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Viruses: Their Types, Features, Variety And Groups

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Viruses are obligate intra-cellular parasites that possibly transmit diseases to all cellular forms of life. Though virologists have conventionally focused on viruses that are important for disease spreading in humans, crops, and domestic animals. Metagenomics sequencing studies for different environmental samples reveals the large virome far and wide in biosphere, minimum of 1031 viral particles are present in atmospheres at any specified time and area, environments including freshwater and marine habitats, metazoan of gastro-intestinal tracts having the number of detectible viruses more than 10 to 100 fold. (Edwards, R. A. & Rohwer, F. 2005, Mokili, J. L. et al. 2012, Rosario, K. & Breitbart, M. 2011, Chow, C. E. & Suttle, C. A. 2015, Wigington, C. H. et al. 2016). The current biomass of staggeringly large virome (globally) have been estimated approximately about two hundred million tones (~75 million blue whales) and of sixty five galaxies if there virions are lengthened end to end (Suttle, C. A. 2013). Organization of viral genetic material and nature, sequences of their genes and their encoded proteins, mechanism of their replication, cellular and intracellular interactions with their hosts are outstandingly diverse (Roossinck, M. J. 2015).

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Contagium vivum fludium (ultravirus) found in tobacco was the reason for the emergence of virology field in the late 1980s. During the first half of the twentieth century, it was the first well studied and become an iconic virus later it was named as TMV (Tobacco Mosaic Virus). In 1935 Wendell M. Stanleyin purified, crystallized and latterly described TMV’s Structure. Molecular Virology was started when genetic information encoded within TMV RNA core was replicated and first reported by Heinz Fraenkel-Conratin in 1950s. (Hadidi and Barbra, 2012). PSTVd (potato spindle tuber viroid), Infectious small RNA virus is a novel class that causes potato spindle tuber disease was first discovered by T.O.Diener in 1971. (Diener, 1971a,b Diener, 1972). Very small non-coding and in circular form RNAs are known as Viroids (Sängeretal., 1976; Owens et al., 1977). Viroids are 247-401 nucleotides in length, without protein coats, single stranded RNAs with internal base pairing at very degree, and are tiniest identified infectious agents. While the actual virus (virions) have encapsidated genome in protein coat. (Hadidi et al., 2003).

The family Geminiviridae shares the morphology of geminate structure containing monopartite or bipartite genome encapsidated withen virions. These are single stranded DNA viruses.

Geminiviruses have the ability to infect both either monocot or dicot plants and also can cause disease in major crops as well as in weeds. Feeding crops by means of their security, are also threatened in tropical and subtropical regions of developing countries worldwide (Moffat, A.S., 1999).

By the development of new molecular tools and the involvement of industrial scale low cost commercial sequencing services, there has been a tremendous increase over the last five years in the rate at which new geminivirus genomes have been characterized. Of the new molecular tools, sequence-independent methodologies based on rolling circle amplification (RCA) that employ ϕ29 DNA polymerase have played a significant role in the discovery of new highly divergent geminiviruses (Haible, D., et al. 2006, Inoue-Nagata, A.K., et al. 2004, Shepherd, D.N., 2008)

There are nine different genera in the family Geminiviridae Begomovirus named Topocuvirus, Curtovirus, Mastrevirus(Brown, J et al. 2012), Becurtovirus, Eragrovirus, Turncurtovirus,( Varsani, A et al. 2014a), Capulavirus, and Grablovirus(Varsani, A et al. 2017 ). Moreover, two highly divergent groups of viruses are still uncharacterized due to incomplete information regarding there morphology and their vectors for transmission. One of these infecting citrus plant assigned as “Citrus chlorotic dwarf associated virus”, while the other infecting mulberry assigned as “Mulberry mosaic dwarf associated virus”( Varsani, A et al. 2017).

Begomovirus is the largest genus of geminiviruses comprising more than 320 species infecting dicot plants.( Zerbini, F.M et al. 2017 ). Begomoviruses are either mono or bipartite, transmitted through whitefly that infects the plants of both New World and Old World (Brown et al., 2015). The vector whitefly Bemisia tabaci is considered to be complex of cryptic species (De Barro et al., 2011). The sequence of specific amino-acids of viral coat protein has specificity for vector B. tabaci (Briddon et al., 1990).

Some begomoviruses, such as Cabbage leaf curl virus (CabLCV), Tomato golden mosaic virus (TGMV) and Africa cassava mosaic virus (ACMV), have genome in two components DNA A and DNA B that are separately encapsidated. Size of these components ranging from 2700-3000 nucleotides. Other begomoviruses, as Tomato yellow leaf curl China virus (TYLCCNV), carries only a single genomic component having similarity with the component of bipartite’s DNA A(Zhou, X., 2013).

The division of begomoviruses New and Old world grouping is based on their geographic origins. In New World group all the members are bipartite by their genome composition, while Old World group can have either bipartite or monopartite genome. Monopartite and bipartite’s genome component DNA A encodes six genes. Coat protein and AV2/V2 proteins are encoded by virion-sense strand, while Rep (replication associated protein or C1/ AC1), TrAP (Transcription Activator Protein or AC2/C2), REn (Replication Enhancer Protein or AC3/C3) and AC4/C4 proteins. Both the components of bipartite DNA A and DNA B are similar in size having difference in their sequences except 200-250 nucleotides within intergenic region known as common region (CR). The CR have a highly conserved stem loop nonanucleotide (TAATATTAC) sequence shared from nanoviruses. (Harrison B, Robinson D. 1999).

Though the DNA A molecule of bipartite begomovirus have the ability to replicate independently to produce new virions, but it cannot produce systematic infection and localization activities without the help of proteins encoded by DNA B, BC1 and BV1 respectively. Several RNA satellite molecules have been reported to associate with plant viruses having RNA gnome. (Simon AE, et al. 2004), but DNA satellite was first identified in 1997 in association with a monopartite begomovirus Tomato leaf curl virus (ToLCV)( Dry IB et al. 1997). After this discovery, association of two classes of satellites molecules (Betasatellites and Alphasatellites) have been found with most of the monopartite begomoviruses.

Betasatellites are also known as DNAβ, are the true pathogenicity determinant molecules in association with most of the begomoviruses having around 1350 nucleotides (which is the half of the helper virus genome size) in single stranded circular DNA form (Briddon RW et al. 2001, Jose J, Usha R. 2003, Saunders K, et al. 2000, Saunders K, et al. 2004, Zhou XP, et al. 2003). Their replication, cell to cell systemic infection within host, encapsidation, transmission to new host through vector all are dependent on their helper viruses. No significant sequence homology have been shared by betasatellites with their helper begomoviruses except a nonanucleotide (TAATATTAC) sequence that plays an important role in the replication of virion strand(Briddon RW et al. 2008). Betasatellites are highly conserved by their genome organization. Sequence conserved region (SCR) of ~120 nucleotides, a single protein (βC1) coding ORF in complementary sense strand DNA, and 160-280 adenine nucleotides (A-rich region) are the components of betasatellite molecule.

Protein encoded by the βC1 ORF is multifunctional, that effects the suppression of transcriptional gene silencing (TGS) and post-transcriptional gene silencing (PTGS), disease complex pathogenicity, and inhibits the plant defense responses. Adenine-rich region contributing ~57-65% part of all known betasatellites is important as for its stuffer function for the systemic movement and maintaining size for efficient encapsidation of betasatellite (Briddon RW et al. 2003, Saunders K, et al. 2000, Zhou XP, et al. 2003). Experimental studies have revealed that A-rich region is has milder effect on disease symptoms and viral DNA in accumulation in infected plants, while has no effect when it was removed from tomato yellow leaf curl china betasatellite (TYLCCNB) for its trans replication in tomato yellow leaf curl china virus (TYLCCNV) (Tao XR, et al. 2006). Deletion of A-rich region decreases the expression of βC1 gene as this region plays a minor role in regulation of βC1 gene promotor activity (Guan CP, Zhou XP. 2006). Some betasatellite support trans-replication under laboratory conditions with New World begomoviruses (Nawaz-ul-Rehman MS et al.2009), but naturally betasatellites are not yet been reported in association with New World begomoviruses although circomics (circular DNA Genomics) assays shows the existence of the betasatellites in symptomatic plants in Brazil (Wyant PS, et al. 2012).

In 1999 association of alphasatellite with vein yellowing disease in a weed Ageratum conyzoides (Saunders K, Stanley J. 1999). They are of half the size of their helper virus, approximately 1375 nucleotides and have only a single ORF, encoding a single alpha-Rep protein. Alphasatellites have predicted hairpin structure as well as A-rich region (~150-200 nucleotides) too. The only ORF encoding protein (alpha-Rep) is of ~37 kDa having 315 amino acids, resembling to nanovirus Rep proteins. The sequences of alpha-Rep proteins are much more conserved than the sequences of full-length alphasatellite molecules (Briddon RW et al. 2004, Xie Y, et al. 2010).

A-rich region contributing ~46-58% part of alphasatellites, is important to distinguish between Rep-encoding components of nanoviruses and begomovirus alphasatellite (Briddon RW et al. 2004). The hairpin structure of nonanucleotides (TAGTATTAC) forms a loop that is common to nanovirusesalso similar to the analog of nonanucleotides (TAATATTAC) of begomoviruses loop. A study on more than 300 plants in china revealed that plants infected with monopartite begomoviruses having alphasatellites also contain betasatellites (Xie Y, et al. 2010).

Contribution to disease symptoms by disease complex (begomovirus-betasatellite) is not obvious. Disease symptoms caused by helpervirus-betasatellite can be attenuated by some of alphasatellites. Nawaz-Ul-Rehman MS et al. (2010) reported the interaction of alpha-Rep from GMusSLA and GDarSLA non-pathogenic alphasatellites associated with CLCuRaV(Cotton leaf curl Rajasthan virus)with CLCuRaV Rep proteins. As betasatellites upon Rep protein of helper begomovirus for their replication so, interaction between helper virus Rep and alpha-Rep proteins may obstruct replication of betasatellite, resulting in dwon-regulation of βC1 protein. They also reported the gene silencing suppressor activities of GMusSLA and GDarSLA alpha-Reps, which is in contrast to CLCuMuV (Cotton leaf curl Multan virus)-encoded V2, C2, and C4 proteins and CLCuMuB-βC1 (Nawaz-Ul-Rehman MS et al. 2010). Surprisingly, association of alphasatellite with CLCuMuV+CLCuMuB have no affect silencing induced by CLCuMuV+CLCuMuB (Amin I, et al. 2011).

Under experimental conditions co-infection of CLCuMuB and CLCuMuV have the ability to cause cotton leaf curl disease (CLCuD), but it is still unclear that how alpha-Rep protein is helpful in silencing suppressor activity in field. Further research is needed to explore whether other alphasatellite Rep proteins have silencing suppressor activities or not. Association of alphasatellites with bipartite begomoviruses have also been found in Brazil (Paprotka T, et al. 2010) and Venezuela (Romay G,et al. 2010). In Singapore unusual type satellites (DNA-2 type alphasatellite members) were reported from Ageratum in New World. From India (Zaffalon V, et al. 2012) and Oman (Idris AM, et al. 2011) DNA-2 are also reported. These DNA-2 type alphasatellites have conserved genome features of alphasatellites, very less homogeneous and are less than 50% identical by their nucleotide sequence identity (Zhou, X 2013). Though the first alphasatellite molecule was discovered about more than 20 years ago, but during either begomoviruses or begomovirus/betasatellite infections the function(s) of alphasatellite are still very little known.

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