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Development and evaluation of Reverse Transcription-Polymer-ase Chain Reaction (RT-PCR) assay for differentiation of Foot and Mouth Disease virus serotype O lineages circulating in India Subramaniam Saravanan1, Gahtori Rekha1, Biswal Jitendra K.1, Ranjan Rajeev1,*, Pattnaik B.1 1ICAR - Directorate of Foot-and-Mouth Disease, Mukteswar-263138, Nainital, Uttarakhand, India *Corresponding author: e-mail: drrajraj@gmail.com
Abstract Foot and mouth disease (FMD) is endemic in India and among the three prevalent serotypes (O, A and Asial), serotype O causes majority of the FMD incidences. Phylogenetic analysis based on the VP1 coding region sequences of FMD serotype O viruses from India has revealed the circulation of two major genetic lineages (Ind2001 and Pan Asia) in recent years. Timely determination of lineage in circulation is essential for effective implementation of FMD control. In present study, a rapid and simple lineage PCR assay to differen-tiate present genetic lineages of serotype O viruses was developed and evaluated. Stretches of lineage specific signature residues were identified and primers were designed. The lineage differentiating PCR assay can be very useful for preliminary identification of serotype O lineages circulating in the country before proceeding with sequencing of VP1 coding region for confirmation, which is time consuming. Top Keywords FMDV, Lineage PCR, Serotype O. Top | ACKNOWLEDGEMENTS Indian Council of Agricultural Research provided necessary facilities to carry out this work. We sincerely thank all the Scientific and Technical Staff associated with network laboratories for providing clinical materials and epidemiological information. |
Top Figures Fig. 1.: Specific amplification of two major lineages of serotype O using lineage differentiating PCR. Lane 1: Lineage Branch A, Lane 1: Lineage Branch B, Lane 3: Ind2001 lineage, Lane 4: Lineage PanAsia; Lane 5–7: Negative control (serotype A, Asial and uninfected BHK-21 culture supernatant), Lane 8: DNA marker
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| Fig. 2.: Neighbour-joining phylogenetic tree estimated at VP1 coding region of representative isolates of FMDV serotype O showing their genetic relationship
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Tables Table 1.: Depiction of lineage differentiating PCR on representative isolates of different lineages of FMDV serotype O that revealed specific amplification (indicated by + symbol)
| Virus-Isolate | Lineage | DHP13 (Serotype O) | Ind2001-1D84F (Ind2001 Lineage) | PanAsia-1D84F (PanAsia Lineage) | INDR2/1975 | Branch B | + | - | - | IND1/1962 | Branch B | + | - | - | IND92/2003 | Branch B | + | - | - | IND452/2001 | Branch B | + | | | IND218/2003 | Branch B | + | - | - | IND218/2003 | Branch B | + | - | - | IND68/1993 | Branch B | + | - | - | IND357/1997 | Branch A | + | - | - | IND120/2002 | Ind2001 | + | + | - | IND83/2001 | Ind2001 | + | + | - | IND44/2002 | Ind2001 | + | + | - | IND35/2002 | Ind2001 | + | + | - | IND144/2002 | Ind2001 | + | + | - | IND74/2002 | Ind2001 | + | + | - | IND65/2002 | Ind2001 | + | + | - | IND81/2002 | Ind2001 | + | + | - | IND119/2002 | Ind2001 | + | + | - | IND357/2007 | PanAsia | + | - | + | IND271/2001 | PanAsia | + | - | + | IND320/2007 | PanAsia | + | - | + | IND335/2005 | PanAsia | + | - | + | IND45/2002 | PanAsia | + | - | + | IND52/2002 | PanAsia | + | - | + | IND307/2002 | PanAsia | + | - | + | IND96/2002 | PanAsia | + | - | + | IND45/2002 | PanAsia | + | - | + |
| | Table 2.: Testing of the clinical materials received from different parts of the country using lineage differentiating PCR
| Sample ID | DHP13 | Ind2001-1D84F | PanAsia-1D84F | Lineage | PD12/2013 | + | - | + | Serotype O/PanAsia | PD631/2013 | + | + | - | Serotype O/Ind2001 | PD632/2013 | + | + | - | Serotype O/Ind2001 | PD1/2013 | + | - | - | Serotype O | PD20/2013 | + | - | - | Serotype O | PD144/2013 | + | + | - | Serotype O/Ind2001 | PD208/2013 | - | - | - | Negative | PD372/2013 | + | + | - | Serotype O/Ind2001 | PD373/2013 | + | + | - | Serotype O/Ind2001 | PD378/2013 | - | - | - | Negative | PD382/2013 | + | - | - | Serotype O | PD385/2013 | + | + | - | Serotype O/Ind2001 | PD386/2013 | + | + | - | Serotype O/Ind2001 | PD388/2013 | + | + | - | Serotype O/Ind2001 | PD391/2013 | + | + | - | Serotype O/Ind2001 | PD408/2013 | + | + | - | Serotype O/Ind2001 | PD428/2013 | + | + | - | Serotype O/Ind2001 | PD437/2013 | + | - | - | Serotype O | PD440/2013 | + | + | - | Serotype O/Ind2001 | PD485/2013 | + | + | - | Serotype O/Ind2001 | PD516/2013 | + | + | - | Serotype O/Ind2001 | PD526/2013 | + | + | - | Serotype O/Ind2001 | PD548/2013 | + | + | - | Serotype O/Ind2001 | PD549/2013 | + | + | - | Serotype O/Ind2001 | PD560/2013 | + | + | - | Serotype O/Ind2001 | PD634/2013 | + | + | - | Serotype O/Ind2001 | PD638/2013 | + | + | - | Serotype O/Ind2001 | PD641/2013 | + | + | - | Serotype O/Ind2001 | PD706/2013 | + | + | - | Serotype O/Ind2001 | PD759/2013 | + | - | - | Serotype O | PD760/2013 | + | + | - | Serotype O/Ind2001 | PD1062/2013 | + | - | - | Serotype O | PD1075/2013 | + | + | - | Serotype O/Ind2001 | PD1078/2013 | + | - | - | Serotype O | PD1373/2013 | + | - | - | Serotype O | PD1379/2013 | + | - | - | Serotype O | PD1503/2013 | + | - | - | Serotype O | PD1513/2013 | + | - | - | Serotype O | PD1517/2013 | + | + | - | Serotype O/Ind2001 | PD1529/2013 | + | + | - | Serotype O/Ind2001 |
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