The Virosphere

 

(Breitbart and Rohwer 2005; Suttle 2007; Andersson and Banfield 2008; Emerman and Malik 2010; Johnson 2010; Krupovic and Bamford 2010; Reyes, Haynes et al. 2010; Walsh and Mohr 2011)

 

Speculation on viruses, cell and genome evolution

 

(Sonea 1987; Tsichlis 1987; Bell 2001; Bubanovic, Najman et al. 2005; Forterre 2005; Claverie 2006; Forterre 2006; Koonin, Senkevich et al. 2006; Suzan-Monti, La Scola et al. 2006; Witzany 2007; Filee, Pouget et al. 2008; Baluska 2009; Bell 2009; Krupovic, Ravantti et al. 2009; Varela, Spencer et al. 2009; Forterre 2010; Gilbert, McDonald et al. 2010; Hughes, Irausquin et al. 2010; Hunter 2010; Koonin 2010; Strassmann and Queller 2010; Van Regenmortel 2010; Villarreal and Witzany 2010; Fischer and Suttle 2011; Roossinck 2011; Villarreal 2011; Williams, Embley et al. 2011; Wu, Wu et al. 2011)

 

Phylogenies and metagenomic analysis of viral sequence components; viral origins by horizontal transfer and symbiogenesis

 

(Holmes and Drummond 2007; Mrazek and Karlin 2007; Bigot, Samain et al. 2008; Filee, Pouget et al. 2008; Williamson, Rusch et al. 2008; Bigot, Renault et al. 2009; Boyer, Yutin et al. 2009; Labonte, Reid et al. 2009; Bousios, Darzentas et al. 2010; Boyer, Madoui et al. 2010; Filee and Chandler 2010; Karam and Miller 2010; Kristensen, Mushegian et al. 2010; Krupovic and Bamford 2010; Lopes, Amarir-Bouhram et al. 2010; Schoenfeld, Liles et al. 2010; Al Rwahnih, Daubert et al. 2011; Caporaso, Knight et al. 2011; Hulo, de Castro et al. 2011)

 

Viral sequences in cellular genomes

 

(Lwoff 1966; Nusse and Varmus 1982; Tsichlis, Lee et al. 1990; Martin, Herniou et al. 1999; Gifford and Tristem 2003; Ryan 2004; Gifford, Kabat et al. 2005; Yohn, Jiang et al. 2005; Fiebig, Hartmann et al. 2006; Jern, Sperber et al. 2006; Tarlinton, Meers et al. 2006; Katzourakis, Tristem et al. 2007; Delaroque and Boland 2008; Eiden 2008; Gifford, Katzourakis et al. 2008; Maeda, Fan et al. 2008; Tarlinton, Meers et al. 2008; Blomberg, Benachenhou et al. 2009; Gilbert, Maxfield et al. 2009; Jaratlerdsiri, Rodriguez-Zarate et al. 2009; Pagarete, Allen et al. 2009; Ryan 2009; Ryan 2009; Varela, Spencer et al. 2009; Wang, Kim et al. 2009; Horie, Honda et al. 2010; Katzourakis and Gifford 2010; Koonin 2010; Kozak 2010; Liu, Fu et al. 2010; Taylor, Leach et al. 2010; van der Kuyl, Cornelissen et al. 2010; Yan, Liu et al. 2010; Beyer, Moll-Rocek et al. 2011; Chiba, Kondo et al. 2011; Huang, Wang et al. 2011; Liu and Eiden 2011)

 

Prokaryotic viruses

 

(Sonea 1987; Prangishvili 2003; Snyder, Stedman et al. 2003; Weinbauer 2004; Prangishvili and Garrett 2005; Lipps 2006; Maaty, Ortmann et al. 2006; Ortmann, Wiedenheft et al. 2006; Prangishvili, Forterre et al. 2006; Srinivasiah, Bhavsar et al. 2008; Basta, Smyth et al. 2009; Pietila, Roine et al. 2009; Sullivan, Krastins et al. 2009; Wang, Kim et al. 2009; Wilson and Edgell 2009; Edgell, Gibb et al. 2010; Petrov, Ratnayaka et al. 2010; Ronning, Losada et al. 2010; Avrani, Wurtzel et al. 2011; Clokie, Millard et al. 2011; Huang, Wang et al. 2011; Krupovic and Forterre 2011; Tadmor, Ottesen et al. 2011)

 

Algal, amoebal and protist viruses

 

(Van Etten and Meints 1999; Van Etten, Graves et al. 2002; Wilson, Tarran et al. 2002; Wilson, Schroeder et al. 2005; Delaroque and Boland 2008; Nagasaki 2008; Zauberman, Mutsafi et al. 2008; Boyer, Yutin et al. 2009; Ogata, Toyoda et al. 2009; Pagarete, Allen et al. 2009; Colson and Raoult 2010; Fischer, Allen et al. 2010; Moliner, Fournier et al. 2010; Raoult 2010; Raoult and Boyer 2010; Thomas and Greub 2010; Arslan, Legendre et al. 2011; Coolen 2011)

 

Invertebrate viruses

 

(Pelisson, Mejlumian et al. 2002; Lambrechts and Scott 2009; Vasilakis, Deardorff et al. 2009; Wang and Jehle 2009; Marquez and Pritham 2010; Dupuy, Periquet et al. 2011; Felix, Ashe et al. 2011; Hoover, Grove et al. 2011)

 

Plant viruses

 

(Turpen 1999; Roossinck 2005; Yano, Panbehi et al. 2005; Roossinck 2010; Al Rwahnih, Daubert et al. 2011; Desbiez, Moury et al. 2011; Elena, Bedhomme et al. 2011; Pantaleo 2011)

 

RNA viruses, including retroviruses

 

(Katzourakis, Gifford et al. 2009; Fujii 2010; Horie, Honda et al. 2010; Felix, Ashe et al. 2011; Simon-Loriere and Holmes 2011)

 

Large Nucleocytoplasmic DNA Viruses

 

(Van Etten and Meints 1999; Van Etten, Graves et al. 2002; Iyer, Balaji et al. 2006; Webb, Strand et al. 2006; Mrazek and Karlin 2007; Filee, Pouget et al. 2008; Boyer, Yutin et al. 2009; Ogata, Toyoda et al. 2009; Webb, Fisher et al. 2009; Wilson, Van Etten et al. 2009; Yutin and Koonin 2009; Yutin, Wolf et al. 2009; Colson and Raoult 2010; Filee and Chandler 2010; Fischer, Allen et al. 2010; Forterre 2010; Koonin and Yutin 2010; Parakkottil Chothi, Duncan et al. 2010; Thomas and Greub 2010; Van Etten, Lane et al. 2010; Arslan, Legendre et al. 2011; Boyer, Azza et al. 2011; Colson, Gimenez et al. 2011; Legendre, Santini et al. 2011; Van Etten 2011; Williams, Embley et al. 2011; Yoshida, Claverie et al. 2011)

 

DNA viruses

 

(Briddon, Patil et al. 2010; Gilbert and Feschotte 2010; Lefeuvre, Harkins et al. 2011)

 

Satellite viruses

 

(Hu, Hsu et al. 2009; Huang, Hu et al. 2010; Krupovic and Cvirkaite-Krupovic 2011)

 

Viral genome packaging and capture of host cell DNA segments

(Guo and Lee 2007; Johnson and Chiu 2007; Roos, Ivanovska et al. 2007; Rao and Feiss 2008; Bright and