Global dynamics of a delayed latent virus model with both virus-to-cell and cell-to-cell transmissions and humoral immunity

In this paper, the dynamical behaviors for multiple delayed latent virus model with virus-to-cell infection and cell-to-cell transmissions and humoral immunity are investigated. The virus-to-cell and cell-to-cell incidence rates are modeled by general nonlinear functions. The basic reproduction number $R_{0}$ R 0 and the humoral immune response number $R_{1}$ R 1 are calculated and proved to be threshold conditions determining the local and global properties of the virus model. The existence of Hopf bifurcation with immune delay as a bifurcation parameter is presented, and the effects of some key parameters on viral dynamics are revealed by numerical simulations.

Double Infection of Onion yellow dwarf virus and Shallot latent virus in Garlic from Several Regions in Indonesia

Viruses have been a problem on garlic cultivations in various countries. There are several viruses reported infecting garlic. Genera Potyvirus and Carlavirus are the most common viruses found infecting garlic. Mixed infection on garlic is often designated as a “garlic viral complex”. These viruses can be transmitted through imported garlic seeds. Therefore, it is necessary to conduct early detection of garlic seeds to prevent the epidemic of these viruses. This study aimed to detect Onion yellow dwarf virus (OYDV) and Shallot latent virus (SLV) on garlic. Garlic samples were obtained from Enrekang, Magelang, Temanggung, Tawangmangu, and Yogyakarta. Total RNA was extracted from the samples and subsequently used for RT-PCR using two pairs of specific primers SLV-F/SLV-R and OYDV-F/OYDV-R. Primary pair SLV-F/SLV-R in amplicons sized 276 bp, while OYDV-F/OYDV-R in amplicons sized 112 bp. RT-PCR results showed that OYDV was found in all samples tested in this study. Meanwhile, double infections (OYDV and SLV) were found in eight out of ten samples tested. These results indicated that double infections on garlic were common in Indonesia.

Detection and Distribution of Viruses Infecting Garlic Crops in Australia

The distribution of viruses in eastern Australian field garlic was evaluated. Detection assays were developed that involved generic RT-PCR for viruses in the Allexivirus, Carlavirus and Potyvirus genera followed by virus-specific colorimetric dot-blot hybridization. Assays targeted the potyviruses (onion yellow dwarf virus (OYDV), shallot yellow stripe virus (SYSV), and leek yellow stripe virus (LYSV)), the carlaviruses (garlic common latent virus (GCLV) and shallot latent virus (SLV)), and the allexiviruses (garlic viruses A, B, C, X (GarVA, -B, -C, -X) and shallot virus X (ShVX)). Virus incidence in crops was consistently high, with most plants infected with at least one virus from each genus. OYDV, LYSV, SLV, and GCLV were commonly detected. Three of the four allexiviruses were in all districts surveyed but varied in incidence, whereas ShVX and SYSV were not detected. There was no association between virus species complement and bulb size, indicating size is not a good predictor of the virus status of planting material. The variation of virus incidence across different Australian growing districts and in different cultivars implies multiple introductions of viruses rather than spread within the country. The genetic diversity observed within coat protein sequences of some virus species also supports multiple separate introductions.

Phylogenetic and diversity analyses of Garlic common latent virus based on the TGB and CP gene sequence

Garlic common latent virus (GarCLV, Carlavirus), in co-infection, often worsens the severity of other Allium viruses on the garlic (Allium sativum Linnaeus). The nucleotide (nt) and amino acid (aa) sequences of the TGB and CP genes were analysed to get the first deep insight into the genomic variations and population structure of GarCLV. Global recombinant-free isolates were clustered into three clades in both the nt-based phylogenetic trees of TGB and CP. The clade 3 isolates shared low similarity percentages among themselves, as well as to the clade 1 and 2 isolates. Most major aa changes in the CP were observed on its 5' and 3' ends. Clade 2 obtained the lowest S, η, k, and π values for both the TGB and CP, which indicated low variations among its isolates. Both TGB and CP have undergone a negative selection, with CP being under stronger negative pressure than TGB. Neutrality tests estimated the non-significant negative values to all clades for TGB and CP, except Tajima's D for clade 2 of the TGB. The results of the K_s*, K_st*, Z*, and Snn tests suggested that all three phylogroups were divergent to each other for both TGB and CP. The high F_st on all the clade comparisons for both TGB and CP showed a large gene flow among three clades.

Actinidia seed-born latent virus is transmitted paternally and maternally at high rates

Actinidia seed-borne latent virus (ASbLV, Betaflexiviridae), was detected at high frequency in healthy seedlings grown from lines of imported seed in a New Zealand post-entry quarantine facility. To better understand how to manage this virus in a dioecious crop species, we developed a rapid molecular protocol to detect infected progeny and to identify a reliable plant tissue appropriate to detect transmission rates from paternal and maternal parents under quarantine environment.The frequency of ASbLV detection from true infection of F1 progeny was distinguished by testing whole seeds and progeny seedling tissues from a controlled cross between two unrelated parents; an ASbLV-infected staminate (male) plant and an uninfected pistillate (female) plant, and the process was repeated with an ASbLV uninfected staminate (male) plant and an infected pistillate (female) plant. Individual whole seeds, or single cotyledons from newly-emerged seedlings, true leaf or a root from those positive-tested seedlings, were assessed for presence of ASbLV by reverse transcription-polymerase chain reaction (RT-PCR) analysis. The virus was detected at a high incidence (98%) in individual seeds, but at a much lower incidence in seedling cotyledons (62%). Since detection results were consistent (P=95%) across the three seedling tissues (i.e. cotyledons, leaves and roots) only cotyledons were tested thereafter to determine ASbLV transmission to F1 progeny. F1 seedlings from three crosses were used to compare transmission rates from infected staminate versus infected pistillate parents. One cross from a single flower used an uninfected pistillate vine pollinated by an infected staminate vine, and two crosses (also from a single flower) used an infected pistillate vine (a sibling of the infected staminate vine), pollinated by either of two unrelated uninfected staminate vines.Cotyledon testing of seedlings from each cross confirmed staminate transmission at high frequency (∼60%), and pistillate transmission at even higher frequency (81% and 86%, respectively).The results show ASbLV is transmitted at very high rates, whether from infected ovules or pollen. Transmission to seedlings is lower than detection in whole seeds perhaps due to ASbLV being sometimes residing on (or within) the seed coat only. The results also show RT-PCR of cotyledons allows non-destructive detection of ASbLV in very young seedlings, and could be used to screen kiwifruit plants in a nursery to avoid virus spread to orchards. Likewise, bulk testing of seed lots can quickly detect infected parent plants (fruit bearing female or male pollinator) already in an orchard.ImportanceActinidia seed-borne latent virus (ASbLV, Betaflexiviridae), was detected at high frequency in healthy seedlings grown from lines of imported seed in a New Zealand post-entry quarantine facility. However there are several technical barriers to detecting the presence of seed transmitted viruses and understanding their biology, which has significance for detection in quarantine and subsequent management under germplasm collections. To overcome this, we developed a rapid molecular protocol to detect infected progeny and to identify a reliable plant tissue appropriate to detect transmission rates from paternal and maternal parents under quarantine environment. Individual whole seeds, or single cotyledons from newly-emerged seedlings, true leaf or a root from those positive-tested seedlings, were assessed for presence of ASbLV by reverse transcription-polymerase chain reaction (RT-PCR) analysis. This was done with seed lots obtained from four separate controlled crosses between ASbLV-infected and ASbLV-uninfected Actinidia chinensis var. deliciosa parents.