Efficient assembly of a large fragment of monkeypox virus genome as a qPCR template using dual-selection based transformation-associated recombination

Assembly of ascovirus HvAV-3h long DNA fragment using the Transformation-Associated Recombination (TAR) approach in yeast cells

BACKGROUND

Synthetic biology is a young but rapidly growing field that allows for assembling long DNA fragments, including complete chromosomes. A key approach for long-DNA assembly is the Transformation Associated Recombination (TAR), which relies on efficient homologous recombination in yeast cells. Recent reports indicate that the TAR method efficiently assembles some human and animal viruses characterized by their large DNA genome size. The application of the TAR method to synthesize long DNA fragments derived from insect viruses is scarce. Therefore, this study aimed to explore the TAR approach for the construction of a long DNA fragment (>44.6 Kb) from the insecticidal Heliothesis virescens ascovirus 3h (HvAV-3h) dsDNA genome to assess the suitability of this approach in genome-wide engineering studies in this family of viruses.

RESULTS

The long DNA fragment assembly process involved three stages: first, we amplified 15 segments of about 2.9-3.2 Kb each via PCR. Next, we recombined these segments through three parallel TAR cycles, producing medium-sized fragments of about 15 Kb. Finally, we assembled these fragments in a single TAR cycle to form a long DNA fragment of about 44.6 kb. We identified some positive clones by colony PCR or restriction digestion pattern. To assess the quality of the assembled DNA fragment, we conducted next-generation sequencing (NGS). A comparative analysis of Sanger sequencing for medium-sized fragments and NGS data from the synthesized long-DNA fragment demonstrated a nearly matched mutation profile, suggesting that the identified mutations and deletions were present at initial synthesis. Both datasets aligned with the reference HvAV-3h strain, revealing three specific nucleotide mutations and three unique mutation regions.

CONCLUSIONS

Overall, the in vivo TAR assembly method efficiently assembled a long DNA fragment derived from the ascovirus genome as a template. The process is cost-effective and can be scaled up to synthesize the entire genome for gene functional studies.

Development of viral infectious clones and their applications based on yeast and bacterial artificial chromosome platforms

Infectious Clones represent a foundational technique in the field of reverse genetics, allowing for the construction and manipulation of full-length viral genomes. The main methods currently used for constructing viral infectious clones include Transformation-associated recombination (TAR), which is based on Yeast Artificial Chromosome (YAC) and Bacterial Artificial Chromosome (BAC). The YAC and BAC systems are powerful tools that enable the clones and manipulation of large DNA fragments, making them well-suited for the construction of full-length viral genomes. These methods have been successfully applied to construct infectious clones for a wide range of viruses, including coronaviruses, herpesviruses, flaviviruses and baculoviruses. The rescued recombinant viruses from these infectious clones have been widely used in various research areas, such as vaccine development, antiviral drug screening, pathogenesis and virulence studies, gene therapy and vector design. However, as different viruses possess unique biological characteristics, the challenge remains in how to rapidly obtain infectious clones for future research. In summary, this review introduced the development and applications of infectious clones, with a focus on the YAC, BAC and combined YAC-BAC technologies. We emphasize the importance of these platforms in various research areas and aim to provide deeper insights that can advance the platform and broaden its application horizons.

Drupacine as a potent SARS-CoV-2 replication inhibitor in vitro

Despite the availability of vaccines and antiviral treatments, the continued emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants and breakthrough infections underscores the need for new, potent antiviral therapies. In a previous study, we established a transcription and replication-competent SARS-CoV-2 virus-like particle (trVLP) system that recapitulates the complete viral life cycle. In this study, we combined high-content screening (HCS) with the SARS-CoV-2 trVLP cell culture system, providing a powerful phenotype-oriented approach to assess the antiviral potential of compounds on a large scale. We screened a library of 3,200 natural compounds and identified drupacine as a potential candidate against SARS-CoV-2 infection. Furthermore, we utilized a SARS-CoV-2 replicon system to demonstrate that drupacine could inhibit viral genome transcription and replication. However, in vitro, enzymatic assays revealed that the inhibition could not be attributed to conventional antiviral targets, such as the viral non-structural proteins nsp5 (MPro) or nsp12 (RdRp). In conclusion, our findings position drupacine as a promising antiviral candidate against SARS-CoV-2, providing a novel scaffold for developing anti-coronavirus disease 2019 therapeutics. Further investigation is required to pinpoint its precise target and mechanism of action.

Development of a multiplex real-time PCR assay for the simultaneous detection of mpox virus and orthopoxvirus infections

Since May 2022, the multi-country outbreak of monkeypox (mpox) has raised a great concern worldwide. Early detection of mpox virus infection is recognized as an efficient way to prevent mpox transmission. Mpox specific detection methods reported up to now are based on the SNPs among mpox virus and other orthopoxviruses. We have therefore developed a real-time PCR based mpox detection method targeting mpox virus specific sequences (N3R and B18Rplus). We have also optimized an orthopoxvirus detection system which targets the highly conserved E9L and D6R genes. The mpox and orthopoxvirus real-time PCR assays have a high sensitivity (1 copy/reaction) and specificity. Mpox viral DNA and clinical samples from mpox patients are detected with the mpox detection system. Furthermore, we have established a multiplex real-time PCR detection system allowing simultaneous and efficient detection of mpox and orthopoxvirus infections.

A review on insights and lessons from COVID-19 to the prevent of monkeypox pandemic

Re-emerging of monkeypox virus (MPXV), a neglected viral zoonotic disease, is a potential global threat. In the current COVID-19 pandemic status, the increasing reporting of positive cases of human MPXV in most countries of the world is a major reason for concern. This paper aims to describe the insights and lessons from COVID-19 pandemic in preventing the impending danger MPXV. In order to prevent further outbreak of disease, identify and control of MPXV transmission routes is necessary. Public health authorities should be vigilant and applied of effective strategies to mitigate the potential spread of MPXV. To address research gaps related to MPX outbreaks, national, regional, and international collaborations are required in time. Finally, the lessons and insights put forward point to the fact that, like the COVID-19 pandemic, people's health by and large depends on the decisions of government officials and people must continue to adhere to health principles. Hence, governments and policymakers must take appropriate precautionary measures to prevent similar crises like COVID-19 in the world.

Monkeypox: An Update on Current Knowledge and Research Advances

The resurgence of the disease in humans that is very similar to smallpox called monkeypox (MPX) disease, caused by the monkeypox virus (MPXV), is the dominant topic of discussion in the scientific and popular press around the world right now. This is taking place as the world celebrates the historic accomplishments made in the fight against the Coronavirus Disease (COVID-19) pandemic MPX is currently thought to pose a risk to the general public's health, particularly in areas with high rates of MPXV infection and close human-wild animal contact. Despite the rarity of MPX outbreaks, they are often caused by human-to-human transmission, especially in households and healthcare settings. Recent decades have seen recurrent outbreaks of the MPX after the smallpox disease was declared eliminated and the consequent cessation of smallpox vaccination programs. MPX has presently spread to several countries throughout the world and posed a global public health emergency, with nearly 45000 confirmed cases in 96 countries and locations, and 12 deaths as of August 24, 2022. Even though this viral illness is thought to be self-limiting, its consequences and feasible pandemic potential seriously jeopardize public health. The main approach to avoiding MPX is to adopt appropriate prevention and control measures, increase awareness of risk factors, and inform the public of the steps they may take to reduce viral exposure. Scientific studies are currently looking at the viability and suitability of the MPX vaccination. This article presents a general introduction to MPXV / MPX along with progress in diagnosis, treatment, vaccination, and prevention and control strategies for tackling this global health emergency.