Sequence analysis of RNA3 of Maize stripe virus associated with stripe disease of sorghum (Sorghum bicolor) in India

Maize stripe virus (MSpV), one of the distinct species of the genus Tenuivirus, has been associated with stripe disease of sorghum in India. In this study, we report the complete sequence analysis of ambisense RNA3 of four MSpV isolates associated with this disease, to confirm its correct identity. The RNA3 of four MSpV-Sorg isolates is 2357 nucleotides in length with two ORFs, one in virion sense (594 nucleotides, non-structural protein 3, NS3) and the other in complementary sense (951 nucleotides, coat protein, CP). The intergenic region between these two ORFs is 653 nucleotides in length, which is rich in U and A residues. The deduced molecular weights of NS3 and CP are ≈22 and ≈34 kDa, respectively. RNA3 has ≈82% sequence identity at nucleotide level with RNA3 of MSpV infecting maize in Florida, USA and Reunion. NS3 and CP ORFs shared ≈94% and ≈95% identities at amino acid levels, respectively with MSpV isolates of maize from Florida and Reunion. The internal non-coding region between two ORFs has 67–68% identity at nucleotide level with the reported MSpV isolates from Florida and Reunion. The sequence identity was more than ≈98% among the four isolates of MSpV-Sorg. Compared to maize-infecting MSpV isolates in USA and Reunion, the sorghum-infecting MSpV isolates in India had more amino acid substitutions in both NS3 and CP. This is the first report of complete sequence analysis of MSpV RNA3 from Asia

Development of duplex RT-PCR for detection of <i>Konjac mosaic virus</i> and Spathiphyllum chlorotic vein banding virus in taro and peace lily

120-122Konjac mosaic virus (KoMV) and Spathiphyllum chlorotic vein banding virus (SCVbV) infecting aroids in Andhra Pradesh, India have recently been reported as distinct potyviruses. Primers were designed based on their partial genome sequence (GenBank A/C EU979524, GQ421462) to detect above viruses by duplex-reverse transcription-polymerase chain reaction (duplex RT-PCR). Using this method, the two viruses were individually detected in limited number of filed/nursery collected Colocasia esculenta (taro) and Spathiphyllum spp. (peace lily). No co-infections with two viruses were traced among the screened samples. However, they were simultaneously detected in the simulated leaf samples of taro and peace lily (1:1, w/w). </span

Targeting the m(6)A RNA modification pathway blocks SARS-CoV-2 and HCoV-OC43 replication

N-6-methyladenosine (m(6)A) is an abundant internal RNA modification, influencing transcript fate and function in uninfected and virus-infected cells. Installation of m(6)A by the nuclear RNA methyltransferase METTL3 occurs cotranscriptionally; however, the genomes of some cytoplasmic RNA viruses are also m(6)A-modified. How the cellular m(6)A modification machinery impacts coronavirus replication, which occurs exclusively in the cytoplasm, is unknown. Here we show that replication of SARS-CoV-2, the agent responsible for the COVID-19 pandemic, and a seasonal human beta-coronavirus HCoV-OC43, can be suppressed by depletion of METTL3 or cytoplasmic m(6)A reader proteins YTHDF1 and YTHDF3 and by a highly specific small molecule METTL3 inhibitor. Reduction of infectious titer correlates with decreased synthesis of viral RNAs and the essential nucleocapsid (N) protein. Sites of m(6)A modification on genomic and subgenomic RNAs of both viruses were mapped by methylated RNA immunoprecipitation sequencing (meRIP-seq). Levels of host factors involved in m(6)A installation, removal, and recognition were unchanged by HCoV-OC43 infection; however, nuclear localization of METTL3 and cytoplasmic m(6)A readers YTHDF1 and YTHDF2 increased. This establishes that coronavirus RNAs are m(6)A-modified and host m(6)A pathway components control beta-coronavirus replication. Moreover, it illustrates the therapeutic potential of targeting the m(6)A pathway to restrict coronavirus reproduction