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Comment
. 2022 Feb;84(2):e24-e26.
doi: 10.1016/j.jinf.2021.12.001. Epub 2021 Dec 5.

Viral metagenomics in nasopharyngeal swabs of Brazilian patients negative for SARS-CoV-2 unveils the presence of Chikungunya virus infection

Tatyane de Souza Cardoso Quintão  1 , Svetoslav Nanev Slavov  2 , Pâmela Maria de Oliveira  3 , Rafael Dos Santos Bezerra  4 , Évelin Mota Cassemiro  3 , Priscilla Pedrette de Melo Alves  5 , Carolina Carvalho Gontijo  6 , Fabiano Dos Anjos Pereira Martins  7 , Helen da Costa Gurgel  5 , Elza Ferreira Noronha  1 , Walter Massa Ramalho  8 , Wildo Navegantes de Araújo  8 , Alex Leite Pereira  9 , Rodrigo Haddad  10
Affiliations
Comment

Viral metagenomics in nasopharyngeal swabs of Brazilian patients negative for SARS-CoV-2 unveils the presence of Chikungunya virus infection

Tatyane de Souza Cardoso Quintão et al. J Infect. 2022 Feb.
No abstract available

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Conflict of interest statement

Declaration of Competing Interest The authors declare that there is no conflict of interest.

Figures

Fig. 1
Fig. 1
Estrutural City location map, CHIKV confirmatory RT-qPCR assay and maximum likelihood tree. A) The Cidade Estrutural has 40,000 inhabitants of whom 4000 are waste pickers and has the lowest HDI of the Federal District of Brazil. The city borders the Brasilia National Forest, which is an environmental protection area of 423.6 km2 characterized by the typical wooded savanna (Cerrado) (landmark 1), and Cabeceira do Valo, where residents often farm vegetables (landmark 2); B) Representative amplification plot of confirmatory RT-qPCR assay showing the CHIKV positive control (observe 1), positive sample from pool 18 (observe 2) and positive sample from pool 11 (3). C) Approximate maximum likelihood tree of the obtained Chikungunya virus (CHIKV) contigs during the metagenomic analysis of nasopharyngeal swabs (2 contigs of 655 and 718 bp belonging to the nonstructural polyprotein). In the phylogenetic reconstruction 397 complete CHIKV genomes obtained from the GenBank were used under the GTR+G4+F nucleotide substitution model with a statistical support of 1000 bootstrap replicates. The phylogenetic tree showed 3 major clades comprising the CHIKV genotypes. Our samples (red dots) were clustered along the CHIKV East-Central-South African genotype, which by far is the most common genotype in Brazil.
See this image and copyright information in PMC

Comment in

Comment on

  • SARS-CoV-2 and co-infections detection in nasopharyngeal throat swabs of COVID-19 patients by metagenomics.
    Van Tan L, Thi Thu Hong N, My Ngoc N, Tan Thanh T, Thanh Lam V, Anh Nguyet L, Nguyen Truc Nhu L, Thi Ha Ny N, Ngoc Quang Minh N, Nguyen Huy Man D, Thi Ty Hang V, Nguyen Quoc Khanh P, Chanh Xuan T, Thanh Phong N, Nguyen Hoang Tu T, Tinh Hien T, Manh Hung L, Thanh Truong N, Min Yen L, Thanh Dung N, Thwaites G, Van Vinh Chau N; for OUCRU COVID-19 research group. Van Tan L, et al. J Infect. 2020 Aug;81(2):e175-e177. doi: 10.1016/j.jinf.2020.06.033. Epub 2020 Jun 17. J Infect. 2020. PMID: 32562797 Free PMC article. No abstract available.

References

    1. Van Tan L., Thi Thu Hong N., My Ngoc N., Tan Thanh T., Thanh Lam V., Anh Nguyet L., et al. SARS-CoV-2 and co-infections detection in nasopharyngeal throat swabs of COVID-19 patients by metagenomics. J Infect. 2020;81:e175–e177. doi: 10.1016/j.jinf.2020.06.033. - DOI - PMC - PubMed
    1. Peddu V., Shean R.C., Xie H., Shrestha L., Perchetti G.A., Minot S.S., et al. Metagenomic Analysis Reveals Clinical SARS-CoV-2 Infection and Bacterial or Viral Superinfection and Colonization. Clin Chem. 2020;66:966–972. doi: 10.1093/clinchem/hvaa106. - DOI - PMC - PubMed
    1. Lansbury L., Lim B., Baskaran V., Lim W.S. Co-infections in people with COVID-19: a systematic review and meta-analysis. J Infect. 2020;81:266–275. doi: 10.1016/j.jinf.2020.05.046. - DOI - PMC - PubMed
    1. Dos Santos Bezerra R., de Melo Jorge D.M., ÍA Castro, Moretto E.L., Scalon de Oliveira L., Ubiali E.M.A., et al. Detection of Influenza A(H3N2) Virus RNA in Donated Blood. Emerg Infect Dis. 2020;26:1621–1623. doi: 10.3201/eid2607.200549. - DOI - PMC - PubMed
    1. Lanciotti R.S., Kosoy O.L., Laven J.J., Panella A.J., Velez J.O., Lambert A.J., et al. Chikungunya virus in US travelers returning from India. Emerg Infect Dis. 2006;13:764–767. doi: 10.3201/eid1305.070015. 2007. - DOI - PMC - PubMed