Create Multiple sequence alignment of your sequences

Use SARS-CoV-2 isoloate Whuan-Hu-1 (NC_045512.2) as the reference.

Download metadata

Metadata from GISAID

Data are available from EpiCoV.

Fileds of GISAID metadata:

#	Column	Example
1	Virus name	hCoV-19/Ireland/LS-NVRL-M35IRL03088/2021
2	Last vaccinated
3	Passage details/history	Original
4	Type	betacoronavirus
5	Accession ID	EPI_ISL_3848896
6	Collection date	2021-08-07
7	Location	Europe / Ireland / Laois
8	Additional location information
9	Sequence length	29715
10	Host	Human
11	Patient age	21-30
12	Gender	unknown
13	Clade	GK
14	Pango lineage	AY.4
15	Pango version	PLEARN-v1.18
16	Variant AA	VOC Delta GK (B.1.617.2+AY.*) first detected in India
17	Substitutions	(N_G215C,NSP3_A1711V,Spike_T95I,…,Spike_L452R)
18	Submission date	2021-07-16
19	Is reference?
20	Is complete?
21	Is high coverage?	True
22	Is low coverage?	True
23	N-Content
24	GC-Content	0.379589505862

Included hosts:

#	Host name	GenBank Common name	Common name
1	Aonyx cinereus	Asian small-clawed otter	otter
2	Arctictis binturong	binturong	binturong
3	canis lupus	gray wolf	wolf
4	Canis lupus	gray wolf	wolf
5	Canis lupus familiaris	gray wolf	wolf
6	Chaetophractus villosus	large hairy armadillo	armadillo
7	Chiroptera	bats	bat
8	Chlorocebus sabaeus	green monkey	monkey
9	Crocuta crocuta	spotted hyena	hyena
10	Cygnus columbianus	tundra swan	swan
11	Environment		environment
12	Felis catus	domestic cat	cat
13	Felis Catus	domestic cat	cat
14	Foreign		human
15	Foreing		human
16	Gorilla	gorilla	gorilla
17	Gorilla gorilla	western gorilla	gorilla
18	Gorilla gorilla gorilla	western lowland gorilla	gorilla
19	Hippopotamus amphibius	hippopotamus	hippo
20	Human	human	human
21	Humano	human	human
22	Laboratory derived		lab
23	Lynx lynx familiaris	Eurasian lynx	lynx
24	Manis javanica	Malayan pangolin	pangolin
25	Manis pentadactyla	Chinese pangolin	pangolin
26	Mesocricetus auratus	golden hamster	hamster
27	Mus musculus	house mouse	mouse
28	Mustela furo	domestic ferret	ferret
29	Mustela putorius furo	domestic ferret	ferret
30	Nasua nasua	ring-tailed coati	coati
31	Neogale vison	American mink	mink
32	Neovison vison	American mink	mink
33	Odocoileus virginianus	white-tailed deer	deer
34	Panthera leo	lion	lion
35	Panthera tigris	tiger	tiger
36	Panthera tigris jacksoni	Malayan tiger	tiger
37	Panthera tigris sondaica	Javan tiger	tiger
38	Panthera tigris tigris	Bengal tiger	tiger
39	Panthera uncia	snow leopard	leopard
40	Phodopus roborovskii	desert hamster	hamster
41	Prionailurus bengalensis euptilurus	Amur leopard cat	cat
42	Prionailurus viverrinus	fishing cat	cat
43	Puma concolor	puma	puma
44	Rhinolophus affinis	intermediate horseshoe bat	bat
45	Rhinolophus bat	horseshoe bat	bat
46	Rhinolophus malayanus	Malayan horseshoe bat	bat
47	Rhinolophus marshalli	Marshall’s horseshoe bat	bat
48	Rhinolophus pusillus	Least horseshoe bat	bat
49	Rhinolophus shameli	Shamel’s horseshoe bat	bat
50	Rhinolophus sinicus	Chinese rufous horseshoe bat	bat
51	Rhinolophus stheno	Lesser brown horseshoe bat	bat
52	unknown		unkonwn

Generate metadata for Taxonum.org visualization:

# Get Virus name (1), Accession ID (5), Collection date (6), Location (7), Host (10)
# Pango lineage (14)
cut -f 1,5,6,7,10,14 gisaid-metadata.tsv > gisaid-metadata-plot.tsv

# Remove leading `hCoV-19/` from Virus name column
perl -lpi -e 's/^hCoV\-19\///' gisaid-metadata-plot.tsv

# Extract country from Location field

# Rebuild virus name to `<virus name>|<Accession number>|<collection date>` format

UShER pre-processed data

Available from UShER’s pre-processed mutation-annotated tree object for public SARS-CoV-2 sequences, which provides these files:

• Protobuf file for use with usher --load-mutation-annotated-tree:
  • public-latest.all.masked.pb[.gz]
• Variant Call Format (VCF) file containing mutations in public sequences, generated from public-latest.all.masked.pb with matUtils extract.
  • public-latest.all.masked.vcf.gz
• Newick tree file:
  • public-latest.all.nwk.gz
• Information about each public sequence, e.g. collection date, location, Nextstrain clade and Pango lineage.
  • public-latest.metadata.tsv.gz

    Dates and locations are not available for some sequences.

• A brief description including date, sources and number of sequences.
  • public-latest.version.txt

Columns of the metadata:

#	Column	Example GenBank	Example Other
1	strain	CHN/20221209-188/2022|OQ048281.1|2022-12-09	100002|LR824035.1|2020-03-05
2	genbank_accession	OQ048281.1	LR824035.1
3	date	2022-12-09	2020-03-05
4	country	China	Switzerland
5	host	Homo sapiens	Homo sapiens
6	completeness
7	length	29769	29903
8	Nextstrain_clade	22B	20A
9	pangolin_lineage	BF.5.1	B.1
10	Nextstrain_clade_usher	22B (Omicron)	20A
11	pango_lineage_usher	BF.5.1	B.1

Included hosts:

#	Host name	GenBank common name	Common name
1			unknown
2	Bos taurus	cattle	cattle
3	Canis lupus	gray wolf	wolf
4	Canis lupus familiaris	gray wolf	wolf
5	Capra hircus	goat	goat
6	Chlorocebus aethiops	grivet	monkey
7	Chlorocebus sabaeus	green monkey	monkey
8	Cricetinae	hamsters	hamster
9	Crocuta crocuta	spotted hyena	hyena
10	Environment		environment
11	Feliformia	cats	cat
12	Felis catus	domestic cat	cat
13	Gorilla	gorilla	gorilla
14	Gorilla gorilla gorilla	western lowland gorilla	gorilla
15	Homo	humans	human
16	Homo sapiens	human	human
17	Iguania	iguanian lizards	lizard
18	Mesocricetus auratus	golden hamster	hamster
19	Mus musculus	house mouse	mouse
20	Mustela lutreola	European mink	mink
21	Mustela putorius furo	domestic ferret	ferret
22	Neogale vison	American mink	mink
23	Odocoileus virginianus	white-tailed deer	deer
24	Ovis aries	sheep	sheep
25	Panthera leo	lion	lion
26	Panthera leo persica	Asiatic lion	lion
27	Panthera tigris	tiger	tiger
28	Panthera tigris jacksoni	Malayan tiger	tiger
29	Prionailurus bengalensis euptilurus	Amur leopard cat	cat
30	Rodentia	rodent
31	Sus scrofa	pig

Generate phylogenetic tree by UShER

UCSC hgPhyloPlace, where will generate a newick format phylogenetic tree.

The tip (taxon) name of this tree is like:

`<virus name>|<Accession number>|<collection date>`

e.g., 

- `CHN/YN-0306-466/2020|MT396241.1|2020-03-06`
- `Ireland/LS-NVRL-M35IRL03088/2021|EPI_ISL_3848896|2021-08-07`

Visualize the phylogenetic tree by Taxonium

Taxonium