Virus World

A U.S. House of Representatives panel yesterday released evidence that a Chinese research team submitted a SARS-CoV-2 genome to a U.S. database on 28 December 2019, nearly 2 weeks before a sequence from another group became public and kick-started the race to develop vaccines and drugs for COVID-19. The revelation, first reported by The Wall Street Journal, renewed allegations that Chinese officials tried to cover up early sequences of the new coronavirus. Lawmakers said the new information also raises the question of whether the U.S. National Institutes of Health’s (NIH’s) GenBank database should somehow flag submissions of pathogen sequences with urgent public health importance. The agency had marked the researcher’s submission as incomplete and deleted the sequence before it became public. The never-completed GenBank submission was “a huge missed opportunity” to start developing drugs, diagnostics, and vaccines earlier, agrees virologist Jeremy Kamil of Louisiana State University Health Shreveport.

The first draft genome sequence of monkeypox virus, taken from a swab of a confirmed case of the current outbreak, was sequenced and released online.   On May 19, a research group led by João Paulo Gomes, PhD, a researcher from the department of infectious diseases, National Institute of Health Doutor Ricardo Jorge (INSA), in Lisbon, Portugal, posted the sequence online on virological.org. There are currently almost 200 (confirmed and suspected) cases of monkeypox associated with the recent outbreak across the world.  The authors write that, “The determination of the genome sequence of the virus causing these infections will certainly contribute to better understand the epidemiology, sources of infection, and transmission patterns.” The work was celebrated by the scientific community almost immediately after being posted, including Trevor Bedford, PhD, a professor of biostatistics, bioinformatics, and epidemiology program in the vaccine and infectious disease division at the Fred Hutch. The first draft sequence of SARS-CoV-2 was made available in a similar fashion. On January 10, 2020, Eddie Holmes, PhD, a virologist and evolutionary biologist at the University of Sydney, tweeted that the first draft sequence of “the coronavirus associated with the Wuhan outbreak” had been posted. Like the monkeypox sequence, it took only weeks to produce the data and post it online. The SARS-CoV-2 sequence was made possible through the work of Yong-Zhen Zhang, PhD, a virologist at Shanghai’s Fudan University.

Monkeypox virus is an enveloped double‐stranded DNA virus with a genome size of around 190 kb. It belongs to the Orthopoxvirus genus of the Poxviridae family. The paper posted on www.virological.org is the first draft genome sequence of the monkeypox virus associated with the major outbreak affecting multiple countries worldwide. The virus, taken from a swab collected on May 4 from skin lesions from a patient, was sequenced using the Oxford Nanopore MinION. The team then quickly performed phylogenetic analysis of the virus. In doing so, they found that the 2022 virus belongs to the West African clade. Indeed, the West African clade has now been confirmed in at least six of the cases in the recent outbreak. There are two clades of monkeypox virus: the West African clade and the Congo Basin (Central African) clade. The West African clade of monkeypox virus infection—which has a lower case fatality ratio (roughly 1%) than the Congo Basin clade (up to 10%)—can lead to severe illness in some individuals.

However, the disease typically resolves.  The phylogenetic analysis also suggests that the virus circulating in the outbreak is most closely related to viruses associated with the exportation of monkeypox virus from Nigeria to several countries—the United Kingdom, Israel, and Singapore—in 2018 and 2019. The findings sparked the interest of Tulio de Oliveira, PhD, professor at Stellenbosch University, Western Cape, South Africa and director of the Centre for Epidemic Response & Innovation (CERI), and the KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP). The authors noted that these data are preliminary, and “will be soon updated upon the release of new genome data.” They also said that these future additions will be important to elucidate the origin and international spread of the currently circulating virus.

Sequence of monkeypox isolate available at Virological:

https://virological.org/t/first-draft-genome-sequence-of-monkeypox-virus-associated-with-the-suspected-multi-country-outbreak-may-2022-confirmed-case-in-portugal/799