RT Journal Article SR Electronic(1) A1 Sanz, Ana I. A1 Fraile, Aurora A1 Garcı́a-Arenal, Fernando A1 Zhou, Xueping A1 Robinson, David J. A1 Khalid, Saif A1 Butt, Tahir A1 Harrison, Bryan D. YR 2000 T1 Multiple infection, recombination and genome relationships among begomovirus isolates found in cotton and other plants in Pakistan JF Journal of General Virology, VO 81 IS 7 SP 1839 OP 1849 DO https://doi.org/10.1099/0022-1317-81-7-1839 PB Microbiology Society, SN 1465-2099, AB Begomoviruses occur in many plant species in Pakistan and are associated with an epidemic of cotton leaf curl disease that has developed since 1985. PCR analysis with primer pairs specific for each of four already sequenced types of DNA-A of cotton leaf curl virus (CLCuV-PK types a, 26, 72b and 804a), or for okra yellow vein mosaic virus (OYVMV), indicated that many individual naturally infected plants of cotton and other malvaceous species contained two or three begomovirus sequences. Similarly, sequence differences among overlapping fragments of begomovirus DNA-A, amplified from individual naturally infected plants, indicated much multiple infection in malvaceous and non-malvaceous species. Some cotton plants contained DNA-A sequences typical of begomoviruses from non-malvaceous species, and some non-malvaceous plants contained sequences typical of CLCuV-PK. Some DNA-A sequences were chimaeric; they each included elements typical of different types of CLCuV-PK, or of different malvaceous and/or non-malvaceous begomoviruses. Often an apparent recombination site occurred at the origin of replication. No complete CLCuV-PK DNA-A sequence was found in malvaceous or non-malvaceous species collected in Pakistan outside the area of the cotton leaf curl epidemic but chimaeric sequences, including a part that was typical of CLCuV-PK DNA-A, did occur there. We suggest that recombination among such pre-existing sequences was crucial for the emergence of CLCuV-PK. Recombination, following multiple infection, could also explain the network of relationships among many of the begomoviruses found in the Indian subcontinent, and their evolutionary divergence, as a group, from begomoviruses causing similar diseases in other geographical regions., UL https://www.microbiologyresearch.org/content/journal/jgv/10.1099/0022-1317-81-7-1839