The Prevalence of the Citrus tristeza virus Trifoliate Resistance Breaking Genotype Among Puerto Rican Isolates

A Comprehensive Analysis of Citrus Tristeza Variants of Bhutan and Across the World

Mandarin orange is economically one of the most important fruit crops in Bhutan. However, in recent years, orange productivity has dropped due to severe infection of citrus tristeza virus (CTV) associated with the gradual decline of citrus orchards. Although the disease incidence has been reported, very limited information is available on genetic variability among the Bhutanese CTV variants. This study used reverse transcription PCR (RT-PCR) to detect CTV in collected field samples and recorded disease incidence up to 71.11% in Bhutan’s prominent citrus-growing regions. To elucidate the extent of genetic variabilities among the Bhutanese CTV variants, we targeted four independent genomic regions (5′ORF1a, p25, p23, and p18) and analyzed a total of 64 collected isolates. These genomic regions were amplified and sequenced for further comparative bioinformatics analysis. Comprehensive phylogenetic reconstructions of the GenBank deposited sequences, including the corresponding genomic locations from 53 whole-genome sequences, revealed unexpected and rich diversity among Bhutanese CTV variants. A resistant-breaking (RB) variant was also identified for the first time from the Asian subcontinent. Our analyses unambiguously identified five (T36, T3, T68, VT, and HA16-5) major, well-recognized CTV strains. Bhutanese CTV variants form two additional newly identified distinct clades with higher confidence, B1 and B2, named after Bhutan. The origin of each of these nine clades can be traced back to their root in the north-eastern region of India and Bhutan. Together, our study established a definitive framework for categorizing global CTV variants into their distinctive clades and provided novel insights into multiple genomic region-based genetic diversity assessments, including their pathogenicity status.

Identification and Characterization of Resistance-Breaking (RB) Isolates of Citrus tristeza virus

Resistance-breaking (RB) strains constitute a clade of biological and genetically distinct isolates of Citrus tristeza virus (CTV) that replicate and move systemically in Poncirus trifoliata (trifoliate orange), resistant to other known strains of CTV. Molecular markers have been developed by comparative genome analysis to allow quick identification of potential RB isolates. Here, methods are described to identify and characterize RB strains by reverse transcription-polymerase chain reaction (RT-PCR), quantitative real-time RT-PCR (RT-qPCR), full-length genome sequencing, and biological indexing.

Titer Variation of Citrus Tristeza Virus in Aphids at Different Acquisition Access Periods and Its Association with Transmission Efficiency

Tristeza, caused by citrus tristeza virus (CTV; Closterovirus, Closteroviridae), is of significant economic importance. Tristeza epidemics have caused severe declines in productivity, and even death, of millions of citrus trees on sour orange rootstock in many regions all over the world. In the field, CTV is most efficiently vectored by the brown citrus aphid (Toxoptera citricida (Kirkaldy)) in a semipersistent manner. The transmission efficiency of the vector is influenced by its acquisition access period (AAP) for CTV. A real-time RT-PCR assay using SYBR Green fluorescent dye was used to estimate the CTV titers in groups of 15 aphids under AAPs after 0.5 to 48 h for three CTV isolates (CT11A, CT16-2, and CTLJ). Similar trends for CTV titer in viruliferous aphids were displayed for the three isolates. The maximum CTV titer was at AAP 6 h for isolates CT11A and CT16-2, and at 4 h for isolate CTLJ. During the AAPs from 0.5 to 6 h, the mean CTV titer of CT16-2 increased from 7.8 × 10⁴ to 1.71 × 10⁷ copies per 15 aphids, and was correlated with an increase in transmission rate from 20 to 90.9%. This suggests that the transmission efficiency is positively correlated with viral titer in the insect from 0.5 h until 6 h AAPs. While a downward trend in CTV titer was observed after a 6-h AAP, the transmission rate remained higher than 90% up to 48 h. These results indicate that factors other than the virus titer in the vector contribute to successful transmission under long acquisition conditions. This is the first detailed quantitative analysis of CTV in its main vector species following different AAPs and its association with transmission efficiency, and should enhance our understanding of T. citricida-CTV interactions.

Pest categorisation of Citrus tristeza virus (non-European isolates)

The Panel on Plant Health performed a pest categorisation of non-European isolates of Citrus tristeza virus (CTV) for the EU territory. CTV is a well characterised virus for which efficient detection assays are available. It is transmitted by vegetative multiplication of infected hosts and by aphid vectors. The most efficient one, Toxoptera citricida, has limited EU presence but another one, Aphis gossypii, is broadly distributed. CTV is reported from a range of countries outside the EU and EU isolates are present in seven of the eight citrus-growing member states. Non-EU isolates are not known to occur in the EU and therefore do not meet one of the criteria for being a Union regulated non-quarantine pest. The natural host range of CTV is restricted to Citrus, Fortunella and Poncirus species. CTV non-EU isolates are listed in Annex IIAI of Directive 2000/29/EC and the main pathway for entry, plants for planting, is closed by the existing legislation. CTV isolates may therefore only enter through minor alternative pathways. They have the potential to subsequently spread through plants for planting and through the action of aphid vectors. CTV non-EU isolates are able to cause severe symptoms on a range of citrus crops that EU isolates do not induce. Overall, non-EU CTV isolates meet all the criteria evaluated by EFSA to qualify as Union quarantine pests. The main knowledge gaps and uncertainties concern (1) the status of Rutaceae species other than Citrus, Fortunella and Poncirus as natural hosts for CTV; (2) the potential undetected presence of non-EU CTV isolates in the EU and in particular the prevalence and biological properties of CTV isolates that may be present in ornamental citrus; and (3) the inability of EU CTV isolates apparently related to non-European stem pitting (SP) isolates to cause SP in sweet orange.

Identification and Characterization of Citrus tristeza virus Isolates Breaking Resistance in Trifoliate Orange in California

Most Citrus tristeza virus (CTV) isolates in California are biologically mild and symptomless in commercial cultivars on CTV tolerant rootstocks. However, to better define California CTV isolates showing divergent serological and genetic profiles, selected isolates were subjected to deep sequencing of small RNAs. Full-length sequences were assembled, annotated and trifoliate orange resistance-breaking (RB) isolates of CTV were identified. Phylogenetic relationships based on their full genomes placed three isolates in the RB clade: CA-RB-115, CA-RB-AT25, and CA-RB-AT35. The latter two isolates were obtained by aphid transmission from Murcott and Dekopon trees, respectively, containing CTV mixtures. The California RB isolates were further distinguished into two subclades. Group I included CA-RB-115 and CA-RB-AT25 with 99% nucleotide sequence identity with RB type strain NZRB-G90; and group II included CA-RB-AT35 with 99 and 96% sequence identity with Taiwan Pumelo/SP/T1 and HA18-9, respectively. The RB phenotype was confirmed by detecting CTV replication in graft-inoculated Poncirus trifoliata and transmission from P. trifoliata to sweet orange. The California RB isolates induced mild symptoms compared with severe isolates in greenhouse indexing tests. Further examination of 570 CTV accessions, acquired from approximately 1960 and maintained in planta at the Central California Tristeza Eradication Agency, revealed 16 RB positive isolates based on partial p65 sequences. Six isolates collected from 1992 to 2011 from Tulare and Kern counties were CA-RB-115-like; and 10 isolates collected from 1968 to 2010 from Riverside, Fresno, and Kern counties were CA-RB-AT35-like. The presence of the RB genotype is relevant because P. trifoliata and its hybrids are the most popular rootstocks in California.