Description of the female, nymph and larva and mitochondrial genome, and redescription of the male, of Ixodes barkeri Barker, 2019 (Acari: Ixodidae) from the short-beaked echidna, Tachyglossus aculeatus, with a consideration of the most suitable subgenus for this tick

Background Ixodes barkeri, a tick with a distinctive ventrolateral horn-like projection on palpal segment 1, was described in 2019 from two male ticks from the Wet Tropics of Far North Queensland, Australia. However, females lie at the core of the taxonomy and subgenus classification of Ixodes, hence we sought specimens of female ticks, successfully recovering females, plus nymphs and larvae. Mitochondrial genomes are also desirable additions to the descriptions of species of ticks particularly with regard to subgenus systematics. So, we sequenced the mt genomes of I. barkeri Barker, 2019 and the possible relatives of I. barkeri that were available to us (I. australiensis Neumann, 1904, I. fecialis Warburton & Nuttall, 1909, and I. woyliei Ash et al. 2017) with a view to discovering which if any of the subgenera of Ixodes would be most suitable for I. barkeri Barker, 2019. Results The female, nymph, larva, and mitochondrial genome of Ixodes barkeri Barker, 2019 are described for the first time and the male of I. barkeri is redescribed in greater detail than previously. So far, I. barkeri is known only from a monotreme, the short-beaked echidna, Tachyglossus aculeatus (Shaw, 1792), from the highland-rainforests of Far North Queensland, Australia. Conclusions Our phylogeny from entire mitochondrial genomes indicated that I. barkeri, and indeed I. woyliei Ash et al. 2017, another tick that was described recently, are best placed in the subgenus Endopalpiger Schulze, 1935.

Visualizations of Topologic Entropy on SARS-CoV-2 Genomes in Multiple Regions

The outbreak of novel coronavirus (SARS-CoV-2) developed into a global pandemic in a few months. The latest study found that the virus belongs to the beta coronavirus family. SARS-CoV-2 is highly similar to Pangolin CoV and BatCoV RaTG. Advanced scientific studies help traceability and vaccine development. In addition to the subgenus classification analysis of the virus, it is interesting for further exploration to focus attention on mutations and their transmissions in different regions. New mutations may be likely to affect the symptoms of the disease and the effectiveness of vaccination. This paper is focused on the study to make error bars and scatter graphs with the support of the metagenetic analysis system MAS. Using SARS-CoV-2 genomes in different countries and regions as input datasets, topological entropy values provide global characteristic quantities based on C4 module for visualization. Sample results show that the method is powerful and useful for consistently integrating all genomes on one unique genomic index map. Various countries have confirmed their specific positions and projections under topologic entropies. Further explorations are required.

Visualizations of Topologic Entropy on SARS-CoV-2 Genomes in Multiple Regions

The outbreak of novel coronavirus (SARS-CoV-2) developed into a global pandemic in a few months. The latest study found that the virus belongs to the beta coronavirus family. SARS-CoV-2 is highly similar to Pangolin CoV and BatCoV RaTG. Advanced scientific studies help traceability and vaccine development. In addition to the subgenus classification analysis of the virus, it is interesting for further exploration to focus attention on mutations and their transmissions in different regions. New mutations may be likely to affect the symptoms of the disease and the effectiveness of vaccination. This paper is focused on the study to make error bars and scatter graphs with the support of the metagenetic analysis system MAS. Using SARS-CoV-2 genomes in different countries and regions as input datasets, topological entropy values provide global characteristic quantities based on C4 module for visualization. Sample results show that the method is powerful and useful for consistently integrating all genomes on one unique genomic index map. Various countries have confirmed their specific positions and projections under topologic entropies. Further explorations are required.

Visualizations of Topologic Entropy on SARS-CoV-2 Genomes in Multiple Regions

The outbreak of novel coronavirus (SARS-CoV-2) developed into a global pandemic in a few months. The latest study found that the virus belongs to the beta coronavirus family. SARS-CoV-2 is highly similar to Pangolin CoV and BatCoV RaTG. Advanced scientific studies help traceability and vaccine development. In addition to the subgenus classification analysis of the virus, it is interesting for further exploration to focus attention on mutations and their transmissions in different regions. New mutations may be likely to affect the symptoms of the disease and the effectiveness of vaccination. This paper is focused on the study to make error bars and scatter graphs with the support of the metagenetic analysis system MAS. Using SARS-CoV-2 genomes in different countries and regions as input datasets, topological entropy values provide global characteristic quantities based on C4 module for visualization. Sample results show that the method is powerful and useful for consistently integrating all genomes on one unique genomic index map. Various countries have confirmed their specific positions and projections under topologic entropies. Further explorations are required.

Partial RdRp sequences offer a robust method for Coronavirus subgenus classification

The recent reclassification of the Riboviria, and the introduction of multiple new taxonomic categories including both subfamilies and subgenera for coronaviruses (family Coronaviridae, subfamily Orthocoronavirinae) represents a major shift in how official classifications are used to designate specific viral lineages. While the newly defined subgenera provide much-needed standardisation for commonly cited viruses of public health importance, no method has been proposed for the assignment of subgenus based on partial sequence data, or for sequences that are divergent from the designated holotype reference genomes. Here, we describe the genetic variation of a partial region of the coronavirus RNA-dependent RNA polymerase (RdRp), which is one of the most used partial sequence loci for both detection and classification of coronaviruses in molecular epidemiology. We infer Bayesian phylogenies from more than 7000 publicly available coronavirus sequences and examine clade groupings relative to all subgenus holotype sequences. Our phylogenetic analyses are largely coherent with genome-scale analyses based on designated holotype members for each subgenus. Distance measures between sequences form discrete clusters between taxa, offering logical threshold boundaries that can attribute subgenus or indicate sequences that are likely to belong to unclassified subgenera both accurately and robustly. We thus propose that partial RdRp sequence data of coronaviruses is sufficient for the attribution of subgenus-level taxonomic classifications and we supply the R package, “MyCoV”, which provides a method for attributing subgenus and assessing the reliability of the attribution.Importance StatementThe analysis of polymerase chain reaction amplicons derived from biological samples is the most common modern method for detection and classification of infecting viral agents, such as Coronaviruses. Recent updates to the official standard for taxonomic classification of Coronaviruses, however, may leave researchers unsure as to whether the viral sequences they obtain by these methods can be classified into specific viral taxa due to variations in the sequences when compared to type strains. Here, we present a plausible method for defining genetic dissimilarity cut-offs that will allow researchers to state which taxon their virus belongs to and with what level of certainty. To assist in this, we also provide the R package ‘MyCoV’ which classifies user generated sequences.

Two new Cryptoxilos species (Hymenoptera:Braconidae:Euphorinae) from New Zealand and Fiji parasitising adult Scolytinae (Coleoptera)

Two new species of Cryptoxilos are described from the South Pacific region. A new species from Auckland, New Zealand, Cryptoxilos thorpei Shaw & Berry, is described and illustrated. This is the first described species of the genus Cryptoxilos from New Zealand. The species is associated with a scolytine bark beetle, Chaetoptelius mundulus (Broun) (Coleoptera : Scolytinae), on a dead Pittosporum tree. A second new species, Cryptoxilos beaveri Shaw & Berry, is described from Fiji, also a new locality record for the genus. The species is associated with cryphaline ambrosia beetles, Hypothenemus curtipennis and Hypothenemus dorsosignatus, in the tree Commersonia bartramia. The existing subgenus classification system is discussed in relation to character states expressed in these two new species. Neither new species can be easily assigned to a subgenus based on the existing system. Given serious problems in the consistent application of the previous subgenus system, we recommend that subgenera be abandoned and we treat subgenus Cryptoxiloides simply as a junior synonym of Cryptoxilos.