Detection of avian metapneumovirus subtype A from wild birds in the State of São Paulo, Brazil

The present study investigated the circulation of avian metapneumovirus (aMPV) in wild birds in Brazil. To do so, 131 samples from 366 oropharyngeal or cloacal swabs collected from 18 species of birds were tested individually or in pools by RT-PCR. Samples detected by RT-PCR were selected for DNA sequencing. Thirteen (9.9%) samples were detected by the RT-PCR targeting the N gene and four out of 13 samples were sequenced. Sequencing results showed a high identity with the aMPV subtype A. Our results confirm the circulation of the aMPV subtype A in wild birds in Brazil even five years after its last detection.

INDEX TERMS:
Detection; avian metapneumovirus; subtype A; wild birds; São Paulo; Brazil; waterfowl; surveillance; aMPV; wildlife animals; birds; viroses

Authorship

Laís S. Rizotto

Postgraduate Program in Experimental Epidemiology of Zoonoses, Faculdade de Medicina Veterinária e Ciência Animal, Universidade de São Paulo (USP), Avenida Prof. Dr. Orlando Marques de Paiva 87, Cidade Universitária, São Paulo, SP 05508-270, Brazil.Universidade de São PauloBrazilSão Paulo, SP, Brazil Postgraduate Program in Experimental Epidemiology of Zoonoses, Faculdade de Medicina Veterinária e Ciência Animal, Universidade de São Paulo (USP), Avenida Prof. Dr. Orlando Marques de Paiva 87, Cidade Universitária, São Paulo, SP 05508-270, Brazil.

Raphael M. Simão

Guilherme P. Scagion

Alessandra A. Simasaki

Departamento de Medicina Veterinária, Faculdade de Zootecnia e Engenharia de Alimentos (FZEA), Universidade de São Paulo (USP), Av. Duque de Caxias Norte 225, Pirassununga, SP 13635-900, Brazil.Universidade de São PauloBrazilPirassununga, SP, Brazil Departamento de Medicina Veterinária, Faculdade de Zootecnia e Engenharia de Alimentos (FZEA), Universidade de São Paulo (USP), Av. Duque de Caxias Norte 225, Pirassununga, SP 13635-900, Brazil.

Leonardo C. Caserta

Laboratório de Virologia Animal, Instituto de Biologia, Universidade de Campinas (Unicamp), Cidade Universitária Zeferino Vaz s/n, Barão Geraldo, Campinas, SP 13083-970, Brazil.Universidade de CampinasBrazilCampinas, SP, Brazil Laboratório de Virologia Animal, Instituto de Biologia, Universidade de Campinas (Unicamp), Cidade Universitária Zeferino Vaz s/n, Barão Geraldo, Campinas, SP 13083-970, Brazil.

Julia C. Benassi

Clarice W. Arns

Helena L. Ferreira ^**Corresponding author: hlage@usp.br

https://orcid.org/0000-0002-3261-3712

*Corresponding author: hlage@usp.br

Conflict of interest statement.- The authors declare no conflict of interest.

SCIMAGO INSTITUTIONS RANKINGS

Figures | Tables

Figures (1)
Tables (1)

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Fig.1.
Phylogenetic tree of avian metapneumovirus (aMPV) samples from Aix galericulata, Dendrocygna viduata, and Falco sparverius. The evolutionary history was inferred using the Maximum Likelihood method based on the Kimura 2-parameter model (Kimura 1980Kimura M. 1980. A simple method for estimating evolutionary rate of base substitutions through comparative studies of nucleotide sequences. J. Mol. Evol. 16(2):111-120. <http://dx.doi.org/10.1007/BF01731581> <PMid:7463489>
https://doi.org/10.1007/BF01731581... ). The tree with the highest log likelihood (-542.1852) is shown. The percentage of trees in which the associated taxa clustered together is shown next to the branches. The initial tree(s) for the heuristic search was obtained automatically by applying the Neighbor-Join and BioNJ algorithms to a matrix of pairwise distances estimated using the Maximum Composite Likelihood (MCL) approach, followed by selection of the topology with a superior log likelihood value. The rate variation model allowed for some sites to be evolutionarily invariable ([+I], 60.7571% sites). The tree is drawn to scale, with branch lengths measured as the number of substitutions per site. The analysis involved 46 nucleotide sequences. The codon positions included were 1st+2nd+3rd+Noncoding. All positions with less than 95% site coverage were eliminated. That is, fewer than 5% alignment gaps, missing data, and ambiguous bases were allowed at any position. There were a total of 115 positions in the final dataset. Evolutionary analyses were conducted using the MEGA7 software (Kumar et al. 2016Kumar S., Stecher G. & Tamura K. 2016. MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol. Biol. Evol. 33(7):1870-1874. <http://dx.doi.org/10.1093/molbev/msw054> <PMid:27004904>
https://doi.org/10.1093/molbev/msw054... ). The aMPVsequences originated from this study are denoted with a ■ symbol.

Thumbnail

Table 1.
Tested samples according to species, number of birds, quantity and swab types (C-cloacal or OP-oropharyngeal swabs)

Fig.1. Phylogenetic tree of avian metapneumovirus (aMPV) samples from Aix galericulata, Dendrocygna viduata, and Falco sparverius. The evolutionary history was inferred using the Maximum Likelihood method based on the Kimura 2-parameter model (Kimura 1980Kimura M. 1980. A simple method for estimating evolutionary rate of base substitutions through comparative studies of nucleotide sequences. J. Mol. Evol. 16(2):111-120. <http://dx.doi.org/10.1007/BF01731581> <PMid:7463489>
https://doi.org/10.1007/BF01731581... ). The tree with the highest log likelihood (-542.1852) is shown. The percentage of trees in which the associated taxa clustered together is shown next to the branches. The initial tree(s) for the heuristic search was obtained automatically by applying the Neighbor-Join and BioNJ algorithms to a matrix of pairwise distances estimated using the Maximum Composite Likelihood (MCL) approach, followed by selection of the topology with a superior log likelihood value. The rate variation model allowed for some sites to be evolutionarily invariable ([+I], 60.7571% sites). The tree is drawn to scale, with branch lengths measured as the number of substitutions per site. The analysis involved 46 nucleotide sequences. The codon positions included were 1st+2nd+3rd+Noncoding. All positions with less than 95% site coverage were eliminated. That is, fewer than 5% alignment gaps, missing data, and ambiguous bases were allowed at any position. There were a total of 115 positions in the final dataset. Evolutionary analyses were conducted using the MEGA7 software (Kumar et al. 2016Kumar S., Stecher G. & Tamura K. 2016. MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol. Biol. Evol. 33(7):1870-1874. <http://dx.doi.org/10.1093/molbev/msw054> <PMid:27004904>
https://doi.org/10.1093/molbev/msw054... ). The aMPVsequences originated from this study are denoted with a ■ symbol.

Table 1. Tested samples according to species, number of birds, quantity and swab types (C-cloacal or OP-oropharyngeal swabs)

Species	Number of birds	C	OP	Number of tested samples (pool/individually)
Dendrocygna viduata ^a	73	73	73	37
Aix galericulata ^{b, c}	61	60	57	32
Dendrocygna autumnalis ^a	10	10	10	5
Aix sponsa ^{b, c}	8	7	8	9
Anas platyrhynchos domestica ^b	6	6	6	12
Chenonetta jubata ^b	4	4	4	4
Cairina moschata ^a	2	2	2	1
Dendrocygna bicolor ^a	1	1	1	1
Cereopsis novahollandiae ^c	1	1	1	2
Cygnus melanocoryphus ^c	1	1	1	2
Cygnus atratus ^c	1	0	1	1
Psittacara leucophthalma ^{c, d}	10	7	7	14
Ara chloropterus ^c	2	0	2	2
Amazona aestiva ^d	1	0	1	1
Columba livia ^a	8	8	8	4
Megascops choliba ^d	1	0	1	1
Ramphastos dicolorus ^d	1	1	0	1
Falco sparverius ^d	1	1	1	2
TOTAL	192	182	184	131

Locations and years where samples were collected: ^a Wild (migratory and resident) birds from Clube de Campo São Paulo, São Paulo/SP (2015), samples were kindly provided by Prof. Dr. Edison L. Durigon of the Laboratory of Clinical and Molecular Virology of the Institute of Biomedical Sciences (ICB-II), University of São Paulo; ^b Captive birds from Commercial Bird house, Pirassununga/SP (2014); ^c Captive birds from Municipal Ecological Park of Americana “Eng. Cid Almeida Franco”, Americana/SP (2013); ^d Wild Birds from Mata Ciliar of Jundiaí (2015), were from different origins such as smuggling, injured birds. Data about those birds is usually not available and sampling was performed upon their arrival. All birds were healthy, without any clinical signs.

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Detection of avian metapneumovirus subtype A from wild birds in the State of São Paulo, Brazil

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[1] *Corresponding author: hlage@usp.br