Genetic Connectivity Between Papaya Ringspot Virus Genomes from Papua New Guinea and Northern Australia, and New Recombination Insights.

Isolates of papaya ringspot virus (PRSV) were obtained from plants of pumpkin (Cucurbita spp.) or cucumber (Cucumis sativus) showing mosaic symptoms growing at Zage in Goroka District in the Eastern Highland Province of Papua New Guinea (PNG) or Bagl in the Mount Hagen District, Western Highlands Province. The samples were sent to Australia on FTA cards where they were subjected to High Throughput Sequencing (HTS). When the coding regions of the six new PRSV genomic sequences obtained via HTS were compared with those of 54 other complete PRSV sequences from other parts of the world, all six grouped together with the 12 northern Australian sequences within major phylogroup B minor phylogroup I, the Australian sequences coming from three widely dispersed locations spanning the north of the continent. Notably, none of the PNG isolates grouped with genomic sequences from the nearby country of East Timor in phylogroup A. The closest genetic match between Australian and PNG sequences was a nucleotide (nt) sequence identity of 96.9%, whereas between PNG and East Timorese isolates it was only 83.1%. These phylogenetic and nt identity findings demonstrate genetic connectivity between PRSV populations from PNG and Australia. Recombination analysis of the 60 PRSV sequences available revealed evidence of 26 recombination events within 18 isolates, only four of which were within major phylogroup B and none of which were from PNG or Australia. Within the recombinant genomes, the P1, Cl, NIa-Pro, NIb, 6K2, and 5'UTR regions contained the highest numbers of recombination breakpoints. After removal of nonrecombinant sequences, four minor phylogroups were lost (IV, VII, VIII, XV), only one of which was in phylogroup B. When genome regions from which recombinationally derived tracts of sequence were removed from recombinants prior to alignment with nonrecombinant genomes, seven previous minor phylogroups within major phylogroup A, and two within major phylogroup B, merged either partially or entirely forming four merged minor phylogroups. The genetic connectivity between PNG and northern Australian isolates and absence of detectable recombination within either group suggests that PRSV isolates from East Timor, rather than PNG, might pose a biosecurity threat to northern Australian agriculture should they prove more virulent than those already present.

Zucchini yellow mosaic virus Genomic Sequences from Papua New Guinea: Lack of Genetic Connectivity with Northern Australian or East Timorese Genomes, and New Recombination Findings.

Zucchini yellow mosaic virus (ZYMV) isolates were obtained in Papua New Guinea (PNG) from cucumber (Cucumis sativus) or pumpkin (Cucurbita spp.) plants showing mosaic symptoms growing at Kongop in the Mount Hagen District, Western Highlands Province, or Zage in the Goroka District, Eastern Highlands Province. The samples were blotted onto FTA cards, which were sent to Australia, where they were subjected to high-throughput sequencing. When the coding regions of the nine new ZYMV genomic sequences found were compared with those of 64 other ZYMV sequences from elsewhere, they grouped together, forming new minor phylogroup VII within ZYMV's major phylogroup A. Genetic connectivity was lacking between ZYMV genomic sequences from PNG and its neighboring countries, Australia and East Timor; the closest match between a PNG and any other genomic sequence was a 92.8% nucleotide identity with a sequence in major phylogroup A's minor phylogroup VI from Japan. When the RDP5.2 recombination analysis program was used to compare 66 ZYMV sequences, evidence was obtained of 30 firm recombination events involving 41 sequences, and all isolates from PNG were recombinants. There were 21 sequences without recombination events in major phylogroup A, whereas there were only 4 such sequences within major phylogroup B. ZYMV's P1, Cl, N1a-Pro, P3, CP, and NIb regions contained the highest evidence of recombination breakpoints. Following removal of recombinant sequences, seven minor phylogroups were absent (I, III, IV, V, VI, VII, and VIII), leaving only minor phylogroups II and IX. By contrast, when a phylogenetic tree was constructed using recombinant sequences with their recombinationally derived tracts removed before analysis, five previous minor phylogroups remained unchanged within major phylogroup A (II, III, IV, V, and VII) while four formed two new merged phylogroups (I/VI and VIII/IX). Absence of genetic connectivity between PNG, Australian, and East Timorese ZYMV sequences, and the 92.8% nucleotide identity between a PNG sequence and the closest sequence from elsewhere, suggest that a single introduction may have occurred followed by subsequent evolution to adapt to the PNG environment. The need for enhanced biosecurity measures to protect against potentially damaging virus movements crossing the seas separating neighboring countries in this region of the world is discussed.

First Complete Genome Sequence of Cucurbit aphid-borne yellows virus from Papua New Guinea.

Analysis of an RNA-Seq library from cucumber leaf RNA revealed the first complete genome sequence of Cucurbit aphid-borne yellows virus (CABYV) from Papua New Guinea. We compared it with 36 complete CABYV genomes from other world regions. It most resembled the genome of South Korean isolate GS6.