Table 3.
Description of the sequences on the representative phylogenetic trees generated for four selected viruses analysed using MEGA 6 or 7 software.
Figure and Table | Long Name (Format: Sample-virus-protein-length-quality-coverage-year) | Short name (Format: Sample-virus-protein-length) | Coverage | No. of nucleotides | Mapping quality threshold | NCBI accession number |
---|---|---|---|---|---|---|
Avian Paramyxovirus 6 from MAD faecal sample | ||||||
2 and 4 | MAD-Avian-paramyxovirus-6-large-polymerase-protein-459nt-Q32-C-9-192-2016 | MAD-APMV6-Pol-459nt | 9–192 | 459 | 32 | MH000419 |
3 and 5 | MAD-Avian-paramyxovirus-6-hemagglutinin-neuraminidase-1839nt-Q32-C-5-103_2016 | MAD-APMV6-HN-1839nt | 5–103 | 1839 | 32 | MH000415 |
4 and 6 | MAD-Avian-paramyxovirus-6-fusion-protein-651nt-Q32-C-2-8-2016 | MAD-APMV6-FP-651nt | 2–8 | 651 | 32 | MH000412 |
Long Name | Short Name (Format: NCBI accession number-virus-country/state) | Country of collection | Collection date | |||
NCBI sequences taken for phylogenetic analysis for APMV6 | ||||||
AB759118-Avian-paramyxovirus-6-viral-cRNA-complete-genome-strain:red-necked-stint/Japan/8KS0813/2008 | AB759118-APMV6-JP | Japan | 2008 | |||
GQ406232-Avian-paramyxovirus-6-strain-duck/Italy/4524-2/07-complete-genome | GQ406232-APMV6-IT | Italy | 2007 | |||
KP762799-Avian-paramyxovirus-6-isolate-red-crested-pochard/Balkhash/5842/2013-complete-genome | KP762799-APMV6-KZ | Kazakhstan | 2013 | |||
AY029299-Avian-paramyxovirus-6-complete-genome | AY029299-APMV6-TW | Taiwan | — | |||
KT962980-Avian-paramyxovirus-6-isolate-teal/Novosibirsk_region/455/2009-complete-genome | KT962980-APMV6-RU | Russia | 2009 | |||
JN571486-Avian-paramyxovirus-6-strain-APMV6/mallard/Belgium/12245/07-nucleoprotein(NP)-phosphoprotein(P)-matrix-protein(M)-fusion-protein(F)-small-hydrophobic-protein(SH)-hemagglutinin-neuramis | JN571486-APMV6-BE | Belgium | 2007 | |||
KF267717-Avian-paramyxovirus-6-isolate-mallard/Jilin/127/2011-complete-genome | KF267717-APMV6-CN | China | 2011 | |||
Deltacoronavirus from the MAD faecal sample | ||||||
5 and 8 | MAD-Deltacoronavirus-Orf1a-10650nt-Q20-C-6-2326−2016 | MAD-DCoV-Orf1a-10650nt | 6–2326 | 10650 | 20 | MH013332 |
6 and 9 | MAD-Deltacoronavirus-Orf1b-polymerase-2076nt-Q20-C-5-475-2016 | MAD-DCoV-RPP-2076nt | 5–475 | 2076 | 20 | MH013331 |
7 and 10 | MAD-Deltacoronavirus-spike-glycoprotein-3702nt-Q20-C-36-6274-2016 | MAD-DCoV-SP-3702nt | 36–6274 | 3702 | 20 | MH013337 |
NCBI sequences taken for phylogenetic analysis for DCoV | ||||||
JQ065049-Common-moorhen coronavirus-HKU21-strain-HKU21-8295-complete-genome | JQ065049-MCoV-CN | China | 2007 | |||
JQ065046-Magpie-robin-coronavirus HKU18-strain-HKU18-chu3-complete-genome | JQ065046-MrCoV-CN | China | 2007 | |||
FJ376622-Munia-coronavirus-HKU13-3514-complete-genome | FJ376622-MuCoV-CN | China | 2007 | |||
FJ376621-Thrush-coronavirus-HKU12-600-complete-genome | FJ376621-TCoV-CN | China | 2007 | |||
MF431743-Porcine-deltacoronavirus-strain-SD-complete-genome | MF431743-PDCoV-CN | China | 2014 | |||
FJ376620-Bulbul-coronavirus-HKU11-796-complete-genome | FJ376620-BCoV-CN | China | 2007 | |||
JQ065047-Night-heron-coronavirus-HKU19-strain-HKU19-6918-complete genome | JQ065047-NhCoV-CN | China | 2007 | |||
JQ065048-Wigeon-coronavirus-HKU20-strain-HKU20-9243-complete-genome | JQ065048-WCoV-CN | China | 2008 | |||
Figure and Table | Long Name (Format: Sample-virus-protein-length-quality-coverage-year) | Short name (Format: Sample-virus-protein-length-year) | Coverage | No. of nucleotides | Mapping quality threshold | NCBI accession number |
Virus related to goose adenovirus 4 (GoA4) and/or duck adenovirus 2 (DuA2) from the MAD faecal sample | ||||||
GoA4 | ||||||
8 and 11 | MAD-Adenovirus-encapsidation-protein-IVa2-279nt-Q20-C-4-69-2016 | MAD-AV-IVa2-279nt | 4–69 | 279 | 20 | MH028885 |
DuA2 | ||||||
9 and 12 | MAD-Adenovirus-III-177nt-Q20-C-21-261-2016 | MAD-AV-III-177nt | 21–261 | 177 | 20 | MH028886 |
10 and 13 | MAD-Adenovirus-pVIII-114nt-Q32-C-19-67-2016 | MAD-AV-pVIII-114nt | 19–67 | 114 | 32 | MH028887 |
NCBI sequences taken for phylogenetic analysis for AV | ||||||
KR135164-Duck-adenovirus-2-strain-CH-GD-12-2014-complete-genome | KR135164-DAd2-CN | China | 2014 | |||
JF510462-Goose-adenovirus-4-strain-P29-complete-genome | JF510462-GAd4-HU | Hungary | — | |||
FN824512-Pigeon-adenovirus-1-complete-genome-strain-IDA4 | FN824512-PAd1-NL | Netherlands | 1995 | |||
KC493646-Fowl-adenovirus-5-strain-340-complete-genome | KC493646-FAd5-IE | Ireland | 1970 | |||
Hubei chryso-like virus 1 from the MUD faecal sample | ||||||
11 and 14 | MUD-Hubei-chryso-like-virus-1-seg1-RdRp-1496nt-Q20-C-4-58-2016 | MUD-HCLV1-s1-Rp-1496nt | 4–58 | 1496 | 20 | MH085092 |
Long Name | Short Name (Format: NCBI accession number-virus-segment-country/state) | Country or State of collection | Collection date | |||
NCBI sequences taken for phylogenetic analysis for HCLV1 | ||||||
Segment 1 | ||||||
MF176368-Hubei-chryso-like-virus-1-strain-mosWSgb49785-segment1-complete-sequence | MF176368-HCLV1-s1-WA | Western Australia | 2015 | |||
MF176309-Hubei-chryso-like-virus-1-strain-mos191gb77171-segment1-complete-sequence | MF176309-HCLV1-s1-WA | Western Australia | 2015 | |||
MF176261-Hubei-chryso-like-virus-1-strain-mos172gb42656-segment1-complete-sequence | MF176261-HCLV1-s1-WA | Western Australia | 2015 | |||
MF176388-Hubei-chryso-like-virus-1-strain-mosWSX51080-segment-1-complete-sequence | MF176388-HCLV1-s1-WA | Western Australia | 2015 | |||
MF176280-Hubei-chryso-like-virus-1-strain-mos172X13576-segment1-complete-sequence | MF176280-HCLV1-s1-WA | Western Australia | 2015 | |||
KX882962-Hubei-chryso-like-virus-1-strain-mosHB233224-hypothetical-protein-gene-partial-cds | KX882962-HCLV1-CN | China | 2013 |
The table gives details of the sequences used for phylogenetic analysis by the Maximum Likelihood method of APMV6, DCoV, AV and HCLV1. The first half of the table for each virus provides details to identify the sample from which the virus was isolated, protein encoded by the consensus sequences that are being analysed, the length of the consensus sequences and gene being analysed, minimum mapping quality threshold used in IGV for the generation of the consensus sequences, the coverage of the consensus sequences from IGV, the year of collection of the sample and the NCBI accession number assigned to the particular consensus sequence. Corresponding short names have been used in the phylogenetic trees which contain the sample, virus, protein and the number of nucleotides. The second half of the table for each virus provides the details of the sequences that were used for the comparative molecular phylogenetic analysis. They were found to be the most closely related sequences to the consensus sequences generated using BLASTN. Corresponding short names have been used in the phylogenetic trees which contain the NCBI accession number, virus and the country of collection. The collection date is given as retrieved from the corresponding NCBI nucleotide reference dataset which together with the country of collection can provide an insight into the possible evolution of the virus through the years.