predominance of DENV-1, an increase of the DENV-4 prevalence, and a switch from DENV-3 to DENV-2 could be linked to an outbreak. Circulating viruses were grouped into Genotype V, Asia/American III and II for DENV-1, -2, -3 and -4, respectively; intragenotypic diversity was detected.Conclusions: The present work highlights the need of comprehensive studies on dynamics of DENV in Colombia to understand transmission of dengue and evaluate the effectiveness of a vaccination programme. [ABSTRACT FROM AUTHOR]

Piscine orthoreovirus genotype 1 (PRV‐1) is widespread in farmed Atlantic salmon (Salmo salar L.) populations in northern Europe, Canada and Chile. PRV‐1 occurs in wild fish in Norway and Canada; however, little information of its geographical distribution in wild populations is currently available, and the effect of PRV‐1 infection in wild populations is currently unknown. In this study, we present the findings of a survey conducted on 1,130 wild salmonids sampled in Denmark, Sweden, Ireland, Faroe Islands, France, Belgium and Greenland between 2008 and 2017. PRV‐1 is reported for the first time in wild salmonids in Denmark, Sweden, Faroe Island and Ireland. The annual PRV‐1 prevalence ranged from 0% in France, Belgium and Greenland to 43% in Faroe Islands. In total, 66 samples tested positive for PRV‐1, including Atlantic salmon broodfish returning to spawn and Atlantic salmon collected at the feeding ground north of Faroe Islands. The phylogenetic analysis of S1 sequences of the PRV‐1 isolates obtained in this survey did not show systematic geographical distribution. This study sheds light on the spread and genetic diversity of the virus identified in populations of free‐living fish and provides rationale for screening wild broodfish used in restocking programmes. [ABSTRACT FROM AUTHOR]

Summary: Recent metagenomic studies have provided an unprecedented wealth of data, which are revolutionizing our understanding of virus diversity. A redrawn landscape highlights viruses as active players in the phytobiome, and surveys have uncovered their positive roles in environmental stress tolerance of plants. Viral infectious clones are key tools for functional characterization of known and newly identified viruses. Knowledge of viruses and their components has been instrumental for the development of modern plant molecular biology and biotechnology. In this review, we provide extensive guidelines built on current synthetic biology advances that streamline infectious clone assembly, thus lessening a major technical constraint of plant virology. The focus is on generation of infectious clones in binary T‐DNA vectors, which are delivered efficiently to plants by Agrobacterium. We then summarize recent applications of plant viruses and explore emerging trends in microbiology, bacterial and human virology that, once translated to plant virology, could lead to the development of virus‐based gene therapies for ad hoc engineering of plant traits. The systematic characterization of plant virus roles in the phytobiome and next‐generation virus‐based tools will be indispensable landmarks in the synthetic biology roadmap to better crops. [ABSTRACT FROM AUTHOR]

Summary: The diversity of archaeal viruses is severely undersampled compared with that of viruses infecting bacteria and eukaryotes, limiting our understanding on their evolution and environmental impacts. Here, we describe the isolation and characterization of four new viruses infecting halophilic archaea from the saline Lake Retba, located close to Dakar on the coast of Senegal. Three of the viruses, HRPV10, HRPV11 and HRPV12, have enveloped pleomorphic virions and should belong to the family Pleolipoviridae, whereas the forth virus, HFTV1, has an icosahedral capsid and a long non‐contractile tail, typical of bacterial and archaeal members of the order Caudovirales. Comparative genomic and phylogenomic analyses place HRPV10, HRPV11 and HRPV12 into the genus Betapleolipovirus, whereas HFTV1 appears to be most closely related to the unclassified Halorubrum virus HRTV‐4. Differently from HRTV‐4, HFTV1 encodes host‐derived minichromosome maintenance helicase and PCNA homologues, which are likely to orchestrate its genome replication. HFTV1, the first archaeal virus isolated on a Haloferax strain, could also infect Halorubrum sp., albeit with an eightfold lower efficiency, whereas pleolipoviruses nearly exclusively infected autochthonous Halorubrum strains. Mapping of the metagenomic sequences from this environment to the genomes of isolated haloarchaeal viruses showed that these known viruses are underrepresented in the available viromes. [ABSTRACT FROM AUTHOR]

Summary: Viruses infecting hyperthermophilic archaea of the phylum Crenarchaeota display enormous morphological and genetic diversity, and are classified into 12 families. Eight of these families include only one or two species, indicating sparse sampling of the crenarchaeal virus diversity. In an attempt to expand the crenarchaeal virome, we explored virus diversity in the acidic, hot spring Umi Jigoku in Beppu, Japan. Environmental samples were used to establish enrichment cultures under conditions favouring virus replication. The host diversity in the enrichment cultures was restricted to members of the order Sulfolobales. Metagenomic sequencing of the viral communities yielded seven complete or near‐complete double‐stranded DNA virus genomes. Six of these genomes could be attributed to polyhedral and filamentous viruses that were observed by electron microscopy in the enrichment cultures. Two icosahedral viruses represented species in the family Portogloboviridae. Among the filamentous viruses, two were identified as new species in the families Rudiviridae and Lipothrixviridae, whereas two other formed a group seemingly distinct from the known virus genera. No particle morphotype could be unequivocally assigned to the seventh viral genome, which apparently represents a new virus type. Our results suggest that filamentous viruses are globally distributed and are prevalent virus types in extreme geothermal environments. [ABSTRACT FROM AUTHOR]

Summary: Marine Group I (MGI) Thaumarchaeota are some of the most abundant microorganisms in the deep ocean and responsible for much of the ammonia oxidation occurring in this environment. In this work, we present 35 sequences assembled from metagenomic samples of the first uncultivated Caudovirales viruses associated with Thaumarchaeota, which we designated marthavirus. Most of the sequences were obtained from cellular metagenomes confirming that they represent an important tool to study environmental viral communities due to cells retrieved while undergoing viral lysis. Metagenomic recruitment showed that this viral population is formed by very divergent entities with high intrapopulation homogeneity. However, metatranscriptomic analyses revealed the same differential expression profile with the capsid as major transcript, indicative of viruses during the lytic cycle. The cobalamine biosynthesis gene cobS, an auxiliary metabolic gene, was also highly expressed during the infection. These analyses expand our understanding of the global diversity of archaeal viruses. [ABSTRACT FROM AUTHOR]

The article explores the potential of viruses, the critical regulators and important components, in manipulating the global ecosystems. It outlines the challenges in thoroughly assessing the influence of viruses in microbial system including the establishment of uncultivated viruses' host linkages and the comprehensive classification of environmental viral diversity. Also presented are stories based on viral genomics and ecological advances to address viral ecology-related questions.

Summary: Viruses represent a driving force in the evolution of microorganisms including those thriving in extreme environments. However, our knowledge of the viral diversity associated to microorganisms inhabiting the deep‐sea hydrothermal vents remains limited. The phylum of Thermotogae, including thermophilic bacteria, is well represented in this environment. Only one virus was described in this phylum, MPV1 carried by Marinitoga piezophila. In this study, we report on the functional and genomic characterization of two new bacterioviruses that infect bacteria from the Marinitoga genus. Marinitoga camini virus 1 and 2 (MCV1 and MCV2) are temperate siphoviruses with a linear dsDNA genome of 53.4 kb and 50.5 kb respectively. Here, we present a comparative genomic analysis of the MCV1 and MCV2 viral genomes with that of MPV1. The results indicate that even if the host strains come from geographically distant sites, their genomes share numerous similarities. Interestingly, heavy metals did not induce viral production, instead the host of MCV1 produced membrane vesicles. This study highlights interaction of mobile genetic elements (MGE) with their hosts and the importance of including hosts‐MGEs' relationships in ecological studies. [ABSTRACT FROM AUTHOR]

The stone fruit genus Prunus, within the family Rosaceae, comprises more than 230 species, some of which have great importance or value as ornamental or fruit crops. Prunus are affected by numerous viruses and viroids linked to the vegetative propagation practices in many of the cultivated species. To date, 44 viruses and three viroids have been described in the 9 main cultivated Prunus species. Seven of these viruses and one viroid have been identified in Prunus hosts within the last 5 years. This work addresses recent advances and prospects in the study of viruses and viroids affecting Prunus species, mostly concerning the detection and characterisation of the agents involved, pathogenesis analysis and the search for new control tools. New sequencing technologies are quickly reshaping the way we can identify and characterise new plant viruses and isolates. Specific efforts aimed at virus identification or data mining of high-throughput sequencing data generated for plant genomics-oriented purposes can efficiently reveal the presence of known or novel viruses. These technologies have also been used to gain a deeper knowledge of the pathogenesis mechanisms at the gene and miRNA expression level that underlie the interactions between Prunus spp. and their main viruses and viroids. New biotechnological control tools include the transfer of resistance by grafting, the use of new sources of resistance and the development of gene silencing strategies using genetic transformation. In addition, the application of next generation sequencing and genome editing techniques will contribute to improving our knowledge of virus-host interactions and the mechanisms of resistance. This should be of great interest in the search to obtain new Prunus cultivars capable of dealing both with known viruses and viroids and with those that are yet to be discovered in the uncertain scenario of climate change. [ABSTRACT FROM AUTHOR]

Viruses have recurrently been hypothesized as instrumental in driving microbial population diversity. Nonetheless, viral mediated co-existence of r/k-strategists, predicted in the Killing-the-Winner (KtW) hypothesis, remains controversial and demands empirical evidence. Therefore, we measured the life strategy parameters that characterize the relevant system Micromonas-Micromonas Virus (MicV). A large number of host and viral strains (37 and 17, respectively) were used in a total of 629 cross-infectivity tests. Algal and viral abundances were monitored by flow cytometry and used to calculate values of growth rate, resistance capacity, and viral production. Two main assumptions of the KtW model, namely (1) a resistance-associated cost on growth and (2) a negative correlation between resistance and viral production capacity, were mildly observed and lacked statistical significance. Micromonas strains infected by more MicV strains presented higher lysis and viral production rates as the number of infectious virus strains increased, suggesting a 'one-gate' regulation of infection in this system. MicV strains demonstrated a vast range of virion production capacity, which unexpectedly grew with increasing host-range. Overall, the significant trends observed in here demonstrate strong co-interactions at different levels between Micromonas and MicV populations, however, the role of viruses as major driving force in phytoplankton fitness wasn't explicitly observed. [ABSTRACT FROM AUTHOR]

Begomoviruses (whitefly-transmitted, single-stranded DNA plant viruses) are among the most damaging pathogens causing epidemics in economically important crops worldwide. Besides cultivated plants, many weed and wild hosts act as virus reservoirs where recombination may occur, resulting in new species. The aim of this study was to further characterise the diversity of begomoviruses infecting two major weed genera, Sida and Leonurus. Total DNA was extracted from samples collected in the states of Rio Grande do Sul, Paraná and Mato Grosso do Sul during the years 2009-2011. Viral genomes were enriched by rolling circle amplification ( RCA), linearised into unit length genomes using various restriction enzymes, cloned and sequenced. A total of 78 clones were obtained: 37 clones from Sida spp. plants and 41 clones from Leonurus sibiricus plants. Sequence analysis indicated the presence of six bipartite begomovirus species and two alphasatellites. In Sida spp. plants we found Sida micrantha mosaic virus ( SiMMV), Euphorbia yellow mosaic virus ( EuYMV), and three isolates that represent new species, for which the following names are proposed: Sida chlorotic mottle virus ( SiCMoV), Sida bright yellow mosaic virus ( SiBYMV) and Sida golden yellow spot virus ( SiGYSV), an Old World-like begomovirus. L. sibiricus plants had a lower diversity of begomoviruses compared to Sida spp., with only Tomato yellow spot virus ( ToYSV) and EuYMV (for the first time detected infecting plants of the genus Leonurus) detected. Two satellite DNA molecules were found: Euphorbia yellow mosaic alphasatellite, for the first time detected infecting plants of the genus Sida, and a new alphasatellite associated with ToYSV in L. sibiricus. These results constitute further evidence of the high species diversity of begomoviruses in non-cultivated hosts, particularly Sida spp. [ABSTRACT FROM AUTHOR]

ABSTRACT The ecology of viruses has been studied only in a limited number of rivers and streams. In light of a recent re-appraisal of the global fluvial surface area, issues such as abundance and production, host mortality and the influence of suspended particles and biofilms are addressed. Viral life cycles, potential impacts of viruses on water biochemistry and carbon flow, and viral diversity are considered. Variability in trophic levels along with the heterogeneous nature and hydrological dynamics of fluvial environments suggest a prevailingly physical control of virus-related processes under lotic conditions and more biological control under lentic conditions. Viral lysis likely contributes to a pool of rapidly cycling carbon in environments typically characterized by high proportions of recalcitrant terrestrial carbon. On average, 33.6% (equalling 0.605 Pg C year−1) of the globally respired carbon from fluvial systems may pass through a viral loop. Virus distribution and the proportion of organic material in horizontal transport versus processes in retention zones remain to be determined in detail. The need for up-scaling the contribution of virus-related processes in fluvial systems is of global relevance. Further, the role of climate change and the effect of anthropogenic alterations of fluvial systems on viruses require attention. The identification of these considerable knowledge gaps should foster future research efforts. [ABSTRACT FROM AUTHOR]

A central focus of population genetics has been examining the contribution of selective and neutral processes in shaping patterns of intraspecies diversity. In terms of selection specifically, surveys of higher organisms have shown considerable variation in the relative contributions of background selection and genetic hitchhiking in shaping the distribution of polymorphisms, although these analyses have rarely been extended to bacteria and viruses. Here, we study the evolution of a ubiquitous, viral pathogen, human cytomegalovirus (HCMV), by analysing the relationship among intraspecies diversity, interspecies divergence and rates of recombination. We show that there is a strong correlation between diversity and divergence, consistent with expectations of neutral evolution. However, after correcting for divergence, there remains a significant correlation between intraspecies diversity and recombination rates, with additional analyses suggesting that this correlation is largely due to the effects of background selection. In addition, a small number of loci, centred on long noncoding RNAs, also show evidence of selective sweeps. These data suggest that HCMV evolution is dominated by neutral mechanisms as well as background selection, expanding our understanding of linked selection to a novel class of organisms. [ABSTRACT FROM AUTHOR]

Heterotrophic bacteria are the major prokaryotic component of the Baltic Sea ice microbiome, and it is postulated that phages are among their major parasites. In this study, we sequenced the complete genomes of six earlier reported phage isolates from the Baltic Sea ice infecting S hewanella sp. and F lavobacterium sp. hosts as well as characterized the phage-host interactions. Based on the genome sequences, the six phages were classified into five new genera. Only two phages, 1/4 and 1/40, both infecting S hewanella sp. strains, showed significant nucleotide sequence similarity to each other and could be grouped into the same genus. These two phages are also related to V ibrio-specific phages sharing approximately 25% of the predicted gene products. Nevertheless, cross-titrations showed that the cold-active phages studied are host specific: none of the seven additionally tested, closely related S hewanella strains served as hosts for the phages. Adsorption experiments of two S hewanella phages, 1/4 and 3/49, conducted at 4° C and at 15° C revealed relatively fast adsorption rates that are, for example, comparable with those of phages infective in mesophilic conditions. Despite the small number of S hewanella phages characterized here, we could already find different types of phage-host interactions including a putative abortive infection. [ABSTRACT FROM AUTHOR]

In 2011, Culicoides ( Diptera: Ceratopogonidae) were collected at 16 locations covering four regions of Belgium with Onderstepoort Veterinary Institute ( OVI) traps and at two locations with Rothamsted suction traps ( RSTs). Quantification of the collections and morphological identification showed important variations in abundance and species diversity between individual collection sites, even for sites located in the same region. However, consistently higher numbers of Culicoides midges were collected at some sites compared with others. When species abundance and diversity were analysed at regional level, between-site variation disappeared. Overall, species belonging to the subgenus Avaritia together with Culicoides pulicaris (subgenus Culicoides) were the most abundant, accounting for 80% and 96% of all midges collected with RSTs and OVI traps, respectively. Culicoides were present during most of the year, with Culicoides obsoletus complex midges found from 9 February until 27 December. Real-time reverse-transcription polymerase chain reaction screening for Schmallenberg virus in the heads of collected midges resulted in the first detection of the virus in August 2011 and identified C. obsoletus complex, Culicoides chiopterus and Culicoides dewulfi midges as putative vector species. At Libramont in the south of Belgium, no positive pools were identified. [ABSTRACT FROM AUTHOR]