International Committee on Taxonomy of Viruses and the 3,142 unassigned species

In 2005, ICTV (International Committee on Taxonomy of Viruses), the official body of the Virology Division of the International Union of Microbiological Societies responsible for naming and classifying viruses, will publish its latest report, the state of the art in virus nomenclature and taxonomy. The book lists more than 6,000 viruses classified in 1,950 species and in more than 391 different higher taxa. However, GenBank contains a staggering additional 3,142 "species" unaccounted for by the ICTV report. This paper reviews the reasons for such a situation and suggests what might be done in the near future to remedy this problem, particularly in light of the potential for a ten-fold increase in virus sequencing in the coming years that would generate many unclassified viruses. A number of changes could be made both at ICTV and GenBank to better handle virus taxonomy and classification in the future

Distribution and diversity of local strains of rice yellow motile virus in Tanzania

Rice (Oryza sativa) is a key staple in Tanzania but its productivity is affected by disease infestation, primary among which is the rice yellow mottle virus (RYMV). Tanzania possesses high RYMV densities and several locations including the Eastern Arc Mountains provide suitable habitat fragmentation that facilitates the diversification process of the virus. However, the distribution pattern and diversity of the local strains of RYMV remain largely unknown and this hinders progress in designing interventions. Efforts were, therefore, made to study the pattern and distribution of RYMV. Collection of isolates was made in May; recovery of virus on a susceptible elite line viz. TXD 220-1-3-3-1 was in June-July and molecular analysis was done in September-December 2005. The sequences of the coat protein (CP) gene of 23 isolates, representative of the three strains of RYMV found in Tanzania, were selected from 52 isolates collected from three regions. The phylogenetic analyses of the CP sequences revealed high (14.8%) nucleotide divergence between strains. Strain S6 was the most divergent with an intra- strain nucleotide divergence of 8.8%; this was consistent with its wide distribution in the region and particularly the eastern part of the Tanzania. Isolates of strains S4 were recorded for the first time in the eastern Arc Mountain region. These formed a monophyletic group with the Lake Malawi strain S4 sub-lineage (percentage identity of 95.4 to 96.8%) and differed from the Lake Victoria strain S4 sub-lineage by 4.5%. Coexistence within the same field of S4, S5 and S6 isolates was observed in the eastern Arc Mountains region. Strong competition between strains of RYMV was suspected from the limited distribution and rarity of strain S5. This study confirm speculations that the Eastern Arc Mountain region is the centre of origin of RYMV. Thus, the high viral load in the Eastern Arc Mountain imply that it is a suitable location for strategic studies aimed at designing control interventions against RYMV

First report of Rice yellow mottle virus on rice in the Democratic Republic of Congo

International audienc

Evaluation of cultural control and resistance‐breeding strategies for suppression of whitefly infestation of cassava at the landscape scale: a simulation modeling approach

Background: The whitefly Bemisia tabaci is an important vector of virus diseases, impacting cassava production in East Africa. To date, breeding efforts in this region have focused on disease resistance. Here we use a spatially‐explicit simulation model to explore how breeding strategies for whitefly resistance will influence the population dynamics of whitefly in the context of regional variation in cassava crop management practices. Results: Simulations indicated that regions with a short cropping cycle and two cropping seasons per year were associated with high whitefly abundance. Nymph mortality and antixenosis resistance mechanisms were more effective than mechanisms that lead to longer whitefly development times. When spatial variation was introduced in heterogeneous landscapes, however, negative consequences of the antixenosis effect were observed in fields containing whitefly susceptible varieties, unless the proportion of whitefly resistant variety in the landscape was low (~10%) or the amount of matrix in the landscape was high (~75%). Conclusion: We show the importance of considering cropping regime and landscape management context when developing and deploying whitefly‐resistant cassava varieties. Recommendations differ significantly between regions. There may also be unintended negative consequences of higher whitefly densities for whitefly susceptible varieties if uptake of the new variety in a landscape is high, depending on the mechanism of resistance and the landscape context. Furthermore, we show that in some cases, such as where there is substantial fallow combined with a short single‐season crop, the management characteristics of the existing cropping regime alone may be effective at controlling whitefly populations

Clustering of magnetic reconnection exhausts in the solar wind: An automated detection study

CONTEXT: Magnetic reconnection is a fundamental process in astrophysical plasmas that enables the dissipation of magnetic energy at kinetic scales. Detecting this process in situ is therefore key to furthering our understanding of energy conversion in space plasmas. However, reconnection jets typically scale from seconds to minutes in situ, and as such, finding them in the decades of data provided by solar wind missions since the beginning of the space era is an onerous task. AIMS: In this work, we present a new approach for automatically identifying reconnection exhausts in situ in the solar wind. We apply the algorithm to Solar Orbiter data obtained while the spacecraft was positioned at between 0.6 and 0.8 AU and perform a statistical study on the jets we detect. METHODS: The method for automatic detection is inspired by the visual identification process and strongly relies on the Walén relation. It is enhanced through the use of Bayesian inference and physical considerations to detect reconnection jets with a consistent approach. RESULTS: Applying the detection algorithm to one month of Solar Orbiter data near 0.7 AU, we find an occurrence rate of seven jets per day, which is significantly higher than in previous studies performed at 1 AU. We show that they tend to cluster in the solar wind and are less likely to occur in the tenuous solar wind (< 10 cm−3 near 0.7 AU). We discuss why the source and the degree of Alfvénicity of the solar wind might have an impact on magnetic reconnection occurrence. CONCLUSIONS: By providing a tool to quickly identify potential magnetic reconnection exhausts in situ, we pave the way for broader statistical studies on magnetic reconnection in diverse plasma environments

Using Solar Orbiter as an upstream solar wind monitor for real time space weather predictions

Coronal mass ejections (CMEs) can create significant disruption to human activities and systems on Earth, much of which can be mitigated with prior warning of the upstream solar wind conditions. However, it is currently extremely challenging to accurately predict the arrival time and internal structure of a CME from coronagraph images alone. In this study, we take advantage of a rare opportunity to use Solar Orbiter, at 0.5\,AU upstream of Earth, as an upstream solar wind monitor. We were able to use real time science quality magnetic field measurements, taken only 12 minutes earlier, to predict the arrival time of a CME prior to reaching Earth. We used measurements at Solar Orbiter to constrain an ensemble of simulation runs from the ELEvoHI model, reducing the uncertainty in arrival time from 10.4\,hours to 2.5\,hours. There was also an excellent agreement in the $B_z$ profile between Solar Orbiter and Wind spacecraft, despite being separated by 0.5\,AU and 10$^{\circ}$ longitude. Therefore, we show that it is possible to predict not only the arrival time of a CME, but the sub-structure of the magnetic field within it, over a day in advance. The opportunity to use Solar Orbiter as an upstream solar wind monitor will repeat once a year, which should further help assess the efficacy upstream in-situ measurements in real time space weather forecasting

Magnetic increases with central current sheets: Observations with Parker Solar Probe

Aims. We report the observation by Parker Solar Probe (PSP) of magnetic structures in the solar wind that present a strong peak in their magnetic field magnitude with an embedded central current sheet. Similar structures have been observed, either at the Earth’s magnetopause and called interlinked flux tubes, or in the solar wind and called interplanetary field enhancements. Methods. In this work, we first investigate two striking events in detail; one occurred in the regular slow solar wind on November 2, 2018 and the other was observed during a heliospheric current sheet crossing on November 13, 2018. They both show the presence of a central current sheet with a visible ion jet and general characteristics consistent with the occurrence of magnetic reconnection. We then performed a survey of PSP data from encounters 1 to 4 and find 18 additional events presenting an increase in the magnetic field magnitude of over 30% and a central current sheet. We performed a statistical study on the 20 "magnetic increases with central current sheet" (MICCS), with 13 observed in the regular slow solar wind with a constant polarity (i.e., identical strahl direction), and 7 which were specifically observed near a heliospheric current sheet (HCS) crossing. Results. We analyze and discuss the general properties of the structures, including the duration, location, amplitude, and magnetic topology, as well as the characteristics of their central current sheet. We find that the latter has a preferential orientation in the TN plane of the RTN frame. We also find no significant change in the dust impact rate in the vicinity of the MICCS under study, leading us to conclude that dust probably plays no role in the MICCS formation and evolution. Our findings are overall consistent with a double flux tube-configuration that would result from initially distinct flux tubes which interact during solar wind propagation

Solar Orbiter observations of the Kelvin-Helmholtz waves in the solar wind

Context. The Kelvin-HeImholtz (KH) instability is a nonlinear shear-driven instability that develops at the interface between shear flows in plasmas. KH waves have been inferred in various astrophysical plasmas, and have been observed in situ at the magnetospheric boundaries of solar-system planets and through remote sensing at the boundaries of coronal mass ejections. // Aims. KH waves are also expected to develop at flow shear interfaces in the solar wind. While they were hypothesized to play an important role in the mixing of plasmas and in triggering solar wind fluctuations, their direct and unambiguous observation in the solar wind was still lacking. // Methods. We report in-situ observations of quasi-periodic magnetic and velocity field variations plausibly associated with KH waves using Solar Orbiter during its cruise phase. They are found in a shear layer in the slow solar wind in the close vicinity of the Heliospheric Current Sheet. Analysis is performed to derive the local configuration of the waves. A 2-D MHD simulation is also set up with approximate empirical values to test the stability of the shear layer. In addition, magnetic spectra of the event are analyzed. Results. We find that the observed conditions satisfy the KH instability onset criterion from the linear theory analysis, and its de- velopment is further confirmed by the simulation. The current sheet geometry analyses are found to be consistent with KH wave development, albeit with some limitations likely owing to the complex 3D nature of the event and solar wind propagation. Addition- ally, we report observations of an ion jet consistent with magnetic reconnection at a compressed current sheet within the KH wave interval. The KH activity is found to excite magnetic and velocity fluctuations with power law scalings that approximately follow k−5/3 and k−2.8 in the inertial and dissipation ranges, respectively. Finally, we discuss reasons for the lack of in-situ KH wave detection in past data. // Conclusions. These observations provide robust evidence of KH wave development in the solar wind. This sheds new light on the process of shear-driven turbulence as mediated by the KH waves with implications for the driving of solar wind fluctuations

Historical Contingencies Modulate the Adaptability of Rice Yellow Mottle Virus

The rymv1-2 and rymv1-3 alleles of the RYMV1 resistance to Rice yellow mottle virus (RYMV), coded by an eIF(iso)4G1 gene, occur in a few cultivars of the Asiatic (Oryza sativa) and African (O. glaberrima) rice species, respectively. The most salient feature of the resistance breaking (RB) process is the converse genetic barrier to rymv1-2 and rymv1-3 resistance breakdown. This specificity is modulated by the amino acid (glutamic acid vs. threonine) at codon 49 of the Viral Protein genome-linked (VPg), a position which is adjacent to the virulence codons 48 and 52. Isolates with a glutamic acid (E) do not overcome rymv1-3 whereas those with a threonine (T) rarely overcome rymv1-2. We found that isolates with T49 had a strong selective advantage over isolates with E49 in O. glaberrima susceptible cultivars. This explains the fixation of the mutation T49 during RYMV evolution and accounts for the diversifying selection estimated at codon 49. Better adapted to O. glaberrima, isolates with T49 are also more prone than isolates with E49 to fix rymv1-3 RB mutations at codon 52 in resistant O. glaberrima cultivars. However, subsequent genetic constraints impaired the ability of isolates with T49 to fix rymv1-2 RB mutations at codons 48 and 52 in resistant O. sativa cultivars. The origin and role of the amino acid at codon 49 of the VPg exemplifies the importance of historical contingencies in the ability of RYMV to overcome RYMV1 resistance

Properties of an Interplanetary Shock Observed at 0.07 and 0.7 au by Parker Solar Probe and Solar Orbiter

Abstract The Parker Solar Probe (PSP) and Solar Orbiter (SolO) missions opened a new observational window in the inner heliosphere, which is finally accessible to direct measurements. On 2022 September 5, a coronal mass ejection (CME)-driven interplanetary (IP) shock was observed as close as 0.07 au by PSP. The CME then reached SolO, which was radially well-aligned at 0.7 au, thus providing us with the opportunity to study the shock properties at different heliocentric distances. We characterize the shock, investigate its typical parameters, and compare its small-scale features at both locations. Using the PSP observations, we investigate how magnetic switchbacks and ion cyclotron waves are processed upon shock crossing. We find that switchbacks preserve their V–B correlation while compressed upon the shock passage, and that the signature of ion cyclotron waves disappears downstream of the shock. By contrast, the SolO observations reveal a very structured shock transition, with a population of shock-accelerated protons of up to about 2 MeV, showing irregularities in the shock downstream, which we correlate with solar wind structures propagating across the shock. At SolO, we also report the presence of low-energy (∼100 eV) electrons scattering due to upstream shocklets. This study elucidates how the local features of IP shocks and their environments can be very different as they propagate through the heliosphere.</jats:p