A giant virus genome is densely packaged by stable nucleosomes

The doublet histones of Marseillevirus are distantly related to the four eukaryotic core histones and wrap DNA to form remarkably similar nucleosomes. By releasing Marseillevirus chromatin from virions into solution and performing genome-wide nuclease digestion and chemical cleavage assays, we find that the higher-order organization of Marseillevirus chromatin differs greatly from that of eukaryotes. Marseillevirus nucleosomes fully protect DNA within virions, without linker DNA or phasing along genes. Likewise, we observe that most nucleosomes reconstituted onto 3-copy tandem repeats of a nucleosome positioning sequence are tightly packed and fully wrapped. We also document repeat generation and instability during viral passage in amoeboid culture. Dense promiscuous packing of fully wrapped nucleosomes rather than 'beads-on-a-string' with genic punctuation suggests a viral genome protection function for doublet histones.

A short plus long-amplicon based sequencing approach improves genomic coverage and variant detection in the SARS-CoV-2 genome

High viral transmission in the COVID-19 pandemic has enabled SARS‐CoV‐2 to acquire new mutations that may impact genome sequencing methods. The ARTIC.v3 primer pool that amplifies short amplicons in a multiplex-PCR reaction is one of the most widely used methods for sequencing the SARS-CoV-2 genome. We observed that some genomic intervals are poorly captured with ARTIC primers. To improve the genomic coverage and variant detection across these intervals, we designed long amplicon primers and evaluated the performance of a short (ARTIC) plus long amplicon (MRL) sequencing approach. Sequencing assays were optimized on VR-1986D-ATCC RNA followed by sequencing of nasopharyngeal swab specimens from fifteen COVID-19 positive patients. ARTIC data covered 94.47% of the virus genome fraction in the positive control and patient samples. Variant analysis in the ARTIC data detected 217 mutations, including 209 single nucleotide variants (SNVs) and eight insertions & deletions. On the other hand, long-amplicon data detected 156 mutations, of which 80% were concordant with ARTIC data. Combined analysis of ARTIC + MRL data improved the genomic coverage to 97.03% and identified 214 high confidence mutations. The combined final set of 214 mutations included 203 SNVs, 8 deletions and 3 insertions. Analysis showed 26 SARS-CoV-2 lineage defining mutations including 4 known variants of concern K417N, E484K, N501Y, P618H in spike gene. Hybrid analysis identified 7 nonsynonymous and 5 synonymous mutations across the genome that were either ambiguous or not called in ARTIC data. For example, G172V mutation in the ORF3a protein and A2A mutation in Membrane protein were missed by the ARTIC assay. Thus, we show that while the short amplicon (ARTIC) assay provides good genomic coverage with high throughput, complementation of poorly captured intervals with long amplicon data can significantly improve SARS-CoV-2 genomic coverage and variant detection.

First report of tomato fruit blotch virus infecting tomatoes in Brazil

Recently, a new blunervirus was reported in tomatoes showing fruit chlorotic lesions. This virus, named tomato fruit blotch virus (ToFBV), was found associated with the tomato fruit blotch disease in Italy and Australia, even though Koch’s postulates were not fulfilled and no viral particles were seen in leaf dips observed with an electron microscope (Ciuffo et al. 2020). In December 2019, symptoms of circular or irregular chlorotic blotches were observed in tomato fruits in an organic farm in Distrito Federal, Brazil. Five different tomato cultivars (2100 plants of cv. Sweet grape, 1700 of Giacomo, 560 of Grazianni, 160 of Tropical, and 160 of DRC 5640) were being grown in two greenhouses and all of them presented the symptoms in at least one fruit, particularly in older fruits. No virus-like symptoms were observed in young and middle leaves, but older leaves could not be examined because they were removed as a routine activity of the farm; and also due to the moderate infestation of the tomato russet mite Aculops lycopersici, associated with leaf and stem necrosis. No viral particles were observed in an electron microscope analysis of symptomatic fruit tissues, and sap inoculation and grafting of stems did not produce any symptom in indicator plants. Two young and asymptomatic plants with the first fruits still in development were removed from another greenhouse of the farm and transported to our greenhouse, but the typical blotch symptoms neither appeared in the fruits nor the necrosis symptoms in the leaves. Serological tests performed for all collected leaf and fruit samples using antibodies produced in-house against common tomato-infecting tospoviruses and potyviruses were negative, as well as a polymerase chain reaction (PCR) detection test for begomoviruses (Rojas et al. 1993). Total RNA from newly collected samples consisting of one symptomatic fruit sample and five asymptomatic leaf samples from distinct plants were individually extracted using RNeasy Plant Mini Kit (Qiagen, Hilden, Germany) and pooled for next generation sequencing (NGS). The library was constructed using TruSeq Stranded Total RNA with Ribo-Zero Plant (Illumina, San Diego, USA) and sequenced at Macrogen, Inc. (Seoul, South Korea) in an Illumina Novaseq6000 platform. The 4,621,977,958 reads obtained were trimmed using Trimommatic 0.35 (Bolger et al. 2014) and contigs were assembled using Velvet (Zerbino and Birney 2008). Following tblastx analysis on Geneious 9.1.8 (Biomatters Ltd.) and BLAST on the NCBI platform (Altschul et al. 1990), seven contigs matching tomato chlorosis virus (ToCV) and five contigs matching ToFBV were identified. Sequences for each of the four genome components of ToFBV (MK517477-MK517480) already present in databases were used as reference using the Map to Reference function in Geneious. A total of 338,402, 78,039, 555,302 and 461,474 reads mapped to virus genome components 1 to 4, respectively, with >99% coverage for each. Four final consensus sequences were used for BLAST analyses on NCBI and presented 97 to 99.7 % nucleotide identity with those used for mapping. These sequences were deposited in GenBank as isolate MAL under accession numbers MW546267 (RNA 1, 5770 nt), MW546268 (RNA 2, 3612 nt), MW546269 (RNA 3, 2826 nt) and MW546270 (RNA 4, 1950 nt). The primer pair Bluner1F (5’-ATTCCTGTTCCTTCGGATAAACTCGT-3’) and Bluner1R (5’-CACACGTGCAGGAAATGGAAAGA-3’) directed to RNA 1 was used to specifically detect the virus. Three leaf samples and two fruit samples, each from a different plant with typical symptoms, were tested positive for ToFBV and negative using ToCV-specific primers in RT-PCR (Dovas et al. 2002). This confirmed that although some plants pooled in the HTS library were infected with ToCV, the chlorotic blotch symptom was clearly associated with the presence of ToFBV. Furthermore, the ~0.5 kbp amplicon for ToFBV-specific primers from one randomly selected sample was sequenced with both primers and the resulting sequence shared 100% nt identity with the RNA 1 of ToFBV isolate Fondi2018 from Italy (MK517477). Then, the virus was detected in the tissue from the surface of another fruit, but not from its internal part, suggesting a superficial infection. The findings presented here are of high phytosanitary significance, given the strong symptoms associated with tomato fruit blotch disease and the identification of ToFBV in the tomato samples from Brazil.

Do Epstein–Barr Virus Mutations and Natural Genome Sequence Variations Contribute to Disease?

Most of the world’s population is infected by the Epstein–Barr virus (EBV), but the incidence of the diseases associated with EBV infection differs greatly in different parts of the world. Many factors may determine those differences, but variation in the virus genome is likely to be a contributing factor for some of the diseases. Here, we describe the main forms of EBV genome sequence variation, and the mechanisms by which variations in the virus genome are likely to contribute to disease. EBV genome deletions or polymorphisms can also provide useful markers for monitoring disease. If some EBV strains prove to be more pathogenic than others, this suggests the possible value of immunising people against infection by those pathogenic strains.

RBD Double Mutations of SARS-CoV-2 Strains Increase Transmissibility through Enhanced Interaction between RBD and ACE2 Receptor

The COVID-19 pandemic, caused by SARS-CoV-2, has led to catastrophic damage for global human health. The initial step of SARS-CoV-2 infection is the binding of the receptor-binding domain (RBD) in its spike protein to the ACE2 receptor in the host cell membrane. Constant evolution of SARS-CoV-2 generates new mutations across its genome including the coding region for the RBD in the spike protein. In addition to the well-known single mutation in the RBD, the recent new mutation strains with an RBD “double mutation” are causing new outbreaks globally, as represented by the delta strain containing RBD L452R/T478K. Although it is considered that the increased transmissibility of double-mutated strains could be attributed to the altered interaction between the RBD and ACE2 receptor, the molecular details remain to be elucidated. Using the methods of molecular dynamics simulation, superimposed structural comparison, free binding energy estimation, and antibody escaping, we investigated the relationship between the ACE2 receptor and the RBD double mutants of L452R/T478K (delta), L452R/E484Q (kappa), and E484K/N501Y (beta, gamma). The results demonstrated that each of the three RBD double mutants altered the RBD structure and enhanced the binding of the mutated RBD to ACE2 receptor. Together with the mutations in other parts of the virus genome, the double mutations increase the transmissibility of SARS-CoV-2 to host cells.

Performance Characteristics of Real-time PCRs for African Swine Fever Virus Genome Detection – comparison of Twelve Kits to an OIE Recommended Method

African swine fever (ASF) is one of the major threats to pig production, and real-time PCR (qPCR) protocols are integral part of ASF laboratory diagnosis. With the pandemic spread of ASF, commercial kits have risen on the market. In Germany, the kits have to go through an approval process and thus, general validation can be assumed. However, they were never compared to each other. In this study, 12 commercial PCR kits were compared to an OIE recommended method. Samples representing different matrices, genome loads, and genotypes were included in a panel that was tested under diagnostic conditions. The comparison included user-friendliness, internal controls, and the time required. All qPCRs were able to detect ASFV genome in different matrices across all genotypes and disease courses. With one exception, there were no significant differences when comparing the overall mean. The overall specificity was 100 % [95 % CI 87.66 - 100], and the sensitivity was between 95 % and 100 % [95 % CI 91.11 - 100]. As can be expected, variability concerned samples with low genome load. Concluding, all tests were fit for purpose. The test system can therefore be chosen based on compatibility and prioritization of the internal control system.

Polerovirus Genomic Variation

The polerovirus (family Solemoviridae, genus Polerovirus) genome consists of single, positive strand RNA organized in overlapping open reading frames (ORFs) that, in addition to others, code for protein 0 (P0, a gene silencing suppressor), a coat protein (CP, ORF3) and a read-through domain (ORF5) that is fused to the CP to form a CP-RT protein. The genus Polerovirus contains 26 virus species that infect a wide variety of plants from cereals to cucurbits, to peppers. Poleroviruses are transmitted by a wide range of aphid species in the genera Rhopalosiphum, Stiobion, Aphis, and Myzus. Aphid transmission is mediated both by the CP and the CP-RT. In viruses, mutational robustness and structural flexibility are necessary for maintaining functionality in genetically diverse sets of host plants and vectors. Under this scenario, within a virus genome, mutations preferentially accumulate in areas that are determinants of host adaptation or vector transmission. In this study, we profiled genomic variation in poleroviruses. Consistent with their multifunctional nature, single nucleotide variation and selection analyses showed that ORFs coding for P0 and the read-through domain within the CP-RT are the most variable and contain the highest frequency of sites under positive selection. An order/disorder analysis showed that protein P0 is not disordered. In contrast, proteins CP-RT and VPg contain areas of disorder. Disorder is a property of multifunctional proteins with multiple interaction partners. Results described here suggest that using contrasting mechanisms, P0, VPg and CP-RT mediate adaptation to host plants, to vectors, and are contributors to the broad host and vector range of poleroviruses. Profiling genetic variation across the polerovirus genome has practical applications in diagnostics, breeding for resistance, identification of susceptibility genes, and contributes to our understanding of virus interactions with their host, vectors, and environment.

Development of a Novel Avian Vaccine Vector Derived From the Emerging Fowl Adenovirus 4

Severe hepatitis-hydropericardium syndrome (HHS) associated with a novel viral genotype, fowl adenovirus 4 (FAdV-4), has emerged and widely spread in China since 2015, causing severe economic losses to the poultry industry. We previously reported that the hexon gene is responsible for pathogenicity and obtained a non-pathogenic hexon-replacement rHN20 strain; however, the lack of information about the non-essential regions for virus replication limits the development of a FAdV-4 vector. This study first established an enhanced green fluorescent protein (EGFP)-indicator virus based on the FAdV-4 reverse genetic technique, effective for batch operations in the virus genome. Based on this, 10 open reading frames (ORFs) at the left end and 13 ORFs at the right end of the novel FAdV-4 genome were deleted separately and identified as non-essential genes for viral replication, providing preliminary insertion sites for foreign genes. To further improve its feasibility as a vaccine vector, seven combinations of ORFs were successfully replaced with EGFP without affecting the immunogenicity of the vector backbone. Finally, a recombinant rHN20-vvIBDV-VP2 strain, expressing the VP2 protein of very virulent infectious bursa disease virus (vvIBDV), was rescued and showed complete protection against FAdV-4 and vvIBDV. Thus, the novel FAdV-4 vector could provide sufficient protection for HHS and efficient exogenous gene delivery. Overall, our findings systemically identified 23 non-essential ORFs for FAdV-4 replication and seven foreign gene insertion regions, providing valuable information for an in-depth understanding of the novel FAdV-4 pathogenesis and development of multivalent vaccines.

Short term but highly efficient Cas9 expression mediated by excisional system using adenovirus vector and Cre

Genome editing techniques such as CRISPR/Cas9 have both become common gene engineering technologies and have been applied to gene therapy. However, the problems of increasing the efficiency of genome editing and reducing off-target effects that induce double-stranded breaks at unexpected sites in the genome remain. In this study, we developed a novel Cas9 transduction system, Exci-Cas9, using an adenovirus vector (AdV). Cas9 was expressed on a circular molecule excised by the site-specific recombinase Cre and succeeded in shortening the expression period compared to AdV, which expresses the gene of interest for at least 6 months. As an example, we chose hepatitis B, which currently has more than 200 million carriers in the world and frequently progresses to liver cirrhosis or hepatocellular carcinoma. The efficiencies of hepatitis B virus genome disruption by Exci-Cas9 and Cas9 expression by AdV directly (Avec) were the same, about 80–90%. Furthermore, Exci-Cas9 enabled cell- or tissue-specific genome editing by expressing Cre from a cell- or tissue-specific promoter. We believe that Exci-Cas9 developed in this study is useful not only for resolving the persistent expression of Cas9, which has been a problem in genome editing, but also for eliminating long-term DNA viruses such as human papilloma virus.