Isolation, Identification, and Whole Genome Analysis of Chicken Infectious Anemia Virus in an Outbreak of Disease in Adult Layer Hens
Abstract
:Simple Summary
Abstract
1. Introduction
2. Materials and Methods
2.1. Sample Collection
2.2. Reagents and Materials
2.3. Primer Design and Synthesis
2.4. Sample Handling
2.4.1. PCR Detection
2.4.2. Virus Isolation and Identification
2.4.3. MDCC-MSB1 Cells Inoculation of CIAV Isolate
2.5. Whole Genome Amplification of CIAV Isolates
2.6. Experimental Infection of 1-Day-Old SPF Chicks with CIAV
2.7. Genome-Wide Bioinformatics Analysis
Genome-Wide Genetic Evolutionary Analysis
3. Results
3.1. Pathological Changes
3.2. PCR Test Results of the Samples
3.3. Virus Isolation Results
3.4. MDCC-MSB1 Culture Results
3.5. Whole Genome Amplification Results
3.6. CIAV GX21121 Pathogenicity to One-Day-Old SPF Chicks
3.7. Genome-Wide Bioinformatics Analysis
4. Discussion
5. Conclusions
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
Appendix A
No. | Accession No. | Country | Isolate | Year | Nucleotides (bp) |
1 | ON596886 | China | GX2112 | 2021 | 2298 |
2 | MH186142 | China | CIAV-Shanxi7 | 2018 | 2291 |
3 | HM134240 | China | \ | 2010 | 2298 |
4 | KU050680 | China | GD-101 | 2015 | 2298 |
5 | KU645520 | China | HN1405 | 2014 | 2298 |
6 | KU845735 | China | CIAV-F10 | 2015 | 2298 |
7 | KX447637 | China | LY-2 | 2016 | 2298 |
8 | KX811526 | China | SD15 | 2015 | 2298 |
9 | KY486144 | China | HLJ15170 | 2015 | 2298 |
10 | KY486151 | China | NX15140 | 2015 | 2298 |
11 | KY486155 | China | LN15170 | 2015 | 2298 |
12 | MK089240 | China | 17CC0509 | 2017 | 2298 |
13 | MK089243 | China | 17SY0902 | 2017 | 2298 |
14 | MK887171 | China | N1 | 2016 | 2298 |
15 | MN103406 | China | GX1904B | 2019 | 2298 |
16 | MN649259 | China | GX1907B | 2019 | 2298 |
17 | MT091001 | China | TBC19 | 2019 | 2298 |
18 | MW423616 | China | TZC1910 | 2019 | 2298 |
19 | MW579762 | China | GX2020-D6 | 2020 | 2298 |
20 | MW660821 | China | SDSPF2020 | 2020 | 2298 |
21 | MZ540762 | China | YN04 | 2020 | 2298 |
22 | MH186141 | China | CIAV-Guangdong11 | 2018 | 2291 |
23 | KF224927 | China | GD-C-12 | 2013 | 2298 |
24 | AF475908 | China | \ | 2002 | 2298 |
25 | MH186138 | China | CIAV-Hebei12 | 2018 | 2293 |
26 | MH186137 | China | CIAV-Heilongjiang16 | 2018 | 2295 |
27 | MZ668717 | China | HN2021-1415 | 2021 | 2298 |
28 | MK770259 | China | XH16 | 2016 | 2298 |
29 | KM496310 | China | SC-PS | 2013 | 2298 |
30 | EF176599 | China | C14 | 2007 | 2298 |
31 | KM496303 | China | SC-HY | 2014 | 2298 |
32 | KM496305 | China | SC-MS | 2014 | 2298 |
33 | KM496307 | China | SC-MZ42A | 2013 | 2298 |
34 | KM496309 | China | SC-NC2 | 2013 | 2298 |
35 | KJ728816 | China | 4 | 2012 | 2298 |
36 | MT795928 | China | 1512TW | 2016 | 2298 |
37 | MT799753 | China | 1635TW | 2017 | 2298 |
38 | MT799771 | China | 1874TW | 2018 | 2298 |
39 | AY846844 | China | TJBD40 | 2004 | 2298 |
40 | AF311892 | Alabama | 98D02152 | 2003 | 2298 |
41 | KJ872514 | Argentina | CAV-18 | 2007 | 2298 |
42 | AF395114 | Bangladesh | BD-3 | 2004 | 2298 |
44 | MG846491 | Brazil | RS/BR/15/1R | 2015 | 2298 |
45 | MT671980 | Brazil | CAV | 2018 | 2298 |
46 | MG827098 | Egypt | CAV-CA1-2015 | 2015 | 2298 |
47 | MG827099 | Egypt | CAV-GZ2-2016 | 2016 | 2298 |
48 | MG827100 | Egypt | CAV-SK4-2017 | 2017 | 2298 |
49 | MH001570 | Egypt | CAV-EG-28 | 2017 | 2298 |
50 | MT268633 | Egypt | EG-ElBeheira-2019 | 2019 | 2298 |
51 | KY053900 | India | CAV/NAM/TANUVAS/09 | 2009 | 2263 |
52 | MZ868644 | India | NIAB-DPR | 2020 | 2298 |
53 | MT239353 | Iran | UT-Zahraee | 2018 | 2298 |
54 | MT813071 | Italy | CIAV/IT/CK/855/17 | 2017 | 2189 |
55 | MT813078 | Italy | CIAV/IT/CK/1188/19 | 2019 | 2186 |
56 | AY040632 | Malaysia | 3-1P60 | 2001 | 2298 |
57 | MZ666102 | Tunisia | CIAV_TN_7-15 | 2019 | 2181 |
58 | MT259325 | Turkey | GDA6K | 2015 | 2296 |
59 | MW219799 | Turkey | CIAV/2011/Akcdg/TUR | 2011 | 2298 |
60 | MW219800 | Turkey | CIAV/2014/Elzg-66/TUR | 2014 | 2298 |
61 | MH536106 | Vietnam | G17.3.1 | 2017 | 2298 |
62 | D10068 | \ | 26P4 (vaccine) | 2007 | 2298 |
63 | AF313470 | USA | Del Ros (vaccine) | 2000 | 2294 |
64 | M81223 | \ | CUX-1 (vaccine) | 1993 | 2298 |
65 | EF683159 | Australia | 3711 (vaccine) | 2007 | 2279 |
66 | MH001564 | Egypt | CAV-EG-26 | 2017 | 2298 |
67 | JF507715 | South Korea | CIAV89-69 | 1991 | 2298 |
68 | AB119448 | Japan | G6 | 2009 | 2298 |
69 | DQ016140 | Slovenia | 69 | 2006 | 1350 |
70 | JQ308213 | Chile | CL37 | 2008 | 1831 |
71 | KY888892 | China | 1102PT01 | 2011 | 1823 |
72 | MK423873 | Vietnam | Vietnam/PT1/17 | 2019 | 1823 |
73 | KP780288 | Vietnam | CAV/Vietnam/HN1/13 | 2018 | 1823 |
74 | DQ991394 | USA | 01-4201 | 2007 | 2298 |
75 | KY888907 | China | 1310CH05 | 2013 | 1823 |
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Primers | (Primer Sequence 5′ to 3′) | Length |
---|---|---|
CIAV ①-F | GACCGATCAACCCAAGCCTCC | 1010 bp |
CIAV ①-R | ATCTTCCCGGTCGCATAAGCA | |
CIAV ②-F | CTTGCCGGTTCTTTAATCACCCT | 751 bp |
CIAV ②-R | CTCTTACCCAGCTGCCACACC | |
CIAV ③-F | CTACATGGCAGCACCCGCATC | 1055 bp |
CIAV ③-R | TCCGGCACATTCTTA(G)AAACCAG | |
CIAV ④-F | AATGAACGCTCTCCAAGAAG | 540 bp |
CIAV ④-R | AGCGGATAGTCATAGTAGAT |
Primers | Pre-Denatured | Denatured × 35 | Annealing × 35 | Extension × 35 | Post Elongation |
---|---|---|---|---|---|
CIAV ① | 95 °C, 5 min | 94 °C, 30 s | 61 °C, 30 s | 72 °C, 70 s | 72 °C, 7 min |
CIAV ② | \ | \ | 62 °C, 30 s | 72 °C, 45 s | 72 °C, 7 min |
CIAV ③ | \ | \ | 58.7 °C, 30 s | 72 °C, 70 s | 72 °C, 7 min |
CIAV ④ | \ | \ | 50.5 °C, 30 s | 72 °C, 30 s | 72 °C, 8 min |
Method | Recombination p Value |
---|---|
RDP | 1.403 × 10−2 |
GENECONV | 2.624 × 10−2 |
BootScan | 3.598 × 10−2 |
MaxChi | 4.106 × 10−3 |
Chimaera | 1.071 × 10−2 |
SiScan | 2.675 × 10−4 |
3Seq | 6.864 × 10−3 |
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Share and Cite
Zeng, Y.; Zhang, H.; Zhang, H. Isolation, Identification, and Whole Genome Analysis of Chicken Infectious Anemia Virus in an Outbreak of Disease in Adult Layer Hens. Vet. Sci. 2023, 10, 481. https://doi.org/10.3390/vetsci10070481
Zeng Y, Zhang H, Zhang H. Isolation, Identification, and Whole Genome Analysis of Chicken Infectious Anemia Virus in an Outbreak of Disease in Adult Layer Hens. Veterinary Sciences. 2023; 10(7):481. https://doi.org/10.3390/vetsci10070481
Chicago/Turabian StyleZeng, Yueyan, Hui Zhang, and Huanrong Zhang. 2023. "Isolation, Identification, and Whole Genome Analysis of Chicken Infectious Anemia Virus in an Outbreak of Disease in Adult Layer Hens" Veterinary Sciences 10, no. 7: 481. https://doi.org/10.3390/vetsci10070481