Public distrust has undermined COVID-19 vaccine acceptance and has become a major public health issue in the battle against SARS-CoV-2 transmission globally. Here we present the first evidence that the vaccination coverage rate is inversely correlated to the mutation frequency of the SARS-CoV-2 delta variant in 16 countries (R²=0.878), strongly indicating that full vaccination against COVID-19 is critical to suppress emergent mutations. We also present a promising tool to forecast new COVID-19 outbreaks. The Tajima’s D test, an evolutionary algorithm, with a threshold value of -2.50 is shown to be an accurate predictor of new outbreaks. We recommend that universal vaccination, as well as mitigation strategies, and genomic surveillance continue to be employed to prevent further viral transmission.

Cardiovascular toxicity has emerged as the leading cause of death in patients undergoing cancer treatment. Thus, cardio-oncology (CO) care must also focus on the prevention and management of related cardiovascular (CV) complications caused by cancer therapy. Neutrophil extracellular traps (NETs)—entities with released DNA, proteases, proinflammatory and prooxidative substances from blasted neutrophils—play an important role in cancer proliferation, propagation metastasis, and incident CV events (acute coronary syndrome, thromboembolic events, and heart failure). Although NETs have been shown to be involved in cancer progression and incident CV events, little is known about their relationship with cardio-oncology, especially on cancer treatment-related cardiovascular toxicity (CTRCT). This review aims to explore the evidence of the impact of NETs on cancer, CV events, and CTRCT, and the possible solutions based on the mechanism of NETs activation and NETs released toxic substances.

On 26 November 2021, the World Health Organization designated the SARS-CoV-2 variant B.1.1.529, Omicron, a variant of concern. However, the phylogenetic and evolutionary dynamics of this variant remain unclear. An analysis of the 131 Omicron variant sequences from November 9 to November 28, 2021 reveals that variants have diverged into at least 6 major subgroups. 86.3% of the cases have an insertion at amino acid 214 (INS214EPE) of the spike protein. Neutrality analysis of DH (−2.814, p <0.001) and Zeng’s E (0.0583, p =1.0) tests suggested that directional selection was the major driving force of Omicron variant evolution. The synonymous ( D _syn ) and nonsynonymous ( D _nonsyn ) polymorphisms of the Omicron variant spike gene were estimated with Tajima’s D statistic to eliminate homogenous effects. Both D ratio ( D _nonsyn / D _syn , 1.57) and Δ D ( D _syn - D _nonsyn , 0.63) indicate that purifying selection operates at present. The low nucleotide diversity (0.00008) and Tajima D value (−2.709, p <0.001) also confirms that Omicron variants had already spread in human population for more than the 6 weeks than has been reported. These results, along with our previous analysis of Delta and Lambda variants, also supports the validity of the Tajima’s D test score, with a threshold value as −2.50, as an accurate predictor of new COVID-19 outbreaks.

Unlike Ff, the packaging signal (PS) and the mechanism of integrative filamentous phage assembly remain largely unknown. Here we revived two Inoviridae prophage sequences, ϕLf2 and ϕLf-UK, as infectious virions lysogenize black rot pathogen Xanthomonas campestris pv. campestris . ϕLf2 and ϕLf-UK genomes consist of 6,363 and 6,062 nucleotides and share 85.8% and 98.7% identity with ϕLf, respectively. To explore their assembly, we first identified 20-26– nucleotide long PS sequences of 10 Xanthomonas phages. These PS consist of a DNA hairpin with the consensus GGX(A/-)CCG(C/T)G sequence in the stem and C/T nucleotides in the loop, both of which are conserved and essential for PS activity. In contrast to Ff, the 5’ to 3‘ orientation of PS sequence is not conserved or critical for their competence. This is the first report to offer insights into the structure and function of integrative phage PS, revealing the diversity of filamentous phage encapsidation.

Here we report the first evidence of recombination of monkeypox genome in natural transmission by analyzing six tandem repeats (TRs) among 415 sequences collected between January to July 2022. The 2022 monkeypox viral population has diverged into 11 subgroups based on various TRs and their copy numbers. Here we identify 8 new recombinants (six from Slovenia, one from Australia, one from Italy). Our results indicate that the monkeypox genome is evolving and expanding quickly during the 2022 pandemic (Zeng’s E = -1.65, Achaz’s Y=-2.52, p< 0.001). We conclude that, In combination with genomic surveillance, TR analysis is a useful tool to monitor and track phylogenetic dynamics of monkeypox transmission.

Viral recombination can rapidly generate new variants and influence outbreak severity. Currently, a method to track viral recombination events at high genomic resolution during natural transmission remains unavailable. Here we describe a novel linkage disequilibrium method and the first report of viral recombination events over time by using single nucleotide polymorphisms (SNPs) as natural genetic markers. Combined with phylogenetic data, we analyzed mpox virus (MPXV) Ib genome during 2023-2025 outbreak and found that 71 recombination events among Ib genomes, yielding a recombination frequency (Rf) and rate of 0.16%/kbp and 0.11%/kbp/year, respectively. Phylogenetic time analysis also shows that recombination began as early as December 23, 2023. Rf of MPXV Ib is 8.8-fold lower compared to vaccinia virus (1.5%/kbp) in vitro . Recombination and linkage hotspots are enriched at both inverted terminal repeat and variable regions of MPXV Ib genome. Our data not only reports the first Rf and rate of natural human transmission in the poxvirus family but also provides a powerful genomic surveillance tool for better understanding transmission and evolution of any viral outbreak globally.