Genomic Analysis of Early Monkeypox Virus Outbreak Strains, Washington, USA

Roychoudhury, Pavitra; Sereewit, Jaydee; Xie, Hong; Nunley, Ethan; Bakhash, Shah Mohamed; Lieberman, Nicole A P; Greninger, Alexander L.

doi:10.3201/eid2903.221446

Cited by 9 publications

(6 citation statements)

References 10 publications

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“…Post-enrichment, the researchers were even able to verify the clade of MPXV (i.e., clade IIb), which was congruous with previous reports. Over in the West, baits were designed using MPXV 2022/MA001 strain to investigate contemporary outbreaks of mpox infections in the USA by enriching MPXV sequences from clinical samples [ 230 ]. Recovering identical genomes between people, researchers were able to trace ongoing community transmissions, but the low genetic diversity of MPXV hampered contact tracing efforts via whole-genome sequencing.…”

Section: Biosurveillance and Emerging Viral Infectious Diseasesmentioning

confidence: 99%

Hybrid-Capture Target Enrichment in Human Pathogens: Identification, Evolution, Biosurveillance, and Genomic Epidemiology

Quek,

2024

Pathogens

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High-throughput sequencing (HTS) has revolutionised the field of pathogen genomics, enabling the direct recovery of pathogen genomes from clinical and environmental samples. However, pathogen nucleic acids are often overwhelmed by those of the host, requiring deep metagenomic sequencing to recover sufficient sequences for downstream analyses (e.g., identification and genome characterisation). To circumvent this, hybrid-capture target enrichment (HC) is able to enrich pathogen nucleic acids across multiple scales of divergences and taxa, depending on the panel used. In this review, we outline the applications of HC in human pathogens—bacteria, fungi, parasites and viruses—including identification, genomic epidemiology, antimicrobial resistance genotyping, and evolution. Importantly, we explored the applicability of HC to clinical metagenomics, which ultimately requires more work before it is a reliable and accurate tool for clinical diagnosis. Relatedly, the utility of HC was exemplified by COVID-19, which was used as a case study to illustrate the maturity of HC for recovering pathogen sequences. As we unravel the origins of COVID-19, zoonoses remain more relevant than ever. Therefore, the role of HC in biosurveillance studies is also highlighted in this review, which is critical in preparing us for the next pandemic. We also found that while HC is a popular tool to study viruses, it remains underutilised in parasites and fungi and, to a lesser extent, bacteria. Finally, weevaluated the future of HC with respect to bait design in the eukaryotic groups and the prospect of combining HC with long-read HTS.

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Section: Biosurveillance and Emerging Viral Infectious Diseasesmentioning

confidence: 99%

Hybrid-Capture Target Enrichment in Human Pathogens: Identification, Evolution, Biosurveillance, and Genomic Epidemiology

Quek,

2024

Pathogens

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“…1A and B ). In detail, members of the B.1.3 lineage reported in Europe, 9 10 North America, 11 and Far East Asia, 12 a common nonsynonymous mutation G190660A; R84K in the NBT03_gp174 protein was observed. Furthermore, in the Far East Asia continent, including the Republic of Korea, Japan, Taiwan, two common mutations were observed: synonymous mutation C3987T and nonsynonymous mutation G105923A; L16F in the OPG124 protein, according to National Center for Biotechnology Information reference sequence NC_063383 coordinates.…”

mentioning

confidence: 95%

Genomic Analysis of Monkeypox Virus During the 2023 Epidemic in Korea

Choi,

Lee,

Lee

et al. 2024

J Korean Med Sci

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We aimed to characterize the genomes of monkeypox virus isolates from the Far East, providing insights into viral transmission and evolution. Genomic analysis was conducted on 8 isolates obtained from patients with monkeypox virus disease in the Republic of Korea between May 2022 and early 2023. These isolates were classified into Clade IIb. Distinct lineages, including B.1.1, A.2.1, and B.1.3, were observed in 2022 and 2023 isolates, with only the B.1.3 lineage detected in six isolates of 2023. These genetic features were specific to Far East isolates (the Republic of Korea, Japan, and Taiwan), distinguishing them from the diverse lineages found in the Americas, Europe, Africa, and Oceania. In early 2023, the prevalence of the B.1.3 lineage of monkeypox virus identified in six patients with no overseas travel history is considered as an indicator of the potential initiation of local transmission in the Republic of Korea.

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“…To date, multiple studies have applied target capture sequencing for the genome analysis of SARS-CoV-2 (9–16). More recently, a group attempted to sequence the monkey pox virus genome using target capture sequencing (17).…”

Section: Introductionmentioning

confidence: 99%

Direct genome sequencing of respiratory viruses from low viral load clinical specimens using target capture sequencing technology

Takemae,

Kuba,

Oba

et al. 2024

Preprint

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The use of metagenomic next-generation sequencing technology to obtain complete viral genome sequences directly from clinical samples with low viral load remains challenging—especially in the case of respiratory viruses—due to the low copy number of viral versus host genomes. To overcome this limitation, target capture sequencing for the enrichment of specific genomes has been developed and applied for direct genome sequencing of viruses. However, as the efficiency of enrichment varies depending on the probes, the type of clinical sample, etc., validation is essential before target capture sequencing can be applied to clinical diagnostics. Here we evaluated the utility of target capture sequencing with a comprehensive viral probe panel for clinical respiratory specimens collected from patients diagnosed with SARS-CoV-2 or influenza type A. We focused on clinical specimens containing low copy numbers of viral genomes. Target capture sequencing yielded approximately 180- and 2000-fold higher read counts of SARS-CoV-2 and influenza A virus, respectively, than metagenomic sequencing when the RNA extracted from specimens contained 59.3 copies/µL of SARS-CoV-2 or 544 copies/µL of influenza A virus, respectively. In addition, the target capture sequencing identified sequence reads in all SARS-CoV-2- or influenza type A-positive specimens with <26 RNA copies/µL, some of which also yielded >70% of the full-length genomes of SARS-CoV-2 or influenza A virus. Furthermore, the target capture sequencing using comprehensive probes identified co-infections with viruses other than SARS-CoV-2, suggesting that this approach will not only detect a wide range of viruses, but also contribute to epidemiological studies.

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Genomic Analysis of Early Monkeypox Virus Outbreak Strains, Washington, USA

Cited by 9 publications

References 10 publications

Hybrid-Capture Target Enrichment in Human Pathogens: Identification, Evolution, Biosurveillance, and Genomic Epidemiology

Hybrid-Capture Target Enrichment in Human Pathogens: Identification, Evolution, Biosurveillance, and Genomic Epidemiology

Genomic Analysis of Monkeypox Virus During the 2023 Epidemic in Korea

Direct genome sequencing of respiratory viruses from low viral load clinical specimens using target capture sequencing technology

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