"Virus Evol"[Journal] - Search Results

Year	Number of Results
2015	20
2016	37
2017	91
2018	42
2019	60
2020	103
2021	126
2022	131
2023	97
2024	131
2025	112
2026	48

1

Evolution of SARS-CoV-2 caused infection in farmed minks: continuous surveillance of an 11-month outbreak at the largest Latvian mink farm.

Zrelovs Ņ, Oļševskis E, Perevoščikovs J, Silamiķelis I, Jakovele A, Lamberga K, Bērziņš A, Brīvība M, Kloviņš J. Zrelovs Ņ, et al. Virus Evol. 2026 Jun 27;12(1):veag038. doi: 10.1093/ve/veag038. eCollection 2026. Virus Evol. 2026. PMID: 42453117 Free PMC article.

2

Experimental evolution of Rc-o319 sarbecovirus spike protein reveals limited ACE2 adaptability.

Moreno-García J, Dufloo J, Sanjuán R. Moreno-García J, et al. Virus Evol. 2026 Jun 23;12(1):veag035. doi: 10.1093/ve/veag035. eCollection 2026. Virus Evol. 2026. PMID: 42416704 Free PMC article.

3

Respiratory virus genomic epidemiology during post-pandemic re-emergence of influenza in Australia.

Rockett RJ, Agius JE, Chandra S, Fong W, Aziz A, Suster CJE, Basile K, Lam C, Chen SC, Dwyer DE, Kok J, Sullivan SG, Barr IG, Sintchenko V, Golubchik T. Rockett RJ, et al. Virus Evol. 2026 Jun 22;12(1):veag036. doi: 10.1093/ve/veag036. eCollection 2026. Virus Evol. 2026. PMID: 42438688 Free PMC article.

4

Continuous in silico screening of fish, amphibians, reptiles, and birds expands the diversity of bornavirids and reveals unexpected genomic architectures.

Eshak MIY, Imai S, Kawasaki J, Kishimoto M, Vences M, Rakotoarison A, Beer M, Rubbenstroth D, Horie M, Pfaff F. Eshak MIY, et al. Virus Evol. 2026 Jun 5;12(1):veag033. doi: 10.1093/ve/veag033. eCollection 2026. Virus Evol. 2026. PMID: 42358456 Free PMC article.

5

Genomic epidemiology and evolutionary analysis of Lassa virus from small mammals suggest bidirectional viral movement across humans and animals.

Happi AN, Ogunsanya OA, Sijuwola AE, Saibu FM, Akano K, Ayinla AO, Daodu RO, Page B, Olumade TJ, Oguzie JU, Oluniyi PE, Adedokun OA, Fadele J, Nwofoke C, Elias OT, Ogundana KE, Lawal OZ, Nosamiefan I, Okolie J, Adelabu A, Lombardi K, Eller LA, Broach E, Prins PA, Heeney JL, Modjarrad K, Njatou TLFA, Parker ZF, McCauley M, Vasan S, Parker E, Collins ND, Michael NL, Happi CT. Happi AN, et al. Virus Evol. 2026 Jun 1;12(1):veag032. doi: 10.1093/ve/veag032. eCollection 2026. Virus Evol. 2026. PMID: 42339070 Free PMC article.

6

Extending the temporal window of arbovirus evolutionary analysis through the recovery of a century-old bandavirus.

Gieraths U, Beheim-Schwarzbach J, Pickin MJ, Beyer A, Begeman L, Hoffmann B, Schlottau K, Beer M, Ulrich RG, Müller T, Freuling CM, Mauno T, van de Bildt M, Mols VC, Corman VM, Weber F, Jones TC, Drosten C. Gieraths U, et al. Virus Evol. 2026 May 26;12(1):veag034. doi: 10.1093/ve/veag034. eCollection 2026. Virus Evol. 2026. PMID: 42382857 Free PMC article.

7

Mapping the global distribution and spread of the Plasmodium vivax-associated virus MaRNAV-1.

Petrone ME, Charon J, Parry RH, Grigg MJ, Piera KA, Westaway JAF, Shioda K, Russell B, Price RN, William T, Kenangalem E, McCarthy JS, Barber BE, Holmes EC, Anstey NM. Petrone ME, et al. Virus Evol. 2026 May 23;12(1):veag031. doi: 10.1093/ve/veag031. eCollection 2026. Virus Evol. 2026. PMID: 42311450 Free PMC article.

8

Extreme GC3 codon bias in a novel brown seaweed virus results in pseudoambigrammatic characteristics.

Dekker RJ, de Leeuw WC, Rauwerda H, van Olst MF, Ensink WA, van Leeuwen SM, Cohen J, Timmermans K, Breit TM, Jonker MJ. Dekker RJ, et al. Virus Evol. 2026 May 23;12(1):veag030. doi: 10.1093/ve/veag030. eCollection 2026. Virus Evol. 2026. PMID: 42294464 Free PMC article.

9

Unravelling viral identity: avoiding the trap of endogenous sequences for viral surveillance of small ruminant oncogenic retroviruses.

Riocreux-Verney B, Verneret M, Dolmazon C, Ashraf S, Atim SA, Navratil V, Leroux C, Turpin J. Riocreux-Verney B, et al. Virus Evol. 2026 May 8;12(1):veag028. doi: 10.1093/ve/veag028. eCollection 2026. Virus Evol. 2026. PMID: 42212305 Free PMC article.

10

The adaptive plasticity of temperate phage λ.

Gandon S, Goel T, Weitz JS, Lion S. Gandon S, et al. Virus Evol. 2026 May 7;12(1):veag026. doi: 10.1093/ve/veag026. eCollection 2026. Virus Evol. 2026. PMID: 42233085 Free PMC article.

11

Metaviromics reveals a high diversity of viruses belonging to the Caliciviridae family in seal feces.

Desdouits M, Schaeffer J, Le Mennec C, Gourmelon M, Le Guyader FS. Desdouits M, et al. Virus Evol. 2026 May 7;12(1):veag029. doi: 10.1093/ve/veag029. eCollection 2026. Virus Evol. 2026. PMID: 42199979 Free PMC article.

12

Linkage-aware inference of fitness from short-read time-series genomic data.

Abdullah SMU, Sohail MS, Louie RHY, Sun Y, Barton JP, McKay MR. Abdullah SMU, et al. Virus Evol. 2026 Apr 25;12(1):veag027. doi: 10.1093/ve/veag027. eCollection 2026. Virus Evol. 2026. PMID: 42181666 Free PMC article.

13

Comprehensive hallmark gene sequence, genomic and structural analysis clarifies new and established taxa within the Picornavirales.

Mayne R, Smith DB, Brown K, Chen YP, Firth AE, Katayama K, Knowles NJ, Simmonds P. Mayne R, et al. Virus Evol. 2026 Apr 20;12(1):veag023. doi: 10.1093/ve/veag023. eCollection 2026. Virus Evol. 2026. PMID: 42110882 Free PMC article.

14

Getting to the root of HIV transmitted founder virus sequences.

Jones BR, Brumme ZL, Hunter E, Joy JB. Jones BR, et al. Virus Evol. 2026 Apr 20;12(1):veag025. doi: 10.1093/ve/veag025. eCollection 2026. Virus Evol. 2026. PMID: 42110881 Free PMC article.

15

Peaked-to-flat transition in quasispecies structure evolution.

Gregori J, Colomer-Castell S, Campos C, Ibañez-Lligoña M, García-Cehic D, Cortese MF, Tabernero D, Riveiro-Barciela M, Buti M, Rando-Segura A, Ferrer R, Pumarola T, Andrés C, González-Sánchez A, Antón A, Rodriguez-Frias F, Quer J. Gregori J, et al. Virus Evol. 2026 Apr 14;12(1):veag024. doi: 10.1093/ve/veag024. eCollection 2026. Virus Evol. 2026. PMID: 42087992 Free PMC article.

16

Single capsid mutations modulating phage adsorption, persistence, and plaque morphology shape evolutionary trajectories in ΦX174.

Reuter M, Sieber M, Reyes-Matte O, Vasileiou C, Böhmker C, Romeyer Dherbey J, Bertels F, Lopez-Garrido J. Reuter M, et al. Virus Evol. 2026 Apr 3;12(1):veag022. doi: 10.1093/ve/veag022. eCollection 2026. Virus Evol. 2026. PMID: 42040904 Free PMC article.

17

Genetic drift acts strongly on influenza virus populations within acute human infections but is obscured by other factors within acutely infected swine.

Shi YT, Martin MA, Weissman DB, Koelle K. Shi YT, et al. Virus Evol. 2026 Apr 1;12(1):veag021. doi: 10.1093/ve/veag021. eCollection 2026. Virus Evol. 2026. PMID: 42027246 Free PMC article.

18

Molecular epidemiology and multi-scale drivers of piscine myocarditis virus dispersal in salmon aquaculture.

Zhao M, Duault H, Fournié G, Solheim MA, Alexandersen S, Matthews C, Soares S, Madhun A, Karlsen M, Hill SC. Zhao M, et al. Virus Evol. 2026 Mar 28;12(1):veag020. doi: 10.1093/ve/veag020. eCollection 2026. Virus Evol. 2026. PMID: 42027247 Free PMC article.

19

Variations and evolution of HIV-1 provirus in peripheral blood under the pressure of ART.

Liang Y, Deng H, Li Q, Zhang C, Li J, Kong Q, Zou Z, Li L, Chen W. Liang Y, et al. Virus Evol. 2026 Mar 28;12(1):veag019. doi: 10.1093/ve/veag019. eCollection 2026. Virus Evol. 2026. PMID: 42021925 Free PMC article.

20

Viral diversity, ecological interconnectedness, and the identification of mammalian chuviruses in Australian microbats.

Ortiz-Baez AS, Mélade J, Van Brussel K, Lang BJ, Lachenauer A, Holmes EC. Ortiz-Baez AS, et al. Virus Evol. 2026 Mar 21;12(1):veag017. doi: 10.1093/ve/veag017. eCollection 2026. Virus Evol. 2026. PMID: 41978731 Free PMC article.

21

Influenza hemagglutinin subtypes have different sequence constraints despite sharing extremely similar structures.

Ahn JJ, Yu TC, Dadonaite B, Radford CE, Bloom JD. Ahn JJ, et al. Virus Evol. 2026 Mar 21;12(1):veag018. doi: 10.1093/ve/veag018. eCollection 2026. Virus Evol. 2026. PMID: 41971714 Free PMC article.

22

Identification and genomic characterization of BA.3.2: a highly divergent BA.3-related SARS-CoV-2 lineage from southern Africa.

Dor G, Kekana D, Hisner R, Martin DP, Korber B, Ernst T, Levy A, Speers D, Turville S, Sintchenko V, Basile K, Sullivan G, Rockett R, Kok J, Schoenmakers J, Gueli F, Lessels R, Baxter C, Wolter N, von Gottberg A, Tegally H, de Oliveira T. Dor G, et al. Virus Evol. 2026 Mar 18;12(1):veag016. doi: 10.1093/ve/veag016. eCollection 2026. Virus Evol. 2026. PMID: 41978732 Free PMC article.

23

Ancestral sequence reconstruction analysis indicates the S1/S2 insertion in the SARS-CoV-2 spike gene likely interrupted a codon.

Chambers MJ, Abdullah M, Sadhu MJ. Chambers MJ, et al. Virus Evol. 2026 Mar 16;12(1):veag015. doi: 10.1093/ve/veag015. eCollection 2026. Virus Evol. 2026. PMID: 41971715 Free article.

24

Anthropozoonotic spillovers reveal sustained long-term cryptic circulation of SARS-CoV-2 within and between Lithuanian mink farms.

Smičius M, Olendraitė I, Bačelis J, Šimaitis A, Gabrielaitė M, Oude Munnink BB, Sikkema RS, Stankevičius A, Janeliūnas Ž, Bušauskas P, Pumputis E, Pilevičienė S, Mačiulskis P, Masiulis M, Paulauskas V, Ščeponavičienė S, Katėnaitė M, Norvilas R, Raugienė L, Jonikas R, Nasvytienė I, Žemeckienė Ž, Tamušauskaitė K, Norkienė M, Vasiliūnaitė E, Žiogienė D, Timinskas A, Šukys M, Šarauskas M, Juozapaitė D, Naumovas D, Pautienius A, Vitkauskienė A, Ugenskienė R, Gedvilaitė A, Čereškevičius D, Griškevičius L, Koopmans M, Malakauskas A, Dudas G. Smičius M, et al. Virus Evol. 2026 Mar 13;12(1):veag014. doi: 10.1093/ve/veag014. eCollection 2026. Virus Evol. 2026. PMID: 41994318 Free PMC article.

25

Genetic and antigenic diversity of rotavirus A in faeces from Danish pigs.

Pedersen K, Goecke NB, Canuti M, Ryt-Hansen P, Weber NR, Cortey M, Larsen LE. Pedersen K, et al. Virus Evol. 2026 Mar 13;12(1):veag013. doi: 10.1093/ve/veag013. eCollection 2026. Virus Evol. 2026. PMID: 41958478 Free PMC article.

26

Continuous phylogeography reveals shifting environmental drivers of highly pathogenic avian influenza H5 spread in Italy, 2016-23.

Fornasiero D, Mulatti P, Fusaro A, Monne I, Gámbaro F, Dellicour S, Scolamacchia F, Martelli L, Faustini G, Ducatez MF, Guinat C. Fornasiero D, et al. Virus Evol. 2026 Mar 9;12(1):veag012. doi: 10.1093/ve/veag012. eCollection 2026. Virus Evol. 2026. PMID: 41907063 Free PMC article.

27

Sequence based virus host prediction: a curated dataset and generalizable framework for training artificial intelligence to identify viruses of humans.

Carbajo AL Jr, Vensko TA, Pellett PE. Carbajo AL Jr, et al. Virus Evol. 2026 Feb 20;12(1):veag009. doi: 10.1093/ve/veag009. eCollection 2026. Virus Evol. 2026. PMID: 41958479 Free PMC article.

28

Evolution and viral properties of the SARS-CoV-2 BA.3.2 subvariant.

Jule Z, Römer C, Hossen T, Sviridchik V, Reedoy K, Ganga Y, Silangwe S, Jackson L, Norman A, Karim F, Kekana D, Mahlangu B, Mnguni A, Nzimande A, Stock N, Bernstein M, Gosnell BI, Moosa MS, Wolter N, Khan K, Neher RA, Sigal A. Jule Z, et al. Virus Evol. 2026 Feb 20;12(1):veag011. doi: 10.1093/ve/veag011. eCollection 2026. Virus Evol. 2026. PMID: 41884606 Free PMC article.

29

Experimental evolution of the host range dynamics in two isolates of potato virus Y.

Morais IJ, Silva JMF, Inoue-Nagata AK, Elena SF. Morais IJ, et al. Virus Evol. 2026 Feb 20;12(1):veag010. doi: 10.1093/ve/veag010. eCollection 2026. Virus Evol. 2026. PMID: 41836771 Free PMC article.

30

Chronic infections can generate SARS-CoV-2-like bursts of viral evolution without epistasis.

Rodríguez-Horta E, Strahan J, Dinner AR, Barton JP. Rodríguez-Horta E, et al. Virus Evol. 2026 Feb 18;12(1):veag008. doi: 10.1093/ve/veag008. eCollection 2026. Virus Evol. 2026. PMID: 41878356 Free PMC article.

31

Begomovirus species demarcation based on genome-sequence identity yields non-monophyletic species: a case study of sweet potato-infecting begomoviruses.

Mauriello MA, Hoyer JS, Julian AD, Crespo-Bellido A, Seah YM, Duffy S. Mauriello MA, et al. Virus Evol. 2026 Feb 16;12(1):veag007. doi: 10.1093/ve/veag007. eCollection 2026. Virus Evol. 2026. PMID: 41836770 Free PMC article.

32

Introduction and inter-species transmission dynamics of high pathogenicity avian influenza H5N1 viruses in Japan 2021-25.

Hew YL, Guinat C, Couty M, Fornasiero D, Hiono T, Isoda N, Sakoda Y. Hew YL, et al. Virus Evol. 2026 Feb 16;12(1):veag005. doi: 10.1093/ve/veag005. eCollection 2026. Virus Evol. 2026. PMID: 41705171 Free PMC article.

33

Genomic analysis of Ostreococcus tauri-infecting viruses reveals a hypervariable region associated with host-virus interactions.

Thomy J, Henri J, Demory D, Sanchez F, Escande ML, Mirambeau G, Grimsley N, Yau S. Thomy J, et al. Virus Evol. 2026 Feb 11;12(1):veaf096. doi: 10.1093/ve/veaf096. eCollection 2026. Virus Evol. 2026. PMID: 41700146 Free PMC article.

34

Clonal interference and changing selective pressures shape the escape of SARS-CoV-2 from hundreds of antibodies.

Haddox HK, Abdel Aziz O, Galloway JG, Kent J, Cooper CR, Jennings-Shaffer C, Dumm W, Temple SD, Bloom JD, Matsen FA 4th. Haddox HK, et al. Virus Evol. 2026 Feb 4;12(1):veaf104. doi: 10.1093/ve/veaf104. eCollection 2026. Virus Evol. 2026. PMID: 41767406 Free PMC article.

35

Deletion detection in SARS-CoV-2 genomes from COVID-19 patients: elimination of false positives.

Jiang N, Dewey CN, Yin J. Jiang N, et al. Virus Evol. 2026 Feb 2;12(1):veag003. doi: 10.1093/ve/veag003. eCollection 2026. Virus Evol. 2026. PMID: 41696605 Free PMC article.

36

Wild birds drive the introduction, maintenance, and spread of H5N1 clade 2.3.4.4b high pathogenicity avian influenza viruses in Spain, 2021-2022.

Cho AY, Lee DH, Fusaro A, Giussani E, Pastori A, Agüero M, Majó N, Bertran K. Cho AY, et al. Virus Evol. 2026 Jan 30;12(1):veag006. doi: 10.1093/ve/veag006. eCollection 2026. Virus Evol. 2026. PMID: 41743171 Free PMC article.

37

The whole genome analysis of four Orf virus strains from Europe and South America.

Cacciabue M, Lozano Calderón LC, Moleres J, Echeverría I, de Pablo L, Glaria I, König G, Peralta A, Reina R. Cacciabue M, et al. Virus Evol. 2026 Jan 28;12(1):veag004. doi: 10.1093/ve/veag004. eCollection 2026. Virus Evol. 2026. PMID: 41727713 Free PMC article.

38

The S190R mutation in RSV-A F protein impairs nirsevimab binding and neutralization capacity.

Cordela S, Harari J, Moirangthem R, Khaleafi R, Kladnitsky O, Duran D, Grunewald M, Bar-On Y. Cordela S, et al. Virus Evol. 2026 Jan 8;12(1):veag002. doi: 10.1093/ve/veag002. eCollection 2026. Virus Evol. 2026. PMID: 41660179 Free PMC article.

39

Intrahost population dynamics of chikungunya virus in humans and naturally infected Aedes mosquitoes reveal transmission-driven diversity.

Banho CA, de Carvalho Marques B, Nascimento OB, Parra MCP, Ferreira MVM, Lemos AP, Magnani GP, Lourenço KL, de Souza BC, Hernandes VM, Brancini ML, Estofolete CF, Júnior JPA, Vasilakis N, Nogueira ML. Banho CA, et al. Virus Evol. 2025 Dec 23;12(1):veaf102. doi: 10.1093/ve/veaf102. eCollection 2026. Virus Evol. 2025. PMID: 41607870 Free PMC article.

40

A phylogenetic contribution to understanding the panzootic spread of African swine fever: from the global to the local scale.

Rossi G, Leitch ECM, Graham J, Biccheri R, Iscaro C, Torresi C, Lycett SJ, Feliziani F, Giammarioli M. Rossi G, et al. Virus Evol. 2025 Dec 24;12(1):veaf103. doi: 10.1093/ve/veaf103. eCollection 2026. Virus Evol. 2025. PMID: 41583793 Free PMC article.

41

Unveiling the RNA virus landscape of Cotesia chilonis: geographic distribution, diversity, and potential roles in parasitoid-host interactions.

Cao Z, Xue C, Wang F, Wang F, Fang Q, Song Q, Ye G. Cao Z, et al. Virus Evol. 2025 Dec 23;12(1):veag001. doi: 10.1093/ve/veag001. eCollection 2026. Virus Evol. 2025. PMID: 41583792 Free PMC article.

42

Coxsackievirus A6 was the predominant pathogen of hand, foot, and mouth disease with frequent recombination and mutations in Shandong Province, 2023.

Wang Z, Wang J, Wang Y, Li Y, Dong Z, Ji J, Liu N, Chong X, Yin N, Zhou Y, Qiu Y, Liu C, Zhao Z, Xu X, Liang H, Kou Z, Wen H. Wang Z, et al. Virus Evol. 2025 Dec 18;12(1):veaf105. doi: 10.1093/ve/veaf105. eCollection 2026. Virus Evol. 2025. PMID: 41583791 Free PMC article.

43

Viral diversity influences T-cell responses to enteric human adenoviruses F40 and F41.

Craven HM, Hoang JP, Mukhopadhyay R, Lambisia AW, Krishna BAC, Ravenhill BJ, Agoti CN, Houldcroft CJ. Craven HM, et al. Virus Evol. 2025 Dec 18;12(1):veaf098. doi: 10.1093/ve/veaf098. eCollection 2026. Virus Evol. 2025. PMID: 41573081 Free PMC article.

44

Human outbreak detection and best practice MPXV analysis and interpretation with squirrel.

O'Toole Á, Kinganda-Lusamaki E, Colquhoun R, Chato C, Scher E, Kent C, Wilkinson S, Quick J, Loman N, Duggan AT, Mbala P, Rambaut A. O'Toole Á, et al. Virus Evol. 2025 Dec 10;12(1):veaf095. doi: 10.1093/ve/veaf095. eCollection 2026. Virus Evol. 2025. PMID: 41573080 Free PMC article.

45

Full genome-based evolutionary analyses of FMD virus serotype A including field outbreak strains isolated from India during the period 2008-22.

Mohapatra JK, Das B, Subramaniam S, Dahiya SS, Rout M, Prusty BR, Singh RP. Mohapatra JK, et al. Virus Evol. 2025 Dec 18;12(1):veaf097. doi: 10.1093/ve/veaf097. eCollection 2026. Virus Evol. 2025. PMID: 41573079 Free PMC article.

46

Contrasting genome composition and codon usage in Listeria monocytogenes temperate versus virulent phages.

Kobakhidze S, Song A, Tang YW, Kotetishvili M. Kobakhidze S, et al. Virus Evol. 2025 Dec 18;12(1):veaf100. doi: 10.1093/ve/veaf100. eCollection 2026. Virus Evol. 2025. PMID: 41573078 Free PMC article.

47

Intra-host GI.1 norovirus evolution is shaped by genetic drift and purifying selection.

Tohma K, Liu P, Koelle K, Sablon O, Pickett T, Mazo I, Moe CL, Parra GI. Tohma K, et al. Virus Evol. 2025 Dec 18;12(1):veaf101. doi: 10.1093/ve/veaf101. eCollection 2026. Virus Evol. 2025. PMID: 41561447 Free article.

48

Single genome amplification and molecular cloning of HIV-1 populations in acute HIV-1 infection: implications for studies on HIV-1 diversity and evolutionary rate.

Hsieh AYY, Hassan AS, Nazziwa J, Lindquist L, Karlson S, Hare J, Kamali A, Karita E, Kilembe W, Price MA, Björkman P, Kaleebu P, Allen S, Hunter E, Gilmour J, Rowland-Jones SL, Sanders EJ, Esbjörnsson J. Hsieh AYY, et al. Virus Evol. 2025 Dec 18;12(1):veaf099. doi: 10.1093/ve/veaf099. eCollection 2026. Virus Evol. 2025. PMID: 41561446 Free PMC article.

49

Ambecovirus, a novel Betacoronavirus subgenus circulating in neotropical bats, sheds new light on bat-borne coronaviruses evolution.

Wallau GDL, Barbier E, Machado LC, da Silva AF, Dias YJM, Dezordi FZ, Tomazatos A, Horváth B, Lins RD, Bernard E, Cadar D. Wallau GDL, et al. Virus Evol. 2025 Dec 6;11(1):veaf094. doi: 10.1093/ve/veaf094. eCollection 2025. Virus Evol. 2025. PMID: 41492410 Free PMC article.

50

The genetic architecture of HIV-1 virulence.

Blanquart F, Wymant C, Hall M, Power R, Golubchik T, Gall A, de Cesare M, Macintyre-Cockett G, Bakker M, Bezemer D, Gabrielaite M, Ong SH, Kendall M, Sauter R, Bannert N, Fellay J, Grabowski MK, Gunsenheimer-Bartmeyer B, Günthard HF, Kivelä P, Kouyos RD, Laeyendecker O, Marvig RL, Meixenberger K, Meyer L, van Sighem A, Bonsall D, van der Valk M, Berkhout B, Kellam P, Cornelissen M, Reiss P, Fraser C. Blanquart F, et al. Virus Evol. 2025 Dec 5;11(1):veaf057. doi: 10.1093/ve/veaf057. eCollection 2025. Virus Evol. 2025. PMID: 41368623 Free PMC article.

51

Biosurveillance of coronaviruses in Rhinolophus bats from South Africa.

Rademan R, Geldenhuys M, Mittal N, Laing ED, Markotter W. Rademan R, et al. Virus Evol. 2025 Dec 1;11(1):veaf093. doi: 10.1093/ve/veaf093. eCollection 2025. Virus Evol. 2025. PMID: 41403853 Free PMC article.

52

The importance of epistasis in the evolution of viral pathogens.

Manivannan SN, Diaz Arenas C, Grubaugh ND, Ogbunugafor CB. Manivannan SN, et al. Virus Evol. 2025 Nov 24;11(1):veaf091. doi: 10.1093/ve/veaf091. eCollection 2025. Virus Evol. 2025. PMID: 41383811 Free PMC article. Review.

53

Correction to: Experimental evidence of vaccine-driven evolution of porcine reproductive and respiratory syndrome virus type 2.

[No authors listed] [No authors listed] Virus Evol. 2025 Nov 22;11(1):veaf092. doi: 10.1093/ve/veaf092. eCollection 2025. Virus Evol. 2025. PMID: 41278020 Free PMC article.

54

Detection and variant characterization of lumpy skin disease virus from dairy cattle in India.

Bajpai M, Khilari A, Likhitkar B, Musale P, Jadhav S, Dhanikachalam V, Kakramkar P, Bhave K, Swaminathan M, Joshi S, Shanmugam D. Bajpai M, et al. Virus Evol. 2025 Nov 20;11(1):veaf090. doi: 10.1093/ve/veaf090. eCollection 2025. Virus Evol. 2025. PMID: 41356691 Free PMC article.

55

Ecology and evolution of influenza A viruses in wild waterfowl in Argentina reveals novel viral genotypes.

Kreps L, Batsche LO, Olivera VS, Crespo-Bellido A, Nelson MI, Perez DR, Rimondi A. Kreps L, et al. Virus Evol. 2025 Nov 6;11(1):veaf088. doi: 10.1093/ve/veaf088. eCollection 2025. Virus Evol. 2025. PMID: 41332916 Free article.

56

Constrained reassortment and genotype-specific traits shape the evolutionary landscape of galbut virus.

Keene-Snickers AH, Brehm AL, Dunham TJ, Gelpi TA, Stenglein MD. Keene-Snickers AH, et al. Virus Evol. 2025 Nov 4;11(1):veaf089. doi: 10.1093/ve/veaf089. eCollection 2025. Virus Evol. 2025. PMID: 41287636 Free PMC article.

57

Emergence of the BA.2.87.1 lineage of SARS-CoV-2 in South Africa, a highly diverged BA.2-related lineage.

Kekana D, Ntozini B, Hisner R, Yousif M, Ntuli P, Ndlovu N, McCarthy K, Mnguni A, Mahlangu B, Nzimande A, Stock N, Tegally H, Davis MA, Moir M, Wilkinson E, Baxter C, Bhiman J, Cohen C, Walaza S, von Gottberg A, de Oliveira T, Wolter N, Martin D. Kekana D, et al. Virus Evol. 2025 Nov 3;11(1):veaf083. doi: 10.1093/ve/veaf083. eCollection 2025. Virus Evol. 2025. PMID: 41293485 Free PMC article.

58

Near real-time data on the human neutralizing antibody landscape to influenza virus to inform vaccine-strain selection in September 2025.

Kikawa C, Huddleston J, Loes AN, Turner SA, Lee J, Barr IG, Cowling BJ, Englund JA, Greninger AL, Harvey R, Hasegawa H, Ho F, Lacombe K, Leung NHL, Lewis NS, Peck H, Watanabe S, Smith DJ, Bedford T, Bloom JD. Kikawa C, et al. Virus Evol. 2025 Nov 3;11(1):veaf086. doi: 10.1093/ve/veaf086. eCollection 2025. Virus Evol. 2025. PMID: 41287634 Free PMC article.

59

Constraint in West Nile virus envelope protein across mosquito, human, and avian host cell environments.

Dorman J, Bakhache W, Pierson TC, Dolan PT. Dorman J, et al. Virus Evol. 2025 Nov 1;11(1):veaf087. doi: 10.1093/ve/veaf087. eCollection 2025. Virus Evol. 2025. PMID: 41306642 Free article.

60

Persistence, spillover, and evolution of co-occurring lineages of lymphocytic choriomeningitis virus.

Mehl C, Adeyemi OA, Möhrer FJ, Wylezich C, Sander S, Schmidt K, Geiger C, Schauerte N, Wurr S, Mätz-Rensing K, Nesseler A, von Graffenried TA, Parker Morgan A, Oestereich L, Günther S, Beer M, Klein C, Cadar D, Kerber R, Höper D, Reiche S, Heckel G, Ulrich RG. Mehl C, et al. Virus Evol. 2025 Oct 31;11(1):veaf085. doi: 10.1093/ve/veaf085. eCollection 2025. Virus Evol. 2025. PMID: 41293484 Free PMC article.

61

Lethal mutagenesis and the transient within-host dynamics of viral adaptation.

Guillemet M, Martin G, Hardy E, Roze D, Gandon S. Guillemet M, et al. Virus Evol. 2025 Oct 28;11(1):veaf084. doi: 10.1093/ve/veaf084. eCollection 2025. Virus Evol. 2025. PMID: 41287635 Free PMC article.

62

Changes in intra-host mycovirus population diversity after vertical and horizontal transmission.

Peranić K, Leigh DM, Popović M, Nuskern L, Ćurković-Perica M, Kupper Q, Rigling D, Ježić M. Peranić K, et al. Virus Evol. 2025 Oct 23;11(1):veaf082. doi: 10.1093/ve/veaf082. eCollection 2025. Virus Evol. 2025. PMID: 41235154 Free PMC article.

63

Beyond the Amazon: vector surveillance and emerging Oropouche virus in South America.

da Silva Brito RD, Farias JP, Birbrair A, de Souza Ferreira LC, Vidal PO, Amorim JH. da Silva Brito RD, et al. Virus Evol. 2025 Oct 15;11(1):veaf081. doi: 10.1093/ve/veaf081. eCollection 2025. Virus Evol. 2025. PMID: 41216607 Free PMC article. No abstract available.

64

Phylogeographic evaluation of the effectiveness of Canadian travel restrictions in reducing SARS-CoV-2 variant importations and burden.

McLaughlin A, Montoya V, Miller RL; Canadian COVID-19 Genomics Network (CanCOGeN) Consortium; Worobey M, Joy JB. McLaughlin A, et al. Virus Evol. 2025 Oct 11;11(1):veaf077. doi: 10.1093/ve/veaf077. eCollection 2025. Virus Evol. 2025. PMID: 41104050 Free PMC article.

65

Correction to: Phylogenetic estimation of the viral fitness landscape of HIV-1 set-point viral load.

[No authors listed] [No authors listed] Virus Evol. 2025 Oct 8;11(1):veaf080. doi: 10.1093/ve/veaf080. eCollection 2025. Virus Evol. 2025. PMID: 41069417 Free PMC article.

66

Intra-host evolution of cell-fusing agent virus following acute infection in Aedes aegypti mosquito.

Uddin MM, Suzuki Y, Logronio DJC, Watanabe K. Uddin MM, et al. Virus Evol. 2025 Sep 30;11(1):veaf079. doi: 10.1093/ve/veaf079. eCollection 2025. Virus Evol. 2025. PMID: 41143102 Free PMC article.

67

Retrospective detection of severe fever with thrombocytopenia syndrome virus (SFTSV) revises timeline of emergence in Thailand.

Perez LJ, Suputtamongkol Y, Hadji A, Phoompoung P, Weiss S, Yamaguchi J, Forberg K, Hodges A, Olivo A, Cloherty GA, Berg MG. Perez LJ, et al. Virus Evol. 2025 Sep 26;11(1):veaf078. doi: 10.1093/ve/veaf078. eCollection 2025. Virus Evol. 2025. PMID: 41143104 Free PMC article.

68

Phylogenetic analysis of pigeon paramyxovirus type 1 detected in the British Isles between 1983 and 2023.

Byrne AMP, Mollett BC, Brown IH, James J, Banyard AC, Ross CS. Byrne AMP, et al. Virus Evol. 2025 Sep 23;11(1):veaf075. doi: 10.1093/ve/veaf075. eCollection 2025. Virus Evol. 2025. PMID: 41089326 Free article.

69

Decoding VZV's evolutionary arsenal: how Beijing strains use recombination and adaptive mutations to thrive.

Han X, Wu C, Deng Y, Zhang L, Wang L, Zhang Z, Zhang X, Mai C, Tan W, Zhao Y. Han X, et al. Virus Evol. 2025 Sep 23;11(1):veaf076. doi: 10.1093/ve/veaf076. eCollection 2025. Virus Evol. 2025. PMID: 41078487 Free PMC article.

70

Tracking down the origin and subsequent spread of SARS-CoV-2 lineage B.1.619.

Bollen N, Hong SL, Potter BI, Lienhard R, Tritten ML, Sierro N, Guedj E, Dulize R, Bornand D, Auberson M, Berthouzoz M, Duvoisin P, Ivanov NV, Peitsch MC, Hill V; Belgium Consortium COVID-19 Genomics; Matheeussen V, Bontems S, Verhasselt B, Degosserie J, Waumans L, Bayon-Vicente G, Reynders M, Cattoir L, Coste V, Valgaeren H, Van Weyenbergh J, Cuypers L, André E, Durkin K, Maes P, Khan K, Huber C, Suchard MA, Maidadi Foudi M, Godwe C, Moumbeket Yifomnjou MH, Landry M, Njouom R, Mbala Kingebeni P, Oluniyi P, Olawoye IB, Happi C, Ayouba A, Peeters M, Behillil S, Simon-Lorière E, Hölzer M, Dellicour S, Dudas G, Baele G. Bollen N, et al. Virus Evol. 2025 Sep 23;11(1):veaf017. doi: 10.1093/ve/veaf017. eCollection 2025. Virus Evol. 2025. PMID: 41031290 Free PMC article.

71

ViralBottleneck: an R package for estimating viral transmission bottlenecks from deep sequencing data using multiple methods.

Zheng B, Johnson PCD, Hughes J. Zheng B, et al. Virus Evol. 2025 Sep 19;11(1):veaf071. doi: 10.1093/ve/veaf071. eCollection 2025. Virus Evol. 2025. PMID: 41089325 Free PMC article.

72

Visualizing and deciphering influenza A(H1N1) pdm09 reassortment in the 2019-23 seasons.

Li TJ, Chen KF, Pekosz A, Gong YN. Li TJ, et al. Virus Evol. 2025 Sep 19;11(1):veaf070. doi: 10.1093/ve/veaf070. eCollection 2025. Virus Evol. 2025. PMID: 41078486 Free PMC article.

73

Tracing the spread and phylogeography of foot-and-mouth disease virus across East and the Horn of Africa.

Makau DN, Arzt J, VanderWaal K. Makau DN, et al. Virus Evol. 2025 Sep 19;11(1):veaf073. doi: 10.1093/ve/veaf073. eCollection 2025. Virus Evol. 2025. PMID: 41069416 Free PMC article.

74

Uncovering hundreds of exogenous and endogenous RNA viral RdRp sequences amongst uncharacterized sequences in public protein databases.

Brown K, Firth AE. Brown K, et al. Virus Evol. 2025 Sep 18;11(1):veaf074. doi: 10.1093/ve/veaf074. eCollection 2025. Virus Evol. 2025. PMID: 41143103 Free PMC article.

75

Identifying impacts of contact tracing on HIV epidemiological inference from phylogenetic data.

Kupperman MD, Ke R, Leitner T. Kupperman MD, et al. Virus Evol. 2025 Sep 18;11(1):veaf068. doi: 10.1093/ve/veaf068. eCollection 2025. Virus Evol. 2025. PMID: 41035850 Free PMC article.

76

Rapid glycoprotein evolution enables variant interactions in herpes simplex virus type 1.

Höfler T, Zeitlow M, Kim JY, Wyler E, Trimpert J. Höfler T, et al. Virus Evol. 2025 Sep 17;11(1):veaf072. doi: 10.1093/ve/veaf072. eCollection 2025. Virus Evol. 2025. PMID: 41058925 Free PMC article.

77

Nuclear trafficking of Anelloviridae capsid protein ORF1 reflects modular evolution of subcellular targeting signals.

Petersen GF, Pavan S, Ariawan D, Tietz O, Nematollahzadeh S, Sarker S, Forwood JK, Alvisi G. Petersen GF, et al. Virus Evol. 2025 Sep 16;11(1):veaf069. doi: 10.1093/ve/veaf069. eCollection 2025. Virus Evol. 2025. PMID: 41041146 Free PMC article.

78

Genetic evolution of swine vesicular disease viruses circulating in Italy from 1992 to the eradication in 2015 and emergence of a recent recombinant strain.

Bregoli A, Benedetti D, Calzolari M, Benevenia R, Di Nardo A, Castelli A, Corsa M, Grazioli S, Chiapponi C, Brocchi E, Pezzoni G. Bregoli A, et al. Virus Evol. 2025 Sep 6;11(1):veaf066. doi: 10.1093/ve/veaf066. eCollection 2025. Virus Evol. 2025. PMID: 41019407 Free PMC article.

79

Plant biosecurity threats detected using metatranscriptomic sequencing of animal gut contents.

Mahar JE, Mifsud JCO, Van Brussel K, Lachenauer AE, Harvey E, Turnbull OMH, Bonat S, Newsome TM, Olsson A, Chiu-Werner A, Jones ME, Holmes EC, Maina S. Mahar JE, et al. Virus Evol. 2025 Sep 5;11(1):veaf067. doi: 10.1093/ve/veaf067. eCollection 2025. Virus Evol. 2025. PMID: 41019406 Free PMC article.

80

Phylogenetic meta-analysis of persistent SARS-CoV-2 infections in immunocompromised individuals highlights the challenges of robust evolutionary rate estimation caused by low genetic diversity.

Översti S, Gaul E, Jensen BO, Kühnert D. Översti S, et al. Virus Evol. 2025 Aug 30;11(1):veaf065. doi: 10.1093/ve/veaf065. eCollection 2025. Virus Evol. 2025. PMID: 41031289 Free PMC article.

81

Amplicon-based analyses of single-nucleotide polymorphisms reveal the genetic structure of a forest insect baculovirus.

Oehlmann C, Fan J, Rihlmann MJ, Lemme H, Müller J, Ruoff B, Wennmann JT, Jehle JA. Oehlmann C, et al. Virus Evol. 2025 Aug 23;11(1):veaf061. doi: 10.1093/ve/veaf061. eCollection 2025. Virus Evol. 2025. PMID: 41104051 Free PMC article.

82

Focal persistence and phylodynamics of Heartland virus in Georgia.

Bellman S, Shariatzadeh N, Ferrell T, Long A, Aeschleman L, Fausett E, Walsh T, Cleary S, Roeske I, Ojeda E, Schwab M, Dakanay H, Telford Iii SR, Goethert HK, Vazquez-Prokopec G, Piantadosi A. Bellman S, et al. Virus Evol. 2025 Aug 23;11(1):veaf064. doi: 10.1093/ve/veaf064. eCollection 2025. Virus Evol. 2025. PMID: 40994726 Free PMC article.

83

Convergent evolution of the G3BP1-binding motif in betacoronavirus nucleocapsid proteins.

Borgogna C, Cislaghi I, Turati S, Mozzi A, Forni D, Cagliani R, Sironi M, Gariglio M. Borgogna C, et al. Virus Evol. 2025 Aug 22;11(1):veaf063. doi: 10.1093/ve/veaf063. eCollection 2025. Virus Evol. 2025. PMID: 40936503 Free PMC article.

84

The recurrent Spike A222V mutation in SARS-CoV-2 enhances replication in primary deer lung cells.

Cereghino C, Tiller K, Kang L, Michalak P, Weger-Lucarelli J. Cereghino C, et al. Virus Evol. 2025 Aug 5;11(1):veaf059. doi: 10.1093/ve/veaf059. eCollection 2025. Virus Evol. 2025. PMID: 40874095 Free PMC article.

85

Sustained cross-species transmission of gammacoronavirus in wild birds revealed by viral characterization in China.

Wang DS, Zou YY, Liu Q, Huang H, Han PY, Zhao JY, Zong LD, Qiu Y, Zhang YZ, Ge XY. Wang DS, et al. Virus Evol. 2025 Aug 4;11(1):veaf060. doi: 10.1093/ve/veaf060. eCollection 2025. Virus Evol. 2025. PMID: 40917815 Free PMC article.

86

Development of avian influenza A(H5) virus datasets for Nextclade enables rapid and accurate clade assignment.

Ort JT, Shepard SS, Zolnoski SA, Lam TT, Davis CT, Neher RA, Moncla LH. Ort JT, et al. Virus Evol. 2025 Aug 4;11(1):veaf058. doi: 10.1093/ve/veaf058. eCollection 2025. Virus Evol. 2025. PMID: 40860043 Free PMC article.

87

Revealing the potential transmission route of Cnaphalocrocis medinalis granulovirus capable of persistently causing granulosis epidemics.

Chen B, Zuo Y, Lv Y, Zhang H, Yang J, Gu Y, Yang J, Yuan M, Yang K. Chen B, et al. Virus Evol. 2025 Jul 25;11(1):veaf055. doi: 10.1093/ve/veaf055. eCollection 2025. Virus Evol. 2025. PMID: 40860044 Free PMC article.

88

Estimates of HIV-1 within-host recombination rates across the whole genome.

Longley H, Bonsall D, Herbeck J, MacIntyre-Cockett G, Chaudron SE, Thomson L, Grayson N, Mujugira A; PANGEA consortium; Fraser C, Lingappa J, Lythgoe K. Longley H, et al. Virus Evol. 2025 Jul 25;11(1):veaf052. doi: 10.1093/ve/veaf052. eCollection 2025. Virus Evol. 2025. PMID: 40740855 Free PMC article.

89

Experimental evidence of vaccine-driven evolution of respiratory syndrome virus type 2.

Pamornchainavakul N, Paploski IAD, Makau DN, Baker JP, Huang J, Ferreira CP, Corzo CA, Rovira A, Cheeran MC, Lycett S, Doeschl-Wilson A, Schroeder DC, VanderWaal K. Pamornchainavakul N, et al. Virus Evol. 2025 Jul 22;11(1):veaf056. doi: 10.1093/ve/veaf056. eCollection 2025. Virus Evol. 2025. PMID: 40831531 Free PMC article.

90

Immune pressure is key to understanding observed patterns of respiratory virus evolution in prolonged infections.

Coats A, Wang YR, Koelle K. Coats A, et al. Virus Evol. 2025 Jul 21;11(1):veaf054. doi: 10.1093/ve/veaf054. eCollection 2025. Virus Evol. 2025. PMID: 40831532 Free PMC article.

91

Correction to: Coevolutionary phage training and Joint application delays the emergence of phage resistance in Pseudomonas aeruginosa.

[No authors listed] [No authors listed] Virus Evol. 2025 Jul 11;11(1):veaf053. doi: 10.1093/ve/veaf053. eCollection 2025. Virus Evol. 2025. PMID: 40655308 Free PMC article.

92

Insights into diversity, host range, and evolution of iflaviruses in Lepidoptera through transcriptome mining.

van Valkengoed D, Bryon A, Ros VID, Kupczok A. van Valkengoed D, et al. Virus Evol. 2025 Jul 7;11(1):veaf051. doi: 10.1093/ve/veaf051. eCollection 2025. Virus Evol. 2025. PMID: 40755814 Free PMC article.

93

Analysis of Piscine orthoreovirus genotype 1 genomes collected over a 32-year period (1988-2020) suggests a fitness peak in salmon hosts with minimal evidence for temporal divergence.

Johnson SC, Turcotte LDM, Siah A, Bradshaw JC, Polinski MP. Johnson SC, et al. Virus Evol. 2025 Jul 3;11(1):veaf033. doi: 10.1093/ve/veaf033. eCollection 2025. Virus Evol. 2025. PMID: 40630922 Free PMC article.

94

Identification of novel hepaciviruses and Sylvilagus-associated viruses via metatranscriptomics in North American lagomorphs.

Jenckel M, Chang WS, Wright EA, Bradley RD, Dusek RJ, Ip HS, Hall RN, Smith IL, Strive T. Jenckel M, et al. Virus Evol. 2025 Jul 2;11(1):veaf050. doi: 10.1093/ve/veaf050. eCollection 2025. Virus Evol. 2025. PMID: 40687189 Free PMC article.

95

Surveillance of coronaviruses in wild aquatic birds in Hong Kong: expanded genetic diversity and discovery of novel subgenus in the Deltacoronavirus.

Ng DYM, Sun W, Sit THC, Brackman CJ, Tse ACN, Bui CHT, Tang AWY, Wong ANC, Tsang ATL, Koo JCT, Cheng SMS, Peiris M, Samborskiy DV, Gorbalenya AE, Chin AWH, Poon LLM. Ng DYM, et al. Virus Evol. 2025 Jul 1;11(1):veaf049. doi: 10.1093/ve/veaf049. eCollection 2025. Virus Evol. 2025. PMID: 40666308 Free PMC article.

96

Identification of a putative new virus from the Jingmenvirus group in ticks from wild animals in Brazil.

Geraldini DB, Bittar C, Possebon FS, Gismene C, Mariutti RB, da Costa VG, Campos GRF, Beltrão RC, Neto GG, Lofego AC, Nogueira ML, Arni RK, Junior JPA, de Freitas Calmon M, Rahal P. Geraldini DB, et al. Virus Evol. 2025 Jun 27;11(1):veaf045. doi: 10.1093/ve/veaf045. eCollection 2025. Virus Evol. 2025. PMID: 40666309 Free PMC article.

97

Phylogenetic insights into the early spread of the SARS-CoV-2 Alpha variant across Europe.

Evans A, Tully DC. Evans A, et al. Virus Evol. 2025 Jun 25;11(1):veaf030. doi: 10.1093/ve/veaf030. eCollection 2025. Virus Evol. 2025. PMID: 40612696 Free PMC article.

98

Correction to: Increase of niche filling with increase of host richness for plant-infecting mastreviruses.

[No authors listed] [No authors listed] Virus Evol. 2025 Jun 16;11(1):veaf046. doi: 10.1093/ve/veaf046. eCollection 2025. Virus Evol. 2025. PMID: 40525130 Free PMC article.

99

Diverse patterns of intra-host genetic diversity in chronically infected SARS-CoV-2 patients.

Ben Zvi A, Rutsinsky N, Jacobi B, Fabian I, Segev ST, Harari S, Meijer S, Paran Y, Stern A. Ben Zvi A, et al. Virus Evol. 2025 Jun 15;11(1):veaf047. doi: 10.1093/ve/veaf047. eCollection 2025. Virus Evol. 2025. PMID: 40662161 Free PMC article.

100

Comprehensive analysis of SARS-CoV-2 Spike evolution: epitope classification and immune escape prediction.

Teruel NFB, Crown M, Rajsbaum R, Bashton M, Najmanovich R. Teruel NFB, et al. Virus Evol. 2025 Jun 11;11(1):veaf027. doi: 10.1093/ve/veaf027. eCollection 2025. Virus Evol. 2025. PMID: 40510757 Free PMC article.

101

Within- and between-host evolutionary effects on viral oncogenicity.

Koizumi Y, Bonsall MB. Koizumi Y, et al. Virus Evol. 2025 Jun 6;11(1):veaf043. doi: 10.1093/ve/veaf043. eCollection 2025. Virus Evol. 2025. PMID: 40606504 Free PMC article.

102

What makes a host a good reservoir? Determinants of the reservoir potential of Nicotiana glauca for tobacco mild green mosaic virus.

de Andrés-Torán R, Fraile A, Bera S, Mora MÁ, McLeish M, García-Arenal F. de Andrés-Torán R, et al. Virus Evol. 2025 Jun 6;11(1):veaf044. doi: 10.1093/ve/veaf044. eCollection 2025. Virus Evol. 2025. PMID: 40584257 Free PMC article.

103

Hantavirus co-circulation in common shrews (Sorex araneus) in Sweden.

Wasberg A, Ecke F, Lindahl JF, Pettersson JH, Lundkvist Å, Ling J. Wasberg A, et al. Virus Evol. 2025 May 28;11(1):veaf038. doi: 10.1093/ve/veaf038. eCollection 2025. Virus Evol. 2025. PMID: 40584256 Free PMC article.

104

Discovery of influenza-like virus clades in invertebrates and the evolutionary history and host-shifting events of Orthomyxoviridae in metazoans.

Leung RWT, Wu Z, Tsang LM, Chu KH, Leung KW, Qin J, Ma KY. Leung RWT, et al. Virus Evol. 2025 May 27;11(1):veaf039. doi: 10.1093/ve/veaf039. eCollection 2025. Virus Evol. 2025. PMID: 40692824 Free PMC article.

105

Lost in the woods: shifting habitats can lead phylogeography astray.

Neher RA. Neher RA. Virus Evol. 2025 May 22;11(1):veaf040. doi: 10.1093/ve/veaf040. eCollection 2025. Virus Evol. 2025. PMID: 40584259 Free PMC article.

106

Paramyxo- and coronavirus diversity and host associations in non-volant small mammals: evidence of viral sharing.

Mortlock M, Geldenhuys M, Keith M, Rademan R, Swanepoel LH, Von Maltitz EF, Kearney T, Markotter W. Mortlock M, et al. Virus Evol. 2025 May 22;11(1):veaf041. doi: 10.1093/ve/veaf041. eCollection 2025. Virus Evol. 2025. PMID: 40584258 Free PMC article.

107

Diverse viral pathogens in Australian canines: limited geographic structure and the first detection of an RNA virus in dingoes.

Mifsud JCO, Harvey E, Van Brussel K, Olsson A, Pitcher BJ, Hall J, Fenton H, Alting BF, Sadiq S, Holmes EC. Mifsud JCO, et al. Virus Evol. 2025 May 22;11(1):veaf042. doi: 10.1093/ve/veaf042. eCollection 2025. Virus Evol. 2025. PMID: 40584255 Free PMC article.

108

Evidence for circulation of high-virulence HIV-1 subtype B variants in the United Kingdom.

Franceschi VB, Drake KO, Bibby DF, Sabin CA, Dunn DT, Mbisa JL, Volz EM. Franceschi VB, et al. Virus Evol. 2025 May 20;11(1):veaf048. doi: 10.1093/ve/veaf048. eCollection 2025. Virus Evol. 2025. PMID: 40662162 Free PMC article.

109

Unravelling dengue serotype 3 transmission in Brazil: evidence for multiple introductions of the 3III_B.3.2 lineage.

Pereira JS, Slavov SN, Brcko IC, Ribeiro G, de Souza VC, Ribeiro IS, De Lima ITT, Borges GAL, Furtado KCL, Chagas SMDS, da Costa PMSSB, Adelino TÉR, Iani FCM, Alcantara LCJ, Hill V, Grubaugh ND, Sampaio SC, Elias MC, Giovanetti M, Lima ARJ. Pereira JS, et al. Virus Evol. 2025 May 18;11(1):veaf034. doi: 10.1093/ve/veaf034. eCollection 2025. Virus Evol. 2025. PMID: 40589497 Free PMC article.

110

The emergence of NY10: insights into the 2012 West Nile Virus outbreak in the United States.

Fautt C, Boudreau MR, Mooney AC, Cohnstaedt LW, Hudson AR, Humphreys JM. Fautt C, et al. Virus Evol. 2025 May 14;11(1):veaf037. doi: 10.1093/ve/veaf037. eCollection 2025. Virus Evol. 2025. PMID: 40574749 Free PMC article.

111

Transition of D3c branch and novel recombination events contribute to the diversity of Coxsackievirus A6 in Beijing, China, from 2019 to 2023.

Zhang X, Li R, Lu R, Wu C, Liang Z, Zhang Z, Huang B, Yang Y, Qi Z, Zhang D, Zhai D, Wang Q, Tan W. Zhang X, et al. Virus Evol. 2025 May 11;11(1):veaf036. doi: 10.1093/ve/veaf036. eCollection 2025. Virus Evol. 2025. PMID: 40574752 Free PMC article.

112

Emergence and transmission dynamics of the FY.4 Omicron variant in Kenya.

Musundi S, Mwanga M, Lambisia A, Morobe JM, Murunga N, Moraa E, Ndwiga L, Cheruiyot R, Musyoki J, Mutunga M, Guzman-Rincon LM, Sande C, Mwangangi J, Bejon P, Ochola-Oyier LI, Nokes DJ, Agoti CN, Nyiro J, Githinji G. Musundi S, et al. Virus Evol. 2025 May 11;11(1):veaf035. doi: 10.1093/ve/veaf035. eCollection 2025. Virus Evol. 2025. PMID: 40574750 Free PMC article.

113

Forecasting influenza A pandemic lineage dominance in the United States using relative reproduction rates.

Zeller MA, Zhang R, Su YCF, Ito K. Zeller MA, et al. Virus Evol. 2025 May 8;11(1):veaf032. doi: 10.1093/ve/veaf032. eCollection 2025. Virus Evol. 2025. PMID: 40458734 Free PMC article.

114

Riboflavin transporter: evidence of a role as entry receptor for chimpanzee endogenous retrovirus.

AbuEed L, Miyake A, Wanjala N, Pramono D, Abdillah D, Imamura M, Shimojima M, Denner J, Kawasaki J, Nishigaki K. AbuEed L, et al. Virus Evol. 2025 May 7;11(1):veaf031. doi: 10.1093/ve/veaf031. eCollection 2025. Virus Evol. 2025. PMID: 40574751 Free PMC article.

115

Eco-evolutionary dynamics of temperate phages in periodic environments.

Goel T, Beckett SJ, Weitz JS. Goel T, et al. Virus Evol. 2025 Apr 29;11(1):veaf019. doi: 10.1093/ve/veaf019. eCollection 2025. Virus Evol. 2025. PMID: 40421433 Free PMC article.

116

Rapid response to fast viral evolution using AlphaFold 3-assisted topological deep learning.

Wee J, Wei GW. Wee J, et al. Virus Evol. 2025 Apr 29;11(1):veaf026. doi: 10.1093/ve/veaf026. eCollection 2025. Virus Evol. 2025. PMID: 40352163 Free PMC article.

117

Exploring genetic signatures of zoonotic influenza A virus at the swine-human interface with phylogenetic and ancestral sequence reconstruction.

Anker KM, Ciucani MM, Nissen JN, Anderson TK, Pedersen AG, Trebbien R. Anker KM, et al. Virus Evol. 2025 Apr 26;11(1):veaf028. doi: 10.1093/ve/veaf028. eCollection 2025. Virus Evol. 2025. PMID: 40655307 Free PMC article.

118

Similarity-weighted entropy for quantifying genetic diversity in viral quasispecies.

Wu J. Wu J. Virus Evol. 2025 Apr 26;11(1):veaf029. doi: 10.1093/ve/veaf029. eCollection 2025. Virus Evol. 2025. PMID: 40376429 Free PMC article.

119

Evolution and adaptation of dengue virus in response to high-temperature passaging in mosquito cells.

Ware-Gilmore F, Jones MJ, Mejia AJ, Dennington NL, Audsley MD, Hall MD, Sgrò CM, Buckley T, Anand GS, Jose J, McGraw EA. Ware-Gilmore F, et al. Virus Evol. 2025 Apr 24;11(1):veaf016. doi: 10.1093/ve/veaf016. eCollection 2025. Virus Evol. 2025. PMID: 40330315 Free PMC article.

120

Virome of Hyalomma and Rhipicephalus ticks from desert of Northwestern China.

Wang N, Lu S, Ye RZ, Li C, Huang JH, Ye G, Li YY, Shen SJ, Shi XY, Zhu DY, Shi W, Zhao L, Jia N, Jiang JF, Cui XM, Sun Y, Cao WC. Wang N, et al. Virus Evol. 2025 Apr 19;11(1):veaf022. doi: 10.1093/ve/veaf022. eCollection 2025. Virus Evol. 2025. PMID: 40356718 Free PMC article.

121

Spatiotemporal dispersion of DENV-1 genotype V in Western Colombia.

Rojas-Gallardo D, Ferrell T, Escobar-Pereira PM, Lopez D, Giraldo B, Restrepo-Chica J, Jimenez-Posada E, Martinez-Gutierrez M, Ruiz-Sáenz J, Key A, Shariatzadeh N, Khosravi D, Martinez MA, Bombin A, Waggoner JJ, Osorio JE, Neufeldt CJ, Collins MH, Cardona-Ospina JA, Piantadosi A. Rojas-Gallardo D, et al. Virus Evol. 2025 Apr 16;11(1):veaf018. doi: 10.1093/ve/veaf018. eCollection 2025. Virus Evol. 2025. PMID: 40395613 Free PMC article.

122

Evolution of Zika virus in Rag1-deficient mice selects for unique envelope glycosylation motif mutants that show enhanced replication fitness.

Nakayama E, Tang B, Stewart R, Cox AL, Yan K, Bishop CR, Dumenil T, Nguyen W, Slonchak A, Sng J, Khromykh AA, Lutzky VP, Rawle DJ, Suhrbier A. Nakayama E, et al. Virus Evol. 2025 Apr 11;11(1):veaf021. doi: 10.1093/ve/veaf021. eCollection 2025. Virus Evol. 2025. PMID: 40291117 Free PMC article.

123

Discovery of additional genomic segments reveals the fluidity of jingmenvirus genomic organization.

Valle C, Parry RH, Coutard B, Colmant AMG. Valle C, et al. Virus Evol. 2025 Apr 7;11(1):veaf023. doi: 10.1093/ve/veaf023. eCollection 2025. Virus Evol. 2025. PMID: 40297511 Free PMC article.

124

Ancient origins and global spread of domestic cat hepatitis B virus.

de Oliveira-Filho EF, Müller SF, Carneiro IO, de Carvalho OV, Alfaro-Alarcón A, Brünink S, Fernandes FD, Anzolini Cassiano MH, Pedroso C, Lehmann F, Jo WK, Moreira-Soto A, Brites C, Netto EM, Ristow LE, Maia RCC, Vogel FSF, de Almeida NR, Müller E, Franke CR, Drexler JF. de Oliveira-Filho EF, et al. Virus Evol. 2025 Apr 5;11(1):veaf025. doi: 10.1093/ve/veaf025. eCollection 2025. Virus Evol. 2025. PMID: 40395614 Free PMC article.

125

Cameroonian blackflies (Diptera: Simuliidae) harbour a plethora of RNA viruses.

De Coninck L, Hadermann A, Ingletto L, Colebunders R, Gamnsi Njamnshi K, Njamnshi AK, Mokili JL, Siewe Fodjo JN, Matthijnssens J. De Coninck L, et al. Virus Evol. 2025 Apr 5;11(1):veaf024. doi: 10.1093/ve/veaf024. eCollection 2025. Virus Evol. 2025. PMID: 40321713 Free PMC article.

126

The virome of the panglobal, wide host-range plant pathogen Phytophthora cinnamomi: phylogeography and evolutionary insights.

Botella L, Hejna O, Kudláček T, Kovačiková K, Rost M, Forgia M, Raco M, Milenković I, Corcobado T, Maia C, Scanu B, Drenth A, Guest DI, Liew ECY, Chi NM, Thu PQ, Chang TT, Fu CH, Kageyama K, Hieno A, Masuja H, Uematsu S, Durán Á, Tarigan M, Junaid M, Nasri N, Sanfuentes E, Čurn V, Webber JF, Brasier CM, Jung MH, Jung T. Botella L, et al. Virus Evol. 2025 Apr 1;11(1):veaf020. doi: 10.1093/ve/veaf020. eCollection 2025. Virus Evol. 2025. PMID: 40352162 Free PMC article.

127

Genomic variants and molecular epidemiological characteristics of dengue virus in China revealed by genome-wide analysis.

Sun B, Xu M, Jia L, Liu H, Li A, Hui L, Wang Z, Liu D, Yan Y. Sun B, et al. Virus Evol. 2025 Mar 17;11(1):veaf013. doi: 10.1093/ve/veaf013. eCollection 2025. Virus Evol. 2025. PMID: 40135062 Free PMC article.

128

Genome data artifacts and functional studies of deletion repair in the BA.1 SARS-CoV-2 spike protein.

Álvarez-Herrera M, Ruiz-Rodriguez P, Navarro-Domínguez B, Zulaica J, Grau B, Bracho MA, Guerreiro M, Aguilar-Gallardo C, González-Candelas F, Comas I, Geller R, Coscollá M. Álvarez-Herrera M, et al. Virus Evol. 2025 Mar 11;11(1):veaf015. doi: 10.1093/ve/veaf015. eCollection 2025. Virus Evol. 2025. PMID: 40308784 Free PMC article.

129

Evolutionary dynamics and molecular epidemiology of H1N1 pandemic 2009 influenza A viruses across swine farms in Denmark.

George S, Ryt-Hansen P, Pedersen AG, Anker KM, Nissen JN, Krog JS, Hjulsager CK, Trebbien R, Larsen LE. George S, et al. Virus Evol. 2025 Mar 7;11(1):veaf014. doi: 10.1093/ve/veaf014. eCollection 2025. Virus Evol. 2025. PMID: 40235651 Free PMC article.

130

FluMut: a tool for mutation surveillance in highly pathogenic H5N1 genomes.

Giussani E, Sartori A, Salomoni A, Cavicchio L, de Battisti C, Pastori A, Varotto M, Zecchin B, Hughes J, Monne I, Fusaro A. Giussani E, et al. Virus Evol. 2025 Mar 7;11(1):veaf011. doi: 10.1093/ve/veaf011. eCollection 2025. Virus Evol. 2025. PMID: 40093844 Free PMC article.

131

Sequence analysis of the hepatitis D virus across genotypes reveals highly conserved regions amidst evidence of recombination.

Chowdhury S, Jacobsen C, Depledge DP, Wedemeyer H, Sandmann L, Kefalakes H. Chowdhury S, et al. Virus Evol. 2025 Feb 27;11(1):veaf012. doi: 10.1093/ve/veaf012. eCollection 2025. Virus Evol. 2025. PMID: 40123834 Free PMC article.

132

Multiple, diverse endogenous giant virus elements within the genome of a brown alga.

Mckeown D, Cormier A, Schroeder D, Couloux A, Tadrent N, Cock JM, Corre E. Mckeown D, et al. Virus Evol. 2025 Feb 27;11(1):veaf009. doi: 10.1093/ve/veaf009. eCollection 2025. Virus Evol. 2025. PMID: 40061209 Free PMC article.

133

Recently reported SARS-CoV-2 genomes suggested to be intermediate between the two early main lineages are instead likely derived.

Pekar JE, Moshiri N, Lemey P, Crits-Christoph A, Débarre F, Goldstein SA, Hensel Z, Rambaut A, Worobey M, Holmes EC, Wertheim JO. Pekar JE, et al. Virus Evol. 2025 Feb 22;11(1):veaf008. doi: 10.1093/ve/veaf008. eCollection 2025. Virus Evol. 2025. PMID: 40040925 Free PMC article.

134

Improvements in RNA and DNA nanopore sequencing allow for rapid genetic characterization of avian influenza.

Perlas A, Reska T, Croville G, Tarrés-Freixas F, Guérin JL, Majó N, Urban L. Perlas A, et al. Virus Evol. 2025 Feb 18;11(1):veaf010. doi: 10.1093/ve/veaf010. eCollection 2025. Virus Evol. 2025. PMID: 40066328 Free PMC article.

135

Genomic surveillance and evolution of Getah virus.

Shen J, Liu S, Liu S, Shen S, Lei M, Xu Q, Li W, He Q, Xu X, Cai X. Shen J, et al. Virus Evol. 2025 Feb 4;11(1):veaf007. doi: 10.1093/ve/veaf007. eCollection 2025. Virus Evol. 2025. PMID: 39989716 Free PMC article.

136

Mamastrovirus species are shaped by recombination and can be reliably distinguished in ORF1b genome region.

Aleshina Y, Lukashev A. Aleshina Y, et al. Virus Evol. 2025 Jan 31;11(1):veaf006. doi: 10.1093/ve/veaf006. eCollection 2025. Virus Evol. 2025. PMID: 39989717 Free PMC article.

137

Correction to: Going beyond consensus genome sequences: An innovative SNP-based methodology reconstructs different Ugandan cassava brown streak virus haplotypes at a nationwide scale in Rwanda.

[No authors listed] [No authors listed] Virus Evol. 2025 Jan 28;11(1):veaf003. doi: 10.1093/ve/veaf003. eCollection 2025. Virus Evol. 2025. PMID: 39877293 Free PMC article.

138

Dispersal dynamics and introduction patterns of SARS-CoV-2 lineages in Iran.

Gustani-Buss EC, Salehi-Vaziri M, Lemey P, Thijssen M, Fereydouni Z, Ahmadi Z, Ranst MV, Maes P, Pourkarim MR, Maleki A. Gustani-Buss EC, et al. Virus Evol. 2025 Jan 27;11(1):veaf004. doi: 10.1093/ve/veaf004. eCollection 2025. Virus Evol. 2025. PMID: 39926479 Free PMC article.

139

Genome sizes of animal RNA viruses reflect phylogenetic constraints.

Takada K, Holmes EC. Takada K, et al. Virus Evol. 2025 Jan 24;11(1):veaf005. doi: 10.1093/ve/veaf005. eCollection 2025. Virus Evol. 2025. PMID: 39906303 Free PMC article.

140

SARS-CoV-2 CoCoPUTs: analyzing GISAID and NCBI data to obtain codon statistics, mutations, and free energy over a multiyear period.

Padhiar NH, Ghazanchyan T, Fumagalli SE, DiCuccio M, Cohen G, Ginzburg A, Rikshpun B, Klein A, Santana-Quintero L, Smith S, Komar AA, Kimchi-Sarfaty C. Padhiar NH, et al. Virus Evol. 2025 Jan 17;11(1):veae115. doi: 10.1093/ve/veae115. eCollection 2025. Virus Evol. 2025. PMID: 39882309 Free PMC article.

141

Expanding the genomic diversity of human anelloviruses.

Modha S, Hughes J, Orton RJ, Lytras S. Modha S, et al. Virus Evol. 2025 Jan 7;11(1):veaf002. doi: 10.1093/ve/veaf002. eCollection 2025. Virus Evol. 2025. PMID: 39839678 Free PMC article.

142

An orphan viral genome with unclear evolutionary status sheds light on a distinct lineage of flavi-like viruses infecting plants.

Xu Z, Zheng L, Gao F, Li Y, Sun Z, Chen J, Zhang C, Li J, Wang X. Xu Z, et al. Virus Evol. 2025 Jan 3;11(1):veaf001. doi: 10.1093/ve/veaf001. eCollection 2025. Virus Evol. 2025. PMID: 39839679 Free PMC article.

143

HIV-1 Vif global diversity and possible APOBEC-mediated response since 1980.

Lewitus E, Li Y, Rolland M. Lewitus E, et al. Virus Evol. 2024 Dec 12;11(1):veae108. doi: 10.1093/ve/veae108. eCollection 2025. Virus Evol. 2024. PMID: 39886100 Free PMC article.

144

Major change in swine influenza virus diversity in France owing to emergence and widespread dissemination of a newly introduced H1N2 1C genotype in 2020.

Richard G, Hervé S, Chastagner A, Quéguiner S, Beven V, Hirchaud E, Barbier N, Gorin S, Blanchard Y, Simon G. Richard G, et al. Virus Evol. 2024 Dec 14;11(1):veae112. doi: 10.1093/ve/veae112. eCollection 2025. Virus Evol. 2024. PMID: 39882310 Free PMC article.

145

Geographic origin and evolution of dengue virus serotypes 1 and 3 circulating in Africa.

Nyathi S, Rezende IM, Walter KS, Thongsripong P, Mutuku F, Ndenga B, Mbakaya JO, Agola G, Vu DM, Bennett S, Mordecai EA, Andrews JR, LaBeaud AD. Nyathi S, et al. Virus Evol. 2024 Dec 30;11(1):veae116. doi: 10.1093/ve/veae116. eCollection 2025. Virus Evol. 2024. PMID: 39839680 Free PMC article.

146

Within-host genetic diversity of SARS-CoV-2 across animal species.

Naderi S, Sagan SM, Shapiro BJ. Naderi S, et al. Virus Evol. 2024 Dec 30;11(1):veae117. doi: 10.1093/ve/veae117. eCollection 2025. Virus Evol. 2024. PMID: 39830312 Free PMC article.

147

Molecular epidemiology, evolution, and transmission dynamics of raccoon rabies virus in Connecticut.

Veytsel G, Desiato J, Chung H, Tan S, Risatti GR, Helal ZH, Jang S, Lee DH, Bahl J. Veytsel G, et al. Virus Evol. 2024 Dec 24;11(1):veae114. doi: 10.1093/ve/veae114. eCollection 2025. Virus Evol. 2024. PMID: 39802825 Free PMC article.

148

A simple phylogenetic approach to analyze hypermutated HIV proviruses reveals insights into their dynamics and persistence during antiretroviral therapy.

Shahid A, Jones BR, Duncan MC, MacLennan S, Dapp MJ, Kuniholm MH, Aouizerat B, Archin NM, Gange S, Ofotokun I, Fischl MA, Kassaye S, Goldstein H, Anastos K, Joy JB, Brumme ZL. Shahid A, et al. Virus Evol. 2024 Nov 11;11(1):veae094. doi: 10.1093/ve/veae094. eCollection 2025. Virus Evol. 2024. PMID: 39802824 Free PMC article.

149

Comprehensive molecular epidemiology of influenza viruses in Brazil: insights from a nationwide analysis.

Brcko IC, de Souza VC, Ribeiro G, Lima ARJ, Martins AJ, Barros CRDS, de Carvalho E, Pereira JS, de Lima LPO, Viala VL, Kashima S, de La Roque DGL, Santos EV, Rodrigues ES, Nunes JA, Torres LS, Caldeira LAV, Palmieri M, Medina CG, de Arruda RA, Lopes RB, Sobrinho GR, Jorge DMM, Arruda E, Mendes ECBDS, Santos HO, de Mello ALES, Pereira FM, Gómez MKA, Nardy VB, Henrique B, Vieira LL, Roll MM, de Oliveira EC, Almeida JDPC, da Silva SF, Borges GAL, Furtado KCL, da Costa PMSSB, Chagas SMDS, Kallás EG, Larh D, Giovanetti M, Nanev Slavov S, Coccuzzo Sampaio S, Elias MC. Brcko IC, et al. Virus Evol. 2024 Nov 23;11(1):veae102. doi: 10.1093/ve/veae102. eCollection 2025. Virus Evol. 2024. PMID: 39802823 Free PMC article.

150

Diversity and cross-species transmission of viruses in a remote island ecosystem: implications for wildlife conservation.

French RK, Anderson S, Cain K, Digby A, Greene TC, Miskelly CM, Muller CG, Taylor MW, Recovery Team K, Geoghegan JL, Holmes EC. French RK, et al. Virus Evol. 2024 Dec 14;11(1):veae113. doi: 10.1093/ve/veae113. eCollection 2025. Virus Evol. 2024. PMID: 39802822 Free PMC article.

151

Kuafuorterviruses, a novel major lineage of reverse-transcribing viruses.

Gong Z, Han GZ. Gong Z, et al. Virus Evol. 2024 Dec 19;10(1):veae110. doi: 10.1093/ve/veae110. eCollection 2024. Virus Evol. 2024. PMID: 39735713 Free PMC article.

152

Recurring incursions and dissemination of novel Eurasian-origin H5Nx avian influenza viruses in Atlantic Canada.

Rahman I, Erdelyan CNG, Signore AV, Ayilara I, Wight J, Jones MEB, Sullivan DS, Lung O, Hisanaga T, Wilhelm SI, Cunningham JT, Ward CRE, Bosch J, Robertson GJ, Gosse K, Baker M, Dawe B, Lair S, Provencher JF, Hargan KE, Berhane Y, Lang AS. Rahman I, et al. Virus Evol. 2024 Dec 17;10(1):veae111. doi: 10.1093/ve/veae111. eCollection 2024. Virus Evol. 2024. PMID: 39722685 Free PMC article.

153

Increase of niche filling with increase of host richness for plant-infecting mastreviruses.

Ben Chéhida S, Devi Bunwaree H, Hoareau M, Moubset O, Julian C, Blondin L, Filloux D, Lavergne C, Roumagnac P, Varsani A, Martin DP, Lett JM, Lefeuvre P. Ben Chéhida S, et al. Virus Evol. 2024 Dec 13;10(1):veae107. doi: 10.1093/ve/veae107. eCollection 2024. Virus Evol. 2024. PMID: 39717705 Free PMC article.

154

On modes of disease transmission and the hidden shape of pandemics: A review of Asymptomatic by Joshua Weitz.

Ogbunugafor CB. Ogbunugafor CB. Virus Evol. 2024 Dec 12;10(1):veae109. doi: 10.1093/ve/veae109. eCollection 2024. Virus Evol. 2024. PMID: 39722684 Free PMC article.

155

Origin, spread, and interspecies transmission of a dominant genotype of BJ/94 lineage H9N2 avian influenza viruses with increased threat.

Zhou Y, Li Y, Chen H, Shu S, Li Z, Sun H, Sun Y, Liu J, Lu L, Pu J. Zhou Y, et al. Virus Evol. 2024 Dec 9;10(1):veae106. doi: 10.1093/ve/veae106. eCollection 2024. Virus Evol. 2024. PMID: 39735714 Free PMC article.

156

A meta-analysis highlights the idiosyncratic nature of tradeoffs in laboratory models of virus evolution.

Kabengele K, Turner WC, Turner PE, Ogbunugafor CB. Kabengele K, et al. Virus Evol. 2024 Dec 6;10(1):veae105. doi: 10.1093/ve/veae105. eCollection 2024. Virus Evol. 2024. PMID: 39717708 Free PMC article.

157

Inferring strain-level mutational drivers of phage-bacteria interaction phenotypes arising during coevolutionary dynamics.

Lucia-Sanz A, Peng S, Leung CYJ, Gupta A, Meyer JR, Weitz JS. Lucia-Sanz A, et al. Virus Evol. 2024 Nov 29;10(1):veae104. doi: 10.1093/ve/veae104. eCollection 2024. Virus Evol. 2024. PMID: 39720789 Free PMC article.

158

Long-term co-circulation of multiple arboviruses in southeast Australia revealed by xeno-monitoring and viral whole-genome sequencing.

Vieira CJSP, Onn MB, Shivas MA, Shearman D, Darbro JM, Graham M, Freitas L, van den Hurk AF, Frentiu FD, Wallau GL, Devine GJ. Vieira CJSP, et al. Virus Evol. 2024 Nov 25;10(1):0. doi: 10.1093/ve/veae103. eCollection 2024. Virus Evol. 2024. PMID: 39678352 Free PMC article.

159

Combined use of pritelivir with acyclovir or foscarnet suppresses evolution of HSV-1 drug resistance.

Schalkwijk HH, Andrei G, Snoeck R. Schalkwijk HH, et al. Virus Evol. 2024 Nov 23;10(1):veae101. doi: 10.1093/ve/veae101. eCollection 2024. Virus Evol. 2024. PMID: 39717706 Free PMC article.

160

Endogenous viral elements: insights into data availability and accessibility.

Ritsch M, Brait N, Harvey E, Marz M, Lequime S. Ritsch M, et al. Virus Evol. 2024 Nov 23;10(1):veae099. doi: 10.1093/ve/veae099. eCollection 2024. Virus Evol. 2024. PMID: 39659497 Free PMC article.

161

Emergence of Omicron FN.1 a descendent of BQ.1.1 in Botswana.

Choga WT, Gustani-Buss E, Tegally H, Maruapula D, Yu X, Moir M, Zuze BJL, James SE, Ndlovu NS, Seru K, Motshosi P, Blenkinsop A, Gobe I, Baxter C, Manasa J, Lockman S, Shapiro R, Makhema J, Wilkinson E, Blackard JT, Lemey P, Lessells RJ, Martin DP, de Oliveira T, Gaseitsiwe S, Moyo S. Choga WT, et al. Virus Evol. 2024 Nov 22;10(1):veae095. doi: 10.1093/ve/veae095. eCollection 2024. Virus Evol. 2024. PMID: 39720788 Free PMC article.

162

Mathematical comparison of protocols for adapting a bacteriophage to a new host.

Bull JJ, Krone SM. Bull JJ, et al. Virus Evol. 2024 Nov 22;10(1):veae100. doi: 10.1093/ve/veae100. eCollection 2024. Virus Evol. 2024. PMID: 39717707 Free PMC article.

163

A critique of the use of species and below-species taxonomic terms for viruses-time for change?

Simmonds P. Simmonds P. Virus Evol. 2024 Nov 22;10(1):veae096. doi: 10.1093/ve/veae096. eCollection 2024. Virus Evol. 2024. PMID: 39697688 Free PMC article.

164

Unraveling the genomic landscape of piscine myocarditis virus: mutation frequencies, viral diversity and evolutionary dynamics in Atlantic salmon.

Amono R, Markussen T, Singh VK, Lund M, Manji F, Mor SK, Evensen Ø, Mikalsen AB. Amono R, et al. Virus Evol. 2024 Nov 21;10(1):veae097. doi: 10.1093/ve/veae097. eCollection 2024. Virus Evol. 2024. PMID: 39717704 Free PMC article.

165

Evolution of a novel engineered tripartite viral genome of a torradovirus.

Turina M, Nerva L, Vallino M, Miotti N, Forgia M, Ciuffo M, Falk BW, Ferriol I. Turina M, et al. Virus Evol. 2024 Nov 20;10(1):0. doi: 10.1093/ve/veae098. eCollection 2024. Virus Evol. 2024. PMID: 39678354 Free PMC article.

166

CovTransformer: A transformer model for SARS-CoV-2 lineage frequency forecasting.

Feng Y, Goldberg EE, Kupperman M, Zhang X, Lin Y, Ke R. Feng Y, et al. Virus Evol. 2024 Nov 14;10(1):veae086. doi: 10.1093/ve/veae086. eCollection 2024. Virus Evol. 2024. PMID: 39659498 Free PMC article.

167

Dimensionality reduction distills complex evolutionary relationships in seasonal influenza and SARS-CoV-2.

Nanduri S, Black A, Bedford T, Huddleston J. Nanduri S, et al. Virus Evol. 2024 Nov 14;10(1):veae087. doi: 10.1093/ve/veae087. eCollection 2024. Virus Evol. 2024. PMID: 39610652 Free PMC article.

168

A phylogenetic assessment of HIV-1 transmission trends among people who inject drugs from Coastal and Nairobi, Kenya.

Kingston H, Nduva G, Chohan BH, Mbogo L, Monroe-Wise A, Sambai B, Guthrie BL, Wilkinson E, Giandhari J, Masyuko S, Sinkele W, de Oliveria T, Bukusi D, Scott J, Farquhar C, Herbeck JT. Kingston H, et al. Virus Evol. 2024 Nov 11;10(1):veae092. doi: 10.1093/ve/veae092. eCollection 2024. Virus Evol. 2024. PMID: 39678353 Free PMC article.

169

Identification of a novel mycovirus belonging to the "flexivirus"-related family with icosahedral virion.

Wu CF, Okada R, Neri U, Chang YC, Ogawara T, Kitaura K, Komatsu K, Moriyama H. Wu CF, et al. Virus Evol. 2024 Nov 6;10(1):veae093. doi: 10.1093/ve/veae093. eCollection 2024. Virus Evol. 2024. PMID: 39697687 Free PMC article.

170

A virus associated with the zoonotic pathogen Plasmodium knowlesi causing human malaria is a member of a diverse and unclassified viral taxon.

Petrone ME, Charon J, Grigg MJ, William T, Rajahram GS, Westaway J, Piera KA, Shi M, Anstey NM, Holmes EC. Petrone ME, et al. Virus Evol. 2024 Nov 6;10(1):veae091. doi: 10.1093/ve/veae091. eCollection 2024. Virus Evol. 2024. PMID: 39619416 Free PMC article.

171

Enhanced detection and molecular modeling of adaptive mutations in SARS-CoV-2 coding and non-coding regions using the c/µ test.

Paradis NJ, Wu C. Paradis NJ, et al. Virus Evol. 2024 Nov 6;10(1):veae089. doi: 10.1093/ve/veae089. eCollection 2024. Virus Evol. 2024. PMID: 39584063 Free PMC article.

172

Community-level variability in Bronx COVID-19 hospitalizations associated with differing population immunity during the second year of the pandemic.

Forster R, Griffen A, Daily JP, Kelly L. Forster R, et al. Virus Evol. 2024 Nov 1;10(1):veae090. doi: 10.1093/ve/veae090. eCollection 2024. Virus Evol. 2024. PMID: 39610653 Free PMC article.

173

Long-read transcriptomics of Ostreid herpesvirus 1 uncovers a conserved expression strategy for the capsid maturation module and pinpoints a mechanism for evasion of the ADAR-based antiviral defence.

Rosani U, Bortoletto E, Zhang X, Huang BW, Xin LS, Krupovic M, Bai CM. Rosani U, et al. Virus Evol. 2024 Oct 17;10(1):veae088. doi: 10.1093/ve/veae088. eCollection 2024. Virus Evol. 2024. PMID: 39555210 Free PMC article.

174

A phylogenetics and variant calling pipeline to support SARS-CoV-2 genomic epidemiology in the UK.

Colquhoun R, O'Toole Á, Hill V, McCrone JT, Yu X, Nicholls SM, Poplawski R, Whalley T, Groves N, Ellaby N, Loman N, Connor T, Rambaut A. Colquhoun R, et al. Virus Evol. 2024 Oct 17;10(1):veae083. doi: 10.1093/ve/veae083. eCollection 2024. Virus Evol. 2024. PMID: 39493537 Free PMC article.

175

Genomic epidemiology reveals the variation and transmission properties of SARS-CoV-2 in a single-source community outbreak.

Zhao N, He M, Wang H, Zhu L, Wang N, Yong W, Fan H, Ding S, Ma T, Zhang Z, Dong X, Wang Z, Dong X, Min X, Zhang H, Ding J. Zhao N, et al. Virus Evol. 2024 Oct 17;10(1):veae085. doi: 10.1093/ve/veae085. eCollection 2024. Virus Evol. 2024. PMID: 39493536 Free PMC article.

176

Evolution of virulence in emerging epidemics: from theory to experimental evolution and back.

Benhamou W, Blanquart F, Choisy M, Berngruber TW, Choquet R, Gandon S. Benhamou W, et al. Virus Evol. 2024 Oct 15;10(1):veae069. doi: 10.1093/ve/veae069. eCollection 2024. Virus Evol. 2024. PMID: 39568860 Free PMC article.

177

On the importance of assessing topological convergence in Bayesian phylogenetic inference.

Brusselmans M, Carvalho LM, L Hong S, Gao J, Matsen Iv FA, Rambaut A, Lemey P, Suchard MA, Dudas G, Baele G. Brusselmans M, et al. Virus Evol. 2024 Oct 15;10(1):veae081. doi: 10.1093/ve/veae081. eCollection 2024. Virus Evol. 2024. PMID: 39534377 Free PMC article.

178

Influenza A virus within-host evolution and positive selection in a densely sampled household cohort over three seasons.

Bendall EE, Zhu Y, Fitzsimmons WJ, Rolfes M, Mellis A, Halasa N, Martin ET, Grijalva CG, Talbot HK, Lauring AS. Bendall EE, et al. Virus Evol. 2024 Oct 3;10(1):veae084. doi: 10.1093/ve/veae084. eCollection 2024. Virus Evol. 2024. PMID: 39444487 Free PMC article.

179

Structural models predict a significantly higher binding affinity between the NblA protein of cyanophage Ma-LMM01 and the phycocyanin of Microcystis aeruginosa NIES-298 compared to the host homolog.

Meza-Padilla I, McConkey BJ, Nissimov JI. Meza-Padilla I, et al. Virus Evol. 2024 Sep 26;10(1):veae082. doi: 10.1093/ve/veae082. eCollection 2024. Virus Evol. 2024. PMID: 39411151 Free PMC article.

180

Correction to: Natural variation in neuraminidase activity influences the evolutionary potential of the seasonal H1N1 lineage hemagglutinin.

[No authors listed] [No authors listed] Virus Evol. 2024 Sep 23;10(1):veae077. doi: 10.1093/ve/veae077. eCollection 2024. Virus Evol. 2024. PMID: 40391285 Free PMC article.

181

Innovation in viruses: fitness valley crossing, neutral landscapes, or just duplications?

Banse P, Elena SF, Beslon G. Banse P, et al. Virus Evol. 2024 Sep 20;10(1):veae078. doi: 10.1093/ve/veae078. eCollection 2024. Virus Evol. 2024. PMID: 39386076 Free PMC article.

182

Evolutionary characterization of the establishment of H6 influenza viruses in domestic geese in China: implications for the position of the host in the ecosystem.

Peng L, Jin Z, Chen P, Zhang Z, Fan X, Hong W, Liu Y, Smith DK, Cheung WY, Wang J, Zhu H, Lam TT, Guan Y. Peng L, et al. Virus Evol. 2024 Sep 14;10(1):veae075. doi: 10.1093/ve/veae075. eCollection 2024. Virus Evol. 2024. PMID: 39777275 Free PMC article.

183

Independent repeated mutations within the alphaviruses Ross River virus and Barmah Forest virus indicates convergent evolution and past positive selection in ancestral populations despite ongoing purifying selection.

Pyke AT, Wilson DJ, Michie A, Mackenzie JS, Imrie A, Cameron J, Doggett SL, Haniotis J, Herrero LJ, Caly L, Lynch SE, Mee PT, Madzokere ET, Ramirez AL, Paramitha D, Hobson-Peters J, Smith DW, Weir R, Sullivan M, Druce J, Melville L, Robson J, Gibb R, van den Hurk AF, Duchene S. Pyke AT, et al. Virus Evol. 2024 Sep 13;10(1):veae080. doi: 10.1093/ve/veae080. eCollection 2024. Virus Evol. 2024. PMID: 39411152 Free PMC article.

184

Historical drivers of HCV Subtypes 1b and 3a in Thailand and 6f in Phetchabun, an HCV endemic area of the country.

Wasitthankasem R, Aiewsakun P, Lapchai S, Raksayot M, Keeratipusana C, Jarupund P, Nakhonsri V, Pimsing N, Tongsima S, Poovorawan Y. Wasitthankasem R, et al. Virus Evol. 2024 Sep 11;10(1):veae079. doi: 10.1093/ve/veae079. eCollection 2024. Virus Evol. 2024. PMID: 39386077 Free PMC article.

185

Contrasting dynamics of two incursions of low-pathogenicity avian influenza virus into Australia.

Wille M, Broz I, Cherrington T, Crawley A, Farrugia B, Ford M, Frost M, Grimsey J, Kirkland PD, Latimore S, Lynch SE, Martin S, Matereke C, Mee PT, Neave MJ, O'Dea M, Read AJ, O'Riley K, Stevens V, Thayaparan S, Zufan S, Ban de Gouvea Pedroso S, Grillo V, Breed AC, Barr IG, Holmes EC, Klaassen M, Wong FYK. Wille M, et al. Virus Evol. 2024 Sep 10;10(1):veae076. doi: 10.1093/ve/veae076. eCollection 2024. Virus Evol. 2024. PMID: 39416286 Free PMC article.

186

The classification, origin, and evolutionary dynamics of severe fever with thrombocytopenia syndrome virus circulating in East Asia.

Sang S, Chen P, Li C, Zhang A, Wang Y, Liu Q. Sang S, et al. Virus Evol. 2024 Sep 6;10(1):veae072. doi: 10.1093/ve/veae072. eCollection 2024. Virus Evol. 2024. PMID: 39310090 Free PMC article.

187

Comprehensive detection and dissection of interlineage recombination events in the SARS-CoV-2 pandemic.

Li JY, Wang HY, Cheng YX, Ji C, Weng S, Han N, Yang R, Zhou HY, Wu A. Li JY, et al. Virus Evol. 2024 Sep 5;10(1):veae074. doi: 10.1093/ve/veae074. eCollection 2024. Virus Evol. 2024. PMID: 39399153 Free PMC article.

188

Phylogenetic evidence of extensive spatial mixing of diverse HIV-1 group M lineages within Cameroon but not between its neighbours.

Godwe C, Goni OH, San JE, Sonela N, Tchakoute M, Nanfack A, Koro FK, Butel C, Vidal N, Duerr R, Martin DP, de Oliveira T, Peeters M, Altfeld M, Ayouba A, Ndung'u T, Tongo M. Godwe C, et al. Virus Evol. 2024 Sep 2;10(1):veae070. doi: 10.1093/ve/veae070. eCollection 2024. Virus Evol. 2024. PMID: 39386075 Free PMC article.

189

SARS-CoV-2 variant replacement constrains vaccine-specific viral diversification.

Dearlove BL, Fries AC, Epsi NJ, Richard SA, Ganesan A, Huprikar N, Lindholm DA, Mende K, Colombo RE, Colombo C, Bai H, Larson DT, Ewers EC, Lalani T, Smith AG, Berjohn CM, Maves RC, Jones MU, Saunders D, Maldonado CJ, Mody RM, Bazan SE, Tribble DR, Burgess T, Simons MP, Agan BK, Pollett SD, Rolland M. Dearlove BL, et al. Virus Evol. 2024 Sep 2;10(1):veae071. doi: 10.1093/ve/veae071. eCollection 2024. Virus Evol. 2024. PMID: 39386074 Free PMC article.

190

Deep mutational scanning of SARS-CoV-2 Omicron BA.2.86 and epistatic emergence of the KP.3 variant.

Taylor AL, Starr TN. Taylor AL, et al. Virus Evol. 2024 Sep 2;10(1):veae067. doi: 10.1093/ve/veae067. eCollection 2024. Virus Evol. 2024. PMID: 39310091 Free PMC article.

191

Intrahost evolution leading to distinct lineages in the upper and lower respiratory tracts during SARS-CoV-2 prolonged infection.

El Moussaoui M, Bontems S, Meex C, Hayette MP, Lejeune M, Hong SL, Dellicour S, Moutschen M, Cambisano N, Renotte N, Bours V, Darcis G, Artesi M, Durkin K. El Moussaoui M, et al. Virus Evol. 2024 Aug 31;10(1):veae073. doi: 10.1093/ve/veae073. eCollection 2024. Virus Evol. 2024. PMID: 39399151 Free PMC article.

192

Cryptic transmission and novel introduction of Dengue 1 and 2 genotypes in Colombia.

Martínez D, Gómez M, Hernández C, Campo-Palacio S, González-Robayo M, Montilla M, Pavas-Escobar N, Tovar-Acero C, Geovo-Arias L, Valencia-Urrutia E, Córdoba-Renteria N, Carrillo-Hernandez MY, Ruiz-Saenz J, Martinez-Gutierrez M, Paniz-Mondolfi A, Patiño LH, Muñoz M, Ramírez JD. Martínez D, et al. Virus Evol. 2024 Aug 31;10(1):veae068. doi: 10.1093/ve/veae068. eCollection 2024. Virus Evol. 2024. PMID: 39347444 Free PMC article.

193

Intra- and inter-subtype HIV diversity between 1994 and 2018 in southern Uganda: a longitudinal population-based study.

Kim S, Kigozi G, Martin MA, Galiwango RM, Quinn TC, Redd AD, Ssekubugu R, Bonsall D, Ssemwanga D, Rambaut A, Herbeck JT, Reynolds SJ, Foley B, Abeler-Dörner L, Fraser C, Ratmann O, Kagaayi J, Laeyendecker O, Grabowski MK. Kim S, et al. Virus Evol. 2024 Aug 24;10(1):veae065. doi: 10.1093/ve/veae065. eCollection 2024. Virus Evol. 2024. PMID: 39399152 Free PMC article.

194

Evolution of the Cytomegalovirus RL11 gene family in Old World monkeys and Great Apes.

Litvin U, Wang ECY, Stanton RJ, Fielding CA, Hughes J. Litvin U, et al. Virus Evol. 2024 Aug 24;10(1):veae066. doi: 10.1093/ve/veae066. eCollection 2024. Virus Evol. 2024. PMID: 39315401 Free PMC article.

195

The tissue virome of black-spotted frogs reveals a diversity of uncharacterized viruses.

Li C, Hu Y, Liu Y, Li N, Yi L, Tu C, He B. Li C, et al. Virus Evol. 2024 Aug 22;10(1):veae062. doi: 10.1093/ve/veae062. eCollection 2024. Virus Evol. 2024. PMID: 39175838 Free PMC article.

196

Prospects for a sequence-based taxonomy of influenza A virus subtypes.

Poon AFY. Poon AFY. Virus Evol. 2024 Aug 17;10(1):veae064. doi: 10.1093/ve/veae064. eCollection 2024. Virus Evol. 2024. PMID: 39247559 Free PMC article.

197

GALV-KoRV-related retroviruses in diverse Australian and African rodent species.

Hayward JA, Tian S, Tachedjian G. Hayward JA, et al. Virus Evol. 2024 Jul 31;10(1):veae061. doi: 10.1093/ve/veae061. eCollection 2024. Virus Evol. 2024. PMID: 39175839 Free PMC article.

198

Investigating the emergence of a zoonotic virus: phylogenetic analysis of European bat lyssavirus 1 in the UK.

Golding ME, Wu G, Wilkie R, Picard-Meyer E, Servat A, Marston DA, Aegerter JN, Horton DL, McElhinney LM. Golding ME, et al. Virus Evol. 2024 Jul 29;10(1):veae060. doi: 10.1093/ve/veae060. eCollection 2024. Virus Evol. 2024. PMID: 39193178 Free PMC article.

199

Opening a 60-year time capsule: sequences of historical poliovirus cold variants shed a new light on a contemporary strain.

Chesnais M, Bujaki E, Filhol T, Caval V, Joffret ML, Martin J, Jouvenet N, Bessaud M. Chesnais M, et al. Virus Evol. 2024 Jul 29;10(1):veae063. doi: 10.1093/ve/veae063. eCollection 2024. Virus Evol. 2024. PMID: 39170726 Free PMC article.

200

Correction to: Cell type-specific adaptation of the SARS-CoV-2 spike.

[No authors listed] [No authors listed] Virus Evol. 2024 Jul 26;10(1):veae057. doi: 10.1093/ve/veae057. eCollection 2024. Virus Evol. 2024. PMID: 39081719 Free PMC article.

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