ABSTRACT
We report the coding-complete genome sequence of Cytomegalovirus humanbeta5 (BR/2023-012844/IEC/NS/2023), recovered from a nasopharyngeal swab collected from a 5-month-old infant with severe acute respiratory syndrome during a respiratory syncytial virus outbreak in Brazil.
KEYWORDS: Cytomegalovirus humanbeta5, Brazil
ANNOUNCEMENT
Human cytomegalovirus (HCMV) is a member of the family Herpesviridae, subfamily Betaherpesvirinae, and genus Cytomegalovirus (1). Its genome consists of a double-stranded DNA molecule of >200 kbp (2). HCMV genomes are most commonly recovered from blood, urine, and saliva, particularly in congenital infections and in immunocompromised individuals (3–7). Recovering viral genomes from upper respiratory tract samples, such as nasopharyngeal swabs, is uncommon because this anatomical site is not routinely examined for HCMV in clinical or surveillance settings. However, obtaining the viral genome from the nasopharynx may provide key insights into viral shedding, reactivation, and coinfection dynamics. Shotgun metagenomics is well suited for recovering viral genomes directly from clinical samples (3). Notably, as of 1 September 2025, only partial HCMV genome sequences from Brazil were available in GenBank (8).
The nasopharyngeal swab analyzed in this study (2023-012844/IEC) was obtained from a 5-month-old infant hospitalized in an intensive care unit in Macapá, Amapá, located in the Brazilian Amazon. The GPS coordinates for sample collection were 0.0388900 and −51.0663900. The sample was collected in April 2023 by the Health Surveillance Secretariat during a respiratory syncytial virus (RSV) outbreak in Brazil. Viral DNA was extracted using the Extracta Kit – Pathogen DNA and RNA MDx, which employs magnetic microparticle technology, following the manufacturer’s instructions. Library preparation and sequencing were performed at the Respiratory Virus Laboratory of the Evandro Chagas Institute. Libraries were constructed using the Illumina Nextera XT DNA Library Preparation Kit (Illumina, San Diego, CA, USA) and sequenced on the Illumina NextSeq 550 System with 2 × 150 bp paired-end reads, generating 39,712,796 read pairs. Quality filtering of reads in FASTQ format was performed using fastp v.0.23.1 (9), and de novo assembly was conducted using MEGAHIT v.1.2.9 (10) (Table 1). Taxonomic classification of contigs was carried out using Kraken2 v.2.1.0 (11) with the Standard-16 database, which identified multiple contigs assigned to Cytomegalovirus. Classification outputs were visualized using the Pavian R package v.1.2 (12). Manual review and open reading frame prediction were performed in Geneious Prime (13), where multiple overlapping contigs were identified. These contigs, supported by read mapping and alignment with MAFFT (14), allowed reconstruction of a coding-complete genome relative to the reference strain (GenBank accession number PP803491). Each contig was additionally confirmed by BLASTn (15).
TABLE 1.
Sequencing and genome metrics
| Metric | Data for BR/2023-012844/IEC/NS/2023 |
|---|---|
| No. of raw reads | 39,712,796 |
| No. of reads after trimming | 36,229,206 |
| Average read length (bp) | 158 |
| Total no. of contigs | 912,240 |
| No. of contigs related to Cytomegalovirus humanbeta5 | 16 |
| Genome size (bp) | 231,043 |
| GC content (%) | 57.5 |
| Coverage (×) | 801.4 |
| N50 | 466 |
| GenBank accession no. | PX246278 |
The 2023-012844_CMV/IEC genome exhibited a typical HCMV genomic organization, with a length of 231,043 bp and 178 predicted genes. The mean read coverage was 801.4×, and the GC content (57.5%) was consistent with other Cytomegalovirus humanbeta5 genomes available in GenBank. The genome displayed high nucleotide identity (>98%) with related HCMV strains available in GenBank (KJ361950; KJ361951; KJ426589; KT726951; KY490088; MT044485), demonstrating the genetic similarity of the 2023-012844/IEC strain to previously characterized isolates. The shotgun metagenomic approach provided evidence of HCMV genomic material in the nasopharynx of an RSV-positive infant with severe acute respiratory syndrome. As RSV infection can modulate host immune responses (16), further investigations are warranted to elucidate viral coinfections, HCMV reactivation, and the potential impact of congenital HCMV infection.
ACKNOWLEDGMENTS
We thank the technical professional from the Health Department of the State of Amapá for collecting the sample, the Central Laboratory of the State of Amapá for sending the sample, and the Evandro Chagas Institute, Ministry of Health, for the financial resources and physical infrastructure to carry out this work.
Contributor Information
Fernando Neto Tavares, Email: fernandotavares@iec.gov.br.
Jelle Matthijnssens, Katholieke Universiteit Leuven, Leuven, Belgium.
DATA AVAILABILITY
The whole genome sequencing project of sample BR/2023-012844/IEC/NS/2023 was deposited in GenBank under accession number PX246278. The accession number for the raw shotgun metagenomic sequencing reads in the NCBI Sequence Read Archive is SRR35176174. This data set is associated with BioProject accession number PRJNA1312120 and BioSample accession number SAMN50854041 (2023-012844/IEC).
ETHICS APPROVAL
The study was approved by the Research Ethics Committee of the Evandro Chagas Institute, Pará, Brazil (approval number 79631424.6.0000.0019).
REFERENCES
- 1. International Committee on Taxonomy of Viruses . 2011. In ICTV ninth report: 2009 taxonomy release. https://ictv.global/report_9th/dsDNA/Herpesvirales/Herpesviridae.
- 2. Murphy E, Shenk TE. 2008. Human Cytomegalovirus, p 1–19. In Human cytomegalovirus. Berlin, Heidelberg. [DOI] [PubMed] [Google Scholar]
- 3. Tsai HP, Yeh CS, Lin IT, Ko WC, Wang JR. 2020. Increasing cytomegalovirus detection rate from respiratory tract specimens by a new laboratory-developed automated molecular diagnostic test. Microorganisms 8:1063. doi: 10.3390/microorganisms8071063 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 4. Griffiths P, Reeves M. 2021. Pathogenesis of human cytomegalovirus in the immunocompromised host. Nat Rev Microbiol 19:759–773. doi: 10.1038/s41579-021-00582-z [DOI] [PMC free article] [PubMed] [Google Scholar]
- 5. Barroso Hernández S, Rodríguez Sabillón JA, Álvarez López Á, García de Vinuesa Calvo E, Calvo Cano A, Robles Pérez-Monteoliva NR. 2023. Enfermedad por citomegalovirus en los pacientes inmunodeprimidos por glomerulonefritis necrosante pauciinmune. Medicina Clínica 160:199–202. doi: 10.1016/j.medcli.2022.07.009 [DOI] [PubMed] [Google Scholar]
- 6. Giorgione V, Krajden Haratz K, Gull I, Brusilov M, Birnbaum R, Blecher Y, Malinger G, Kaplan A, Beer G, Kapusta L. 2023. Myocardial function in fetuses with congenital cytomegalovirus infection. Fetal Diagn Ther 50:430–437. doi: 10.1159/000533280 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 7. Ozdemir E, Sarac Sivrikoz T, Sarsar K, Tureli D, Onel M, Demirci M, Yapar G, Yurtseven E, Has R, Agacfidan A, Kirkoyun Uysal H. 2024. Evaluation of congenital cytomegalovirus infection in pregnant women admitted to a university hospital in Istanbul. Viruses 16:414. doi: 10.3390/v16030414 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 8. National Center for Biotechnology Information . 2025.. NCBI virus sequences for discorevy. Available from: https://www.ncbi.nlm.nih.gov/labs/virus/vssi/#/virus?SeqType_s=Nucleotide&VirusLineage_ss=Human%20betaherpesvirus%205,%20taxid:10359&utm_source=nuccore&utm_medium=referral
- 9. Chen S, Zhou Y, Chen Y, Gu J. 2018. Fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics 34:i884–i890. doi: 10.1093/bioinformatics/bty560 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 10. Li D, Luo R, Liu C-M, Leung C-M, Ting H-F, Sadakane K, Yamashita H, Lam T-W. 2016. MEGAHIT v1.0: A fast and scalable metagenome assembler driven by advanced methodologies and community practices. Methods 102:3–11. doi: 10.1016/j.ymeth.2016.02.020 [DOI] [PubMed] [Google Scholar]
- 11. Wood DE, Lu J, Langmead B. 2019. Improved metagenomic analysis with Kraken 2. Genome Biol 20:257. doi: 10.1186/s13059-019-1891-0 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 12. Breitwieser FP, Salzberg SL. 2020. Pavian: interactive analysis of metagenomics data for microbiome studies and pathogen identification. Bioinformatics 36:1303–1304. doi: 10.1093/bioinformatics/btz715 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 13. Kearse M, Moir R, Wilson A, Stones-Havas S, Cheung M, Sturrock S, Buxton S, Cooper A, Markowitz S, Duran C, Thierer T, Ashton B, Meintjes P, Drummond A. 2012. Geneious Basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics 28:1647–1649. doi: 10.1093/bioinformatics/bts199 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 14. Katoh K, Standley DM. 2013. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol 30:772–780. doi: 10.1093/molbev/mst010 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 15. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. 1990. Basic local alignment search tool. J Mol Biol 215:403–410. doi: 10.1016/S0022-2836(05)80360-2 [DOI] [PubMed] [Google Scholar]
- 16. Heinonen S, Velazquez VM, Ye F, Mertz S, Acero-Bedoya S, Smith B, Bunsow E, Garcia-Mauriño C, Oliva S, Cohen DM, Moore-Clingenpeel M, Peeples ME, Ramilo O, Mejias A. 2020. Immune profiles provide insights into respiratory syncytial virus disease severity in young children. Sci Transl Med 12:eaaw0268. doi: 10.1126/scitranslmed.aaw0268 [DOI] [PubMed] [Google Scholar]
Associated Data
This section collects any data citations, data availability statements, or supplementary materials included in this article.
Data Availability Statement
The whole genome sequencing project of sample BR/2023-012844/IEC/NS/2023 was deposited in GenBank under accession number PX246278. The accession number for the raw shotgun metagenomic sequencing reads in the NCBI Sequence Read Archive is SRR35176174. This data set is associated with BioProject accession number PRJNA1312120 and BioSample accession number SAMN50854041 (2023-012844/IEC).