Investigation of some viruses in alfalfa production areas of Muş province using multiplex RT-PCR method and molecular characterization of some virus isolates

In 2023, survey studies were conducted in Muş province and its districts to detect the presence of alfalfa viruses (AMV, BYMV, CMV, CYVV) in alfalfa cultivation areas. The multiplex RT-PCR method was used to test for the presence of alfalfa viruses. Molecular characterization of the coat protein and movement protein genes of the AMV virus detected in Muş was performed. A total of 479 fresh alfalfa leaf samples were collected from alfalfa fields in Muş. AMV was detected in 17 out of the 479 tested alfalfa samples. The general infection rate of alfalfa viruses in Muş was found to be 3.54%. None of the samples tested positive for BYMV, CMV, or CYVV. Three positive AMV isolates were randomly selected, and the coat protein genes and movement protein genes were characterized molecularly. The full-length coat protein genes of the viruses AMV 121 (GenBank Accession No: PP760451), AMV 199 (GenBank Accession No: PP781953), and AMV 217 (GenBank Accession No: PP781954) were cloned, as well as the full-length movement protein genes of AMV 121 (GenBank Accession No: PP760452), AMV 199 (GenBank Accession No: PP781955), and AMV 217 (GenBank Accession No: PP781956). The nucleotide sequences of these genes were determined using next-generation sequencing (NGS). The CP gene nucleotide sequences of the current isolates showed similarity rates ranging from 94% to 100% with other isolates from Turkey and from 93% to 100% with isolates worldwide, respectively. On the other hand, the MP genes displayed nucleotide homology ranging from 93% to 100% with other isolates from Turkey and from 92% to 100% with isolates worldwide. This study reports the presence of AMV in alfalfa cultivation areas in Muş province for the first time.