Table 2.

Summary of Antarctic bird- and mammal-associated viruses identified through sequencing based approaches, including respective accession numbers of the partial and full genome sequences.

	Virus taxonomy				Notes
ID	Family	Genus	Species & virus	Host	Method	Sample type	Location	Year of collection	Accession #	Reference
A	Togaviridae	Alphavirus	Southern elephant seal virus [Southern elephant seal virus (SES virus)]	Southern elephant seals (Mirounga leonina)	Virus cultured in BHK-21 cells virus from blood sucking lice Lepidophthirus macrorhini and used in viral neutralization assay for serology. Negative stain electron microscopy. RT-PCR and Sanger sequencing of capsid protein gene.	Lepidophthirus macrorhini and serum from southern elephant seal virus	Macquarie Island	–	AF315122 HM147990	Forrester et al. (2012) and La Linn et al. (2001)
B	Paramyxoviridae	Avulavirus	Avian avulavirus 1 [New castle disease virus (NDV)]	Adélie penguins (Pygoscelis adeliae)	RT-PCR and real-time PCR targeting F gene of NDV, virus culture, haemagglutination test using antigen against B1 NDV strain, Sanger sequencing.	Cloacal/tracheal swabs and serum samples	King George Island	2006	HM143848–HM143850	Thomazelli et al. (2010)
C			Avian avulavirus 10 [Avian paramyxovirus 10 (APMV10)]	Rockhopper penguins (Eudyptes chrysocome)	Real-time RT-PCR, hemagglutination assay, binaxNOW influenza A&B test, hemagglutination inhibition assay, ELISA, electron microscopy, Sanger sequencing.	Cloacal/tracheal swabs and serum samples	Falkland Islands	2007	HM147142, HM755886–HM755888 (updated following the publication of Goraichuk et al. (2017)	Miller et al. (2010)
D				Rockhopper penguins (Eudyptes chrysocome)	Complete genome sequencing using Illumina and Sanger sequencing.	Cloacal/tracheal swabs and serum samples	Falkland Islands	2007	HM147142, HM755886–HM755888	Goraichuk et al. (2017)
E			Unclassified [Avian paramyxovirus 15, 16, 17 (APMV15, APMV16, APMV17)]	Gentoo penguins (Pygoscelis papua)	Hemagglutination assay, RT-PCR and Sanger sequencing.	Virus isolated from 12 cloacal swabs, 5 confirmed by sequencing	Kopaitic Island	2014 − 2016	KY452442–KY452444	Neira et al. (2017)
F	Orthomyxoviridae	Influenzavirus A	Influenzavirus A [Avian Influenza A virus H5N5]	Chinstrap penguins (Pygoscelis antarctica)	RT-PCR, HTS, ELISA using nucleoprotein, hemagglutination assay.	Cloacal/tracheal swabs and serum samples	Antarctic peninsula	2015	GISAID #s [EPI774530-EPI774536, EPI774538- EPI774539]; [EPI774527- EPI774529]	Hurt et al. (2016)
G			Influenzavirus A [Avian influenza A virus H11N2]	Adélie penguins (Pygoscelis adeliae)	RT-PCR, virus culture, ELISA, whole genome Sanger sequencing.	Cloacal/tracheal swabs and serum samples	Rada Covadonga, Antarctic Peninsula and King George Island	2013	KJ729348–KJ729379	Hurt et al. (2014)
H	Papillomaviridae	Treisepsilonpapillomavirus	Treisetapapillomavirus 1 [Pygoscelis adeliae papillomavirus 1]	Adélie penguins (Pygoscelis adeliae)	HTS-informed approach, genome recovered by abutting primers, cloned and Sanger sequenced.	Faeces	Cape Crozier, Ross Island	2012/2013	KJ173785	Varsani et al. (2014)
I			Unclassified [Pygoscelis adeliae papillomavirus 2]	Adélie penguins (Pygoscelis adeliae)	HTS-informed approach, genome recovered by abutting primers, cloned and Sanger sequenced.	Cloacal swab	Cape Crozier, Ross Island	2014	MF168943	Van Doorslaer et al. (2017)
J	Polyomaviridae	Gammapolyomavirus	Pygoscelis adeliae polyomavirus 1 [Adelie penguin polyomavirus (AdPyV)]	Adélie penguins (Pygoscelis adeliae)	HTS-informed approach, genome recovered by abutting primers, cloned and Sanger sequenced.	Faeces	Cape Royds, Ross Island	2012/2013	KP033140	Varsani et al. (2015)
K		unassigned	Trematomus pennellii polyomavirus 1 [Sharp-spined notothenia polyomavirus (SspPyV)]	Sharp spined notothen (Trematomus pennellii)	HTS-informed approach, genome recovered by abutting primers, cloned and Sanger sequenced.	Stomach and liver samples	Ross Sea	2012/2013	KP768176	Buck et al. (2016)
L		Betapolyomavirus	Leptonychotes weddellii polyomavirus 1 [Weddell seal polyomavirus (WsPyV)]	Weddell seal (Leptonychotes weddellii)	HTS-informed approach, genome recovered by abutting primers, cloned and Sanger sequenced.	Kidney	Ross Sea	2014	KX533457	Varsani et al. (2017)
M	Adenoviridae	Siadenovirus	Penguin siadenovirus A [Chinstrap penguin adenovirus (CSPAdV)]	Chinstrap penguins (Pygoscelis antarctica)	PCR of protein VI and capsid protein hexon genes.	Lung, liver, kidney, heart, intestine, trachea samples	King George Island	2009/2010	KC593379–KC593386	Lee et al. (2014)
N			Penguin siadenovirus A [Chinstrap penguin adenovirus (CSPAdV)]	Chinstrap penguins (Pygoscelis antarctica)	RACE PCR, Sanger sequencing of whole genome.	Lung, liver, kidney, heart, intestine, trachea samples	King George Island	2008–2013	KP144329–KP144330	Lee et al. (2016)
O			Penguin siadenovirus A [Gentoo penguin adenvirus (GPAdV)]	Gentoo penguins (Pygoscelis papua)	RACE PCR, Sanger sequencing of whole genome.	lung, liver, kidney, heart, intestine, trachea, feces	King George Island	2008–2013	KP279746–KP279747	Lee et al. (2016)
P			Skua siadenovirus A [South polar skua adenovirus 1 (SPSAdV 1)]	South Polar skua (Stercorarius maccormicki)	Nested PCR, RACE PCR, Sanger sequencing of whole genome.	kidney	King George Island	2007–2009	HM585353 (full genome) JM585354-HM585358	Park et al. (2012)
Q	Poxviridae	Parapoxvirus	Unassigned [Seal poxvirus]	Weddell seal (Leptonychotes weddellii)	Electron microscopy, PCR of B2L gene, sequencing of B2L gene.	Neck skin lesion from a single seal	Queen Maud Land	2001	AJ622900	Tryland et al. (2005)
R	Anelloviridae	unassigned	Unassigned [Torque teno Leptonychotes weddelli virus 1,-2(TTLwV1 & TTLwV2)]	Weddell seal (Leptonychotes weddellii)	HTS-informed approach, genome recovered by abutting primers, cloned and Sanger sequenced.	Vaginal, nasal and faecal samples	Ross Sea	November-February 2014–2015	KY246479–KY246627	Fahsbender et al. (2017)
S			Unassigned [Torque teno Leptonychotes weddelli virus 1 (TTLwV1)	South Polar skua (Stercorarius maccormicki)	HTS-informed approach, genome recovered by abutting primers, cloned and Sanger sequenced.	Faecal sample	Ross Sea	November/December 2014	KY246476–KY246478	Fahsbender et al. (2017)

cDNA: complementary DNA.

ELISA: Enzyme-linked immunosorbent assay.

PCR: Polymerase chain reaction.

HTS: High throughput sequencing.

RACE: Rapid Amplification of cDNA ends.

RT-PCT: Reverse transcription PCR.