Subgenotype VII.1.1 Newcastle Disease Virus Evolution and Spread in the Russian Federation in 2019–2023
Abstract
1. Introduction
2. Materials and Methods
2.1. Sampling
2.2. Sample Preparation
2.3. Virus Isolation
2.4. RNA Extraction
2.5. Real-Time Reverse Transcription-Polymerase Chain Reaction (Real-Time RT-PCR)
2.6. Reverse Transcription (RT) and Polymerase Chain Reaction (PCR) for Determination of Complete F and HN Gene Sequences
2.7. Sequencing
2.8. Alignment and Editing of Nucleotide Sequences
2.9. Dataset for Phylogenetic and Evolutionary Analysis
2.10. Evolutionary Analysis of Nucleotide Sequences Using BEAST and BEAUTI Software
2.11. Mapping
3. Results
3.1. Sampling
3.2. Phylogenetic Analysis
3.3. Evolutionary Analysis of Nucleotide Sequence Variability of NDVisolates
4. Discussion
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Data Availability Statement
Conflicts of Interest
References
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No. | Isolate | Sampling Region | Species | Sampling Date | Accession F/HN |
---|---|---|---|---|---|
1 | NDV/Ck/Rus/Krasnodar/207/2019 | Krasnodar Krai | Chicken | 29 January 2019 | PV490921 PV490946 |
2 | NDV/Ck/Rus/Chechnya/819/2019 | Chechen Republic | Chicken | 13 March 2019 | PV490922 PV490947 |
3 | NDV/Ck/Rus/Stavropol/923/2019 | Stavropol Krai | Chicken | 18 April 2019 | PV490923 PV490948 |
4 | NDV/Ck/Rus/Primorsk/1134/2019 | Primorsky Krai | Chicken | 6 May 2019 | PV490924 PQ641107 |
5 | NDV/Ck/Rus/Saratov/2017/2019 | Saratov Oblast | Chicken | 1 August 2019 | PV490925 PQ641108 |
6 | NDV/Ck/Rus/Zabaikalsk/2346/2019 | Zabaikalsky Krai | Chicken | 4 September 2019 | PV490926 PV490949 |
7 | NDV/Ck/Rus/Omsk/2366/2019 | Omsk Oblast | Chicken | October 2019 | PV490927 PV490950 |
8 | NDV/poultry/Rus/Kursk/2819/2019 | Kursk Oblast | Chicken | November 2019 | PV490928 PV490951 |
9 | NDV/Ck/Rus/Primorsk/3087/2019 | Primorsky Krai | Chicken | 10 December 2019 | PV490929 PV490952 |
10 | NDV/Ck/Rus/Kursk/68/2020 | Kursk Oblast | Chicken | January 2020 | PV490930 PQ641109 |
11 | NDV/Ck/Rus/Kursk/142/2020 | Kursk Oblast | Chicken | January 2020 | PV490931 PQ641110 |
12 | NDV/Ck/Rus/Vladimir/709/2020 | Vladimir Oblast | Chicken | 30 April 2020 | PV490932 PV490953 |
13 | NDV/Ck/Rus/Vladimir/1464/2020 | Vladimir Oblast | Chicken | 4 September 2020 | PV490933 PQ641111 |
14 | NDV/Ck/Rus/Vladimir/1474/2020 | Vladimir Oblast | Chicken | 7 September 2020 | PV490934 PQ641112 |
15 | NDV/Ck/Rus/Vladimir/1553/2020 | Vladimir Oblast | Chicken | 14 September 2020 | PV490935 PQ641113 |
16 | NDV/Ck/Rus/Vladimir/1715/2020 | Vladimir Oblast | Chicken | 7 October 2020 | PV490936 PQ641114 |
17 | NDV/Ck/Rus/Ingushetia/1750/2020 | Republic of Ingushetia | Chicken | 13 August 2020 | PV490937 PV490954 |
18 | NDV/Ck/Rus/Vladimir/1931/2020 | Vladimir Oblast | Chicken | 5 November 2020 | PV490938 PQ641115 |
19 | NDV/Ck/Rus/Vladimir/2125/2020 | Vladimir Oblast | Chicken | 1 December 2020 | PV490939 PQ641116 |
20 | NDV/Ck/Rus/Chechny/2191/2020 | Chechen Republic | Chicken | 7 December 2020 | PV490940 PQ641117 |
21 | NDV/Ck/Rus/N.Novgorod/667/2021 | Nizhny Novgorod Oblast | Chicken | 1 May 2021 | PV490941 PQ641118 |
22 | NDV/Ck/Rus/Vladimir/1035/2021 | Vladimir Oblast | Chicken | 20 July 2021 | PV490942 PQ641119 |
23 | NDV/Ck/Rus/Khanty-Mansi/1240/2021 | Khanty-Mansi Autonomous Okrug | Chicken | 9 August 2021 | PV490943 PV490955 |
24 | NDV/Ck/Rus/Primorsk/1472/2021 | Primorsky Krai | Chicken | 6 September 2021 | PV490944 PQ641120 |
25 | NDV/poultry/Rus/Vladimir/2271/2021 | Vladimir Oblast | Chicken | 28 December 2021 | PV490945 PV490956 |
26 | NDV/Ck/Rus/Vladimir/1114/2022 | Vladimir Oblast | Chicken | 8 June 2022 | PQ641093 PQ641121 |
27 | NDV/poultry/Rus/Saratov/2403/2022 | Saratov Oblast | Chicken | October 2022 | PQ641094 PQ641122 |
28 | NDV/Ck/Rus/Samara/2453/2022 | Samara Oblast | Chicken | 26 October 2022 | PQ641095 PQ641123 |
29 | NDV/poultry/Rus/Bashkortostan/2776/2022 | Republic of Bashkortostan | Chicken | 5 December 2022 | PQ641092 |
30 | NDV/quail/Rus/Mari El/128/2023 | Mari El Republic | Quail | 25 January 2023 | PQ641096 PQ641124 |
31 | NDV/Ck/Rus/Samara/761/2023 | Samara Oblast | Chicken | April 2023 | PQ641097 PQ641125 |
32 | NDV/Ck/Rus/N.Novgorod/1230/2023 | Nizhny Novgorod Oblast | Chicken | May 2023 | PQ641098 PQ641126 |
33 | NDV/Ck/Rus/Irkutsk/1317/2023 | Irkutsk Oblast | Chicken | 24 May 2023 | PQ641099 PQ641127 |
34 | NDV/Ck/Rus/Vladimir/2042/2023 | Vladimir Oblast | Chicken | 15 August 2023 | PQ641100 PQ641128 |
35 | NDV/Ck/Mari El/2090/2023 | Mari El Republic | Chicken | 8 August 2023 | PQ641101 PQ641129 |
36 | NDV/Ck/Rus/Khanty-Mansi/2285/2023 | Khanty-Mansi Autonomous Okrug | Chicken | 23 August 2023 | PQ641102 PQ641130 |
37 | NDV/Ck/Rus/Vladimir/2501/2023 | Vladimir Oblast | Chicken | October 2023 | PQ641103 PQ641131 |
38 | NDV/Ck/Rus/Vladimir/2546/2023 | Vladimir Oblast | Chicken | October 2023 | PQ641104 PQ641132 |
39 | NDV/Ck/Rus/Mari El/3061/2023 | Mari El Republic | Chicken | 22 November 2023 | PQ641105 PQ641133 |
40 | NDV/Ck/Rus/Khabarovsk/3162/2023 | Khabarovsk Krai | Chicken | 21 November 2023 | PQ641106 PQ641134 |
Summary Statistics | Models Used and Parameter Estimates | |||
---|---|---|---|---|
GTR | HKY | |||
Strict Model | Relaxed Model | Strict Model | Relaxed Model | |
Substitution Accumulation Rate Per Site Per Year for the RF Isolates | ||||
Mean | 1.8 × 10−3 | 2.0 × 10−3 | 1.8 × 10−3 | 2.0 × 10−3 |
Standard deviation of mean | 3.4310 × 10−4 | 5.47 × 10−4 | 3.47 × 10−4 | 5.50 × 10−4 |
Date of tree root node for the group of Iranian and Russian isolates | ||||
Mean | 2008.9373 | 2008.9651 | 2007.8821 | 2008.5288 |
Standard deviation of mean | 1.5625 | 1.5531 | 2.935 | 2.2313 |
Date of the most recent common ancestor of the group of Russian isolates | ||||
Mean | 2016.7133 | 2016.739 | 2015.7992 | 2016.4382 |
Standard deviation of mean | 0.8278 | 0.8222 | 1.6926 | 1.1471 |
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Guseva, N.A.; Kolosov, S.N.; Zinyakov, N.G.; Kozlov, A.A.; Shcherbakova, L.O.; Chvala, I.A.; Andriyasov, A.V.; Yin, R.; Andreychuk, D.B.; Chvala, I.A. Subgenotype VII.1.1 Newcastle Disease Virus Evolution and Spread in the Russian Federation in 2019–2023. Viruses 2025, 17, 1319. https://doi.org/10.3390/v17101319
Guseva NA, Kolosov SN, Zinyakov NG, Kozlov AA, Shcherbakova LO, Chvala IA, Andriyasov AV, Yin R, Andreychuk DB, Chvala IA. Subgenotype VII.1.1 Newcastle Disease Virus Evolution and Spread in the Russian Federation in 2019–2023. Viruses. 2025; 17(10):1319. https://doi.org/10.3390/v17101319
Chicago/Turabian StyleGuseva, Nelly A., Sergey N. Kolosov, Nikolay G. Zinyakov, Anton A. Kozlov, Lydia O. Shcherbakova, Irina A. Chvala, Artem V. Andriyasov, Renfu Yin, Dmitry B. Andreychuk, and Ilya A. Chvala. 2025. "Subgenotype VII.1.1 Newcastle Disease Virus Evolution and Spread in the Russian Federation in 2019–2023" Viruses 17, no. 10: 1319. https://doi.org/10.3390/v17101319
APA StyleGuseva, N. A., Kolosov, S. N., Zinyakov, N. G., Kozlov, A. A., Shcherbakova, L. O., Chvala, I. A., Andriyasov, A. V., Yin, R., Andreychuk, D. B., & Chvala, I. A. (2025). Subgenotype VII.1.1 Newcastle Disease Virus Evolution and Spread in the Russian Federation in 2019–2023. Viruses, 17(10), 1319. https://doi.org/10.3390/v17101319