Abstract
Phylogenetic analysis of 34 monkeypox virus genome sequences isolated from patients in Minas Gerais, Brazil, revealed initial importation events in early June 2022, then community transmission within the state. All generated genomes belonged to the B.1 lineage responsible for a global mpox outbreak. These findings can inform public health measures.
Keywords: Monkeypox virus, mpox, viruses, zoonoses, sexually transmitted diseases, genomic surveillance, Minas Gerais, Brazil
Human mpox (formerly monkeypox) is an emerging zoonotic disease caused by monkeypox virus (MPXV) (1,2). Since the 1970s, mpox outbreaks in humans have occurred sporadically, mainly in Africa (3). In early May 2022, mpox emerged worldwide, and case numbers increased substantially (4). On July 23, 2022, the World Health Organization (WHO) declared the mpox outbreak a Public Health Emergency of International Concern (5).
Genomic surveillance might be considered a fundamental approach to tracking circulating strains and investigating viral spread (6–8). By October 2022, Brazil had reported 12,378 mpox cases, and the state of Minas Gerais, located in southeast Brazil, reported a total of 838 cases through epidemiologic week 41 (9).
We selected 34 human MPXV-positive samples collected in Minas Gerais during June–September 2022 for whole-genome sequencing at the Central Laboratory of Public Health of Minas Gerais. The selected samples had cycle threshold values <30 and available epidemiologic patient data. The study was approved by the research ethics committee of the Ezequiel Dias Foundation (approval no. 62702222.6.0000.9507).
We extracted viral DNA from lesion exudate and sequenced with the Ion Torrent PGM platform (Thermo Fisher Scientific, https://www.thermofisher.com) using a set of MPXV-specific primers designed for this study by using the primalscheme platform version 1.3.2 (https://pypi.org/project/primalscheme) (Appendix Table 1). We used the MPXV reference genome (GenBank accession no. NC_063383.1) to perform genome assembly by using Burrows-Wheeler Aligner version 0.7.17 (https://github.com/lh3/bwa), SAMtools version 1.11 (https://github.com/samtools), and iVar version 1.0 (https://github.com/andersen-lab/ivar). We used Nextclade version 2.8.1 (Nextstrain, https://clades.nextstrain.org) to assess genome quality and classification.
We used MAFFT version 7.310 (https://mafft.cbrc.jp) to align the 34 genomes obtained from this study with an additional 218 MPXV genomes collected from GISAID (https://www.gisaid.org) until October 3, 2022 (Appendix Table 2). We used BEAST version 1.10.4 (https://beast.community) to infer the Bayesian phylogeny. The Brazilian Ministry of Health Notifiable Diseases Information System provided weekly notified cases of MPXV infection in Minas Gerais.
Epidemiologic data revealed that the highest number (n = 112) of MPXV cases in Minas Gerais were reported during epidemiologic week 31 (Appendix Figure 1). The data also highlight that the metropolitan region of Belo Horizonte had the highest concentration (n = 608) of confirmed cases during June–September (Appendix Figure 2).
Using patients’ clinical records, we found that 55.9% (19/34) were HIV-positive and 23.5% (8/34) reported active sexually transmitted infection. Among the screened samples, 33 were from male patients and 1 was from a female patient; patients were 22–46 (mean 32.5) years of age. The most frequent signs and symptoms were rash (34/34, 100%), lymphadenopathy (22/34, 64.7%), and fever (21/34, 61.8%) (Appendix Figure 3). Among mpox patients, 17 reported no travel history, 15 reported travel history to the state of São Paulo, Brazil, and 1 each reported travel to London and to Portugal.
Using the Ion Torrent PGM platform, we obtained a total number of 34 MPXV genome sequences. Genome coverage was 76.2%–97.5% (mean 87%) and had an average depth of 391× (Table). All the genomes generated in this study belonged to lineages B.1 (n = 13), B.1.1 (n = 19), B.1.2 (n = 1), and B.1.9 (n = 1), which are lineages responsible for the 2022 outbreak (7,8).
Table. Summary statistics of assembled genomes from genomic surveillance of monkeypox virus, Minas Gerais, Brazil, 2022*.
| Sample ID | Collection date | Mapped reads | Mean read depth | Coverage, % | Lineage | GISAID ID |
|---|---|---|---|---|---|---|
| 311257928† | 2022 Jun 28 | 241,791 | 208.5 | 90.3 | B.1 | EPI_ISL_13780332 |
| 311261010 | 2022 Jul 1 | 520,016 | 473.6 | 86.5 | B.1.1 | EPI_ISL_16650224 |
| 311261273 | 2022 Jul 1 | 478,258 | 447.8 | 90.7 | B.1 | EPI_ISL_16650225 |
| 311261816 | 2022 Jul 4 | 318,530 | 244.3 | 84.9 | B.1 | EPI_ISL_16650230 |
| 311261841 | 2022 Jul 4 | 388,417 | 347.0 | 93.5 | B.1 | EPI_ISL_16650229 |
| 311262116‡ | 2022 Jul 4 | 334,589 | 234.4 | 83.3 | B.1 | EPI_ISL_16650231 |
| 311262133 | 2022 Jul 4 | 362,965 | 331.9 | 85.3 | B.1.1 | EPI_ISL_16650228 |
| 311262224 | 2022 Jul 4 | 449,397 | 420.0 | 91.4 | B.1 | EPI_ISL_16650226 |
| 311262265 | 2022 Jul 4 | 427,206 | 399.6 | 93.6 | B.1.1 | EPI_ISL_16650227 |
| 311262687 | 2022 Jul 5 | 353,768 | 282.2 | 76.2 | B.1.1 | EPI_ISL_16650233 |
| 311262723 | 2022 Jul 5 | 342,256 | 266.3 | 81.8 | B.1 | EPI_ISL_16650234 |
| 311263370 | 2022 Jul 5 | 388,951 | 308.5 | 80.5 | B.1.1 | EPI_ISL_16650232 |
| 311265338 | 2022 Jul 5 | 344,341 | 299.7 | 82.5 | B.1.1 | EPI_ISL_16650238 |
| 311263885 | 2022 Jul 6 | 296,827 | 256.8 | 78.4 | B.1 | EPI_ISL_16650236 |
| 311263902 | 2022 Jul 6 | 394,450 | 332.8 | 79.2 | B.1.1 | EPI_ISL_16650235 |
| 311264859 | 2022 Jul 7 | 393,675 | 342.8 | 81.0 | B.1.1 | EPI_ISL_16650237 |
| 311266133 | 2022 Jul 8 | 345,305 | 290.7 | 79.1 | B.1.1 | EPI_ISL_16650239 |
| 311266186 | 2022 Jul 8 | 354,920 | 274.4 | 87.8 | B.1 | EPI_ISL_16650240 |
| 311266233 | 2022 Jul 8 | 284,916 | 239.2 | 82.9 | B.1.1 | EPI_ISL_16650241 |
| 311266796 | 2022 Jul 11 | 384,836 | 358.5 | 82.2 | B.1.9 | EPI_ISL_16650243 |
| 311267285 | 2022 Jul 11 | 351,311 | 325.0 | 79.4 | B.1.1 | EPI_ISL_16650242 |
| 311267311 | 2022 Jul 11 | 341,773 | 320.4 | 81.0 | B.1.1 | EPI_ISL_16650244 |
| 311267938 | 2022 Jul 12 | 330,526 | 300.1 | 77.1 | B.1.1 | EPI_ISL_16650245 |
| 311271087§ | 2022 Jul 15 | 581,432 | 594.2 | 97.5 | B.1.1 | EPI_ISL_16650246 |
| 311283035 | 2022 Aug 5 | 590,550 | 584.0 | 96.3 | B.1 | EPI_ISL_16650248 |
| 311287351 | 2022 Aug 12 | 565,565 | 557.1 | 96.5 | B.1.1 | EPI_ISL_16650247 |
| 311288391 | 2022 Aug 15 | 533,148 | 528.6 | 97.1 | B.1.1 | EPI_ISL_16650249 |
| 311291580 | 2022 Aug 22 | 520,820 | 554.3 | 91.7 | B.1 | EPI_ISL_16650262 |
| 311294876 | 2022 Aug 26 | 567,700 | 528.8 | 97.0 | B.1 | EPI_ISL_16650251 |
| 311297067 | 2022 Aug 31 | 539,498 | 454.0 | 94.7 | B.1.2 | EPI_ISL_16650253 |
| 311300630 | 2022 Sep 8 | 532,582 | 549.0 | 88.9 | B.1.1 | EPI_ISL_16650258 |
| 311300699 | 2022 Sep 8 | 476,181 | 514.3 | 82.5 | B.1 | EPI_ISL_16650255 |
| 311303564 | 2022 Sep 13 | 533,191 | 563.8 | 95.9 | B.1.1 | EPI_ISL_16650260 |
| 311309205 | 2022 Sep 26 | 546,501 | 564.2 | 92.9 | B.1.1 | EPI_ISL_16650265 |
*Genome assembly performed by using Burrows-Wheeler Aligner version 0.7.17 (https://github.com/lh3/bwa) and iVar version 1.0 (https://github.com/andersen-lab/ivar) pipeline and lineage ID was assigned to each genome by using Nextclade version 2.8.1 (Nextstrain, https://clades.nextstrain.org). GISAID, https://www.gisaid.org. ID, identification. †First confirmed mpox case in Minas Gerais; patient had travel history to London, UK. ‡Patient had travel history to Portugal and São Paulo, Brazil. §First mpox death reported in Minas Gerais.
Our phylogenetic reconstruction revealed that all genomes from the 2022 mpox outbreak grouped together (Figure). Most of the genomes we obtained from Minas Gerais grouped with MPXV genomes isolated from other regions of Brazil (Figure). Our phylogenetic reconstruction revealed that the first mpox case reported in Minas Gerais, isolated from a patient with a travel history to London, UK (GISAID accession no. EPI_ISL_13780332), grouped with a genome sequence from the United Kingdom (GISAID accession no. EPI_ISL_14439774).
Figure.
Bayesian phylogenetic tree of 34 genome sequences generated during genomic surveillance of monkeypox virus, Minas Gerais, Brazil, 2022. The tree also includes 218 reference strains available at GISAID (https://www.gisaid.org), accessed October 3, 2022. Colors represent different sampling locations. Posterior probability support is shown at key nodes for clade I, IIa, and IIb. Scale bar indicates nucleotide substitutions per site.
We also sequenced a sample from the first confirmed mpox death in Brazil, which was reported in late July 2022. That sample was collected from a patient who resided in Minas Gerais and was in treatment for diffuse large B-cell lymphoma and HIV (10). The genome from that patient’s sample belonged to the B.1.1 lineage, and in our phylogenetic reconstruction, it clustered with genome sequences isolated from Minas Gerais and from other states in Brazil.
Overall, our data revealed that an mpox case detected in Minas Gerais in early 2022 was related to a likely importation event, probably associated with a traveler returning from the United Kingdom, and then sustained MPXV community transmission. The first confirmed death reported in Minas Gerais was associated with a local MPXV infection described in a patient who reported several underlying conditions. These results contribute to genomic MPXV surveillance in Minas Gerais and increase the number of genome sequences from this virus available in GISAID. These findings and the available data can help future studies aiming to improve diagnostic protocols and vaccine development.
Additional information on genomic surveillance of monkeypox virus, Minas Gerais, Brazil.
Acknowledgments
We thank all authors who have kindly deposited and shared genome data on GISAID (Appendix Table 2).
This study was financed by the Central Public Health Laboratory of Minas Gerais (Ezequiel Dias Foundation), the Brazilian Ministry of Health (grant no. SCON2021-00180), Pan American Health Organization PAHO/WHO and the National Institutes of Health (grant no. U01 AI151698) for the United World Arbovirus Research Network (UWARN). M.G. is funded by PON Ricerca e Innovazione (Research and Innovation) 2014-2020. Laboratório de Vírus and CT-Vacinas received funding from the Ministry of Science, Technology and Innovation, Brazil. G.d.S.T. is a researcher with the National Council for Scientific and Technological Development (CNPq), Brazil.
Biography
Dr. Guimarães is a research scientist and analyst at the Ezequiel Dias Foundation. Her research interests and work include the molecular diagnosis and sequencing of SARS-CoV-2, monkeypox virus, and arboviruses, including dengue, Zika, chikungunya, and yellow fever viruses, and other pathogens of importance to public health.
Footnotes
Suggested citation for this article: Guimarães NR, Tomé LMR, Lamounier LO, Silva MVF, Lima MT, da Costa AVB, et al. Genomic surveillance of monkeypox virus, Minas Gerais, Brazil, 2022. Emerg Infect Dis. 2023 May [date cited]. https://doi.org/10.3201/eid2906.230113
These authors contributed equally to this article.
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Supplementary Materials
Additional information on genomic surveillance of monkeypox virus, Minas Gerais, Brazil.