Human G3P[4] rotavirus obtained in Japan, 2013, possibly emerged through a human–equine rotavirus reassortment event

In 2009, the co-circulation of H5N1 and H1N1pdm09 raised concerns that a reassortment event may lead to highly pathogenic influenza strains. H1N1pdm09 and H5N1 are able to infect the same target cells of the lower respiratory tract. To investigate the capacity of the emergence of reassortant viruses, we characterized viruses obtained from the co-infection of cells with H5N1 (A/Turkey/13/2006) and H1N1pdm09 (A/Lyon/969/2009 H1N1). In our analysis, all the screened reassortants possessed the PB2, HA, and NP segments from H5N1 and acquired one or two of the H1N1pdm09 segments. Moreover, the in vivo infections showed that the acquisition of the NS segment from H1N1pdm09 increased the virulence of H5N1 in mice. We conclude, therefore, that reassortment can occur between these two viruses, even if this process has never been detected in nature.

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The Segment Matters: Probable Reassortment of Tilapia Lake Virus (TiLV) Complicates Phylogenetic Analysis and Inference of Geographical Origin of New Isolate from Bangladesh

Viruses ◽

10.3390/v12030258 ◽

2020 ◽

Vol 12 (3) ◽

pp. 258 ◽

Cited By ~ 7

Author(s):

Dominique L. Chaput ◽

David Bass ◽

Md. Mehedi Alam ◽

Neaz Al Hasan ◽

Grant D. Stentiford ◽

...

Keyword(s):

Phylogenetic Analysis ◽

Geographical Origin ◽

Rna Virus ◽

Geographic Origin ◽

South American ◽

Reassortment Event ◽

Coding Regions ◽

Whole Genomes ◽

History Of ◽

Negative Sense

Tilapia lake virus (TiLV), a negative sense RNA virus with a 10 segment genome, is an emerging threat to tilapia aquaculture worldwide, with outbreaks causing over 90% mortality reported on several continents since 2014. Following a severe tilapia mortality event in July 2017, we confirmed the presence of TiLV in Bangladesh and obtained the near-complete genome of this isolate, BD-2017. Phylogenetic analysis of the concatenated 10 segment coding regions placed BD-2017 in a clade with the two isolates from Thailand, separate from the Israeli and South American isolates. However, phylogenetic analysis of individual segments gave conflicting results, sometimes clustering BD-2017 with one of the Israeli isolates, and splitting pairs of isolates from the same region. By comparing patterns of topological difference among segments of quartets of isolates, we showed that TiLV likely has a history of reassortment. Segments 5 and 6, in particular, appear to have undergone a relatively recent reassortment event involving Ecuador isolate EC-2012 and Israel isolate Til-4-2011. The phylogeny of TiLV isolates therefore depends on the segment sequenced. Our findings illustrate the need to exercise caution when using phylogenetic analysis to infer geographic origin and track the movement of TiLV, and we recommend using whole genomes wherever possible.

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Evolution and rapid spread of a reassortant A(H3N2) virus that predominated the 2017–2018 influenza season

Virus Evolution ◽

10.1093/ve/vez046 ◽

2019 ◽

Vol 5 (2) ◽

Cited By ~ 3

Author(s):

Barney I Potter ◽

Rebecca Kondor ◽

James Hadfield ◽

John Huddleston ◽

John Barnes ◽

...

Keyword(s):

North American ◽

Influenza Season ◽

H3n2 Virus ◽

Amino Acid Substitutions ◽

H1n1 Pandemic ◽

Reassortment Event ◽

Antigenic Analysis ◽

Viral Genomes ◽

Rapid Spread ◽

2009 H1n1

Abstract The 2017–2018 North American influenza season caused more hospitalizations and deaths than any year since the 2009 H1N1 pandemic. The majority of recorded influenza infections were caused by A(H3N2) viruses, with most of the virus’s North American diversity falling into the A2 clade. Within A2, we observe a subclade which we call A2/re that rose to comprise almost 70 per cent of A(H3N2) viruses circulating in North America by early 2018. Unlike most fast-growing clades, however, A2/re contains no amino acid substitutions in the hemagglutinin (HA) segment. Moreover, hemagglutination inhibition assays did not suggest substantial antigenic differences between A2/re viruses and viruses sampled during the 2016–2017 season. Rather, we observe that the A2/re clade was the result of a reassortment event that occurred in late 2016 or early 2017 and involved the combination of the HA and PB1 segments of an A2 virus with neuraminidase (NA) and other segments a virus from the clade A1b. The success of this clade shows the need for antigenic analysis that targets NA in addition to HA. Our results illustrate the potential for non-HA drivers of viral success and necessitate the need for more thorough tracking of full viral genomes to better understand the dynamics of influenza epidemics.

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Molecular Characterisation of a Rare Reassortant Porcine-Like G5P[6] Rotavirus Strain Detected in an Unvaccinated Child in Kasama, Zambia

Pathogens ◽

10.3390/pathogens9080663 ◽

2020 ◽

Vol 9 (8) ◽

pp. 663

Author(s):

Wairimu M. Maringa ◽

Peter N. Mwangi ◽

Julia Simwaka ◽

Evans M. Mpabalwani ◽

Jason M. Mwenda ◽

...

Keyword(s):

Phylogenetic Analyses ◽

The Other ◽

Interspecies Transmission ◽

Whole Genome ◽

Molecular Characterisation ◽

Human Origin ◽

Reassortment Event ◽

Reassortant Strain ◽

Unvaccinated Child ◽

Cognate Gene

A human-porcine reassortant strain, RVA/Human-wt/ZMB/UFS-NGS-MRC-DPRU4723/2014/G5P[6], was identified in a sample collected in 2014 from an unvaccinated 12 month old male hospitalised for gastroenteritis in Zambia. We sequenced and characterised the complete genome of this strain which presented the constellation: G5-P[6]-I1-R1-C1-M1-A8-N1-T1-E1-H1. The genotype A8 is often observed in porcine strains. Phylogenetic analyses showed that VP6, VP7, NSP2, NSP4, and NSP5 genes were closely related to cognate gene sequences of porcine strains (e.g., RVA/Pig-wt/CHN/DZ-2/2013/G5P[X] for VP7) from the NCBI database, while VP1, VP3, VP4, and NSP3 were closely related to porcine-like human strains (e.g., RVA/Human-wt/CHN/E931/2008/G4P[6] for VP1, and VP3). On the other hand, the origin of the VP2 was not clear from our analyses, as it was not only close to both porcine (e.g., RVA/Pig-tc/CHN/SWU-1C/2018/G9P[13]) and porcine-like human strains (e.g., RVA/Human-wt/LKA/R1207/2009/G4P[6]) but also to three human strains (e.g., RVA/Human-wt/USA/1476/1974/G1P[8]). The VP7 gene was located in lineage II that comprised only porcine strains, which suggests the occurrence of independent porcine-to-human reassortment events. The study strain may have collectively been derived through interspecies transmission, or through reassortment event(s) involving strains of porcine and porcine-like human origin. The results of this study underline the importance of whole-genome characterisation of rotavirus strains and provide insights into interspecies transmissions from porcine to humans.

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Phylogenetic Analysis Reveals a Correlation between the Expansion of Very Virulent Infectious Bursal Disease Virus and Reassortment of Its Genome Segment B

Journal of Virology ◽

10.1128/jvi.00585-06 ◽

2006 ◽

Vol 80 (17) ◽

pp. 8503-8509 ◽

Cited By ~ 76

Author(s):

Chung-Chau Hon ◽

Tsan-Yuk Lam ◽

Alexei Drummond ◽

Andrew Rambaut ◽

Yiu-Fai Lee ◽

...

Keyword(s):

Phylogenetic Analysis ◽

Population Dynamics ◽

Disease Virus ◽

Infectious Bursal Disease Virus ◽

Genome Segment ◽

Infectious Bursal Disease ◽

Reassortment Event ◽

The Past ◽

Bursal Disease ◽

Past Population

ABSTRACT Infectious bursal disease virus (IBDV) is a birnavirus causing immunosuppressive disease in chickens. Emergence of the very virulent form of IBDV (vvIBDV) in the late 1980s dramatically changed the epidemiology of the disease. In this study, we investigated the phylogenetic origins of its genome segments and estimated the time of emergence of their most recent common ancestors. Moreover, with recently developed coalescence techniques, we reconstructed the past population dynamics of vvIBDV and timed the onset of its expansion to the late 1980s. Our analysis suggests that genome segment A of vvIBDV emerged at least 20 years before its expansion, which argues against the hypothesis that mutation of genome segment A is the major contributing factor in the emergence and expansion of vvIBDV. Alternatively, the phylogeny of genome segment B suggests a possible reassortment event estimated to have taken place around the mid-1980s, which seems to coincide with its expansion within approximately 5 years. We therefore hypothesize that the reassortment of genome segment B initiated vvIBDV expansion in the late 1980s, possibly by enhancing the virulence of the virus synergistically with its existing genome segment A. This report reveals the possible mechanisms leading to the emergence and expansion of vvIBDV, which would certainly provide insights into the scope of surveillance and prevention efforts regarding the disease.

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Surveillance in eastern India (2007-2009) revealed reassortment event involving ns and PB1-F2 gene segments among co-circulating influenza a subtypes

Virology Journal ◽

10.1186/1743-422x-9-3 ◽

2012 ◽

Vol 9 (1) ◽

pp. 3 ◽

Cited By ~ 2

Author(s):

Mehuli Sarkar ◽

Shampa Chanda ◽

Sekhar Chakrabarti ◽

Jaydeep Mazumdar ◽

Anirban Ganguly ◽

...

Keyword(s):

Influenza A ◽

Reassortment Event ◽

Eastern India

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Genetic characterization of a novel G9P[23] rotavirus A strain identified in southwestern China with evidence of a reassortment event between human and porcine strains

Archives of Virology ◽

10.1007/s00705-019-04188-y ◽

2019 ◽

Vol 164 (4) ◽

pp. 1229-1232

Author(s):

Danyu Chen ◽

Long Zhou ◽

Yiming Tian ◽

Xuan Wu ◽

Lan Feng ◽

...

Keyword(s):

Genetic Characterization ◽

Southwestern China ◽

Reassortment Event ◽

Rotavirus A

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Distribution of two distinct rotavirus B (RVB) strains in the north-central Bangladesh and evidence for reassortment event among human RVB revealed by whole genomic analysis

Infection Genetics and Evolution ◽

10.1016/j.meegid.2016.11.001 ◽

2017 ◽

Vol 47 ◽

pp. 77-86 ◽

Cited By ~ 2

Author(s):

Meiji Soe Aung ◽

Samsoon Nahar ◽

Satoru Aida ◽

Shyamal Kumar Paul ◽

Muhammad Akram Hossain ◽

...

Keyword(s):

Genomic Analysis ◽

Reassortment Event ◽

North Central ◽

The North

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Tomato Chlorotic Spot Virus (TCSV) Putatively Incorporated a Genomic Segment of Groundnut Ringspot Virus (GRSV) Upon a Reassortment Event

Viruses ◽

10.3390/v11020187 ◽

2019 ◽

Vol 11 (2) ◽

pp. 187 ◽

Cited By ~ 4

Author(s):

João Silva ◽

Athos de Oliveira ◽

Mariana de Almeida ◽

Richard Kormelink ◽

Tatsuya Nagata ◽

...

Keyword(s):

Evolutionary History ◽

Nucleotide Diversity ◽

Ringspot Virus ◽

Parental Genotype ◽

Biological Traits ◽

Reassortment Event ◽

Spot Virus ◽

Chlorotic Spot ◽

History Of ◽

Event Based

Tomato chlorotic spot virus (TCSV) and groundnut ringspot virus (GRSV) share several genetic and biological traits. Both of them belong to the genus Tospovirus (family Peribunyaviridae), which is composed by viruses with tripartite RNA genome that infect plants and are transmitted by thrips (order Thysanoptera). Previous studies have suggested several reassortment events between these two viruses, and some speculated that they may share one of their genomic segments. To better understand the intimate evolutionary history of these two viruses, we sequenced the genomes of the first TCSV and GRSV isolates ever reported. Our analyses show that TCSV and GRSV isolates indeed share one of their genomic segments, suggesting that one of those viruses may have emerged upon a reassortment event. Based on a series of phylogenetic and nucleotide diversity analyses, we conclude that the parental genotype of the M segment of TCSV was either eliminated due to a reassortment with GRSV or it still remains to be identified.

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Evolution and rapid spread of a reassortant A(H3N2) virus that predominated the 2017-2018 influenza season

10.1101/543322 ◽

2019 ◽

Author(s):

Barney I. Potter ◽

Rebecca Garten ◽

James Hadfield ◽

John Huddleston ◽

John Barnes ◽

...

Keyword(s):

North American ◽

Influenza Season ◽

H3n2 Virus ◽

Amino Acid Substitutions ◽

H1n1 Pandemic ◽

Reassortment Event ◽

Antigenic Analysis ◽

Viral Genomes ◽

Rapid Spread ◽

2009 H1n1

The 2017-2018 North American influenza season caused more hospitalizations and deaths than any year since the 2009 H1N1 pandemic. The majority of recorded influenza infections were caused by A(H3N2) viruses, with most of the virus’s North American diversity falling into the A2 clade. Within A2, we observe a subclade which we call A2/re that rose to comprise almost 70% of A(H3N2) viruses circulating in North America by early 2018. Unlike most fast-growing clades, however, A2/re contains no amino acid substitutions in the hemagglutinin (HA) segment. Moreover, HI assays did not suggest substantial antigenic differences between A2/re viruses and viruses sampled during the 2016-2017 season. Rather, we observe that the A2/re clade was the result of a reassortment event that occurred in late 2016 or early 2017 and involved the combination of the HA and PB1 segments of an A2 virus with neuraminidase (NA) and other segments a virus from the clade A1b. The success of this clade shows the need for antigenic analysis that targets NA in addition to HA. Our results illustrate the potential for non-HA drivers of viral success and necessitate the need for more thorough tracking of full viral genomes to better understand the dynamics of influenza epidemics.

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