Intra-Host Co-Existing Strains of SARS-CoV-2 Reference Genome Uncovered by Exhaustive Computational Search.

The COVID-19 pandemic caused by SARS-CoV-2 has had a severe impact on people worldwide. The reference genome of the virus has been widely used as a template for designing mRNA vaccines to combat the disease. In this study, we present a computational method aimed at identifying co-existing intra-host strains of the virus from RNA-sequencing data of short reads that were used to assemble the original reference genome. Our method consisted of five key steps: extraction of relevant reads, error correction for the reads, identification of within-host diversity, phylogenetic study, and protein binding affinity analysis. Our study revealed that multiple strains of SARS-CoV-2 can coexist in both the viral sample used to produce the reference sequence and a wastewater sample from California. Additionally, our workflow demonstrated its capability to identify within-host diversity in foot-and-mouth disease virus (FMDV). Through our research, we were able to shed light on the binding affinity and phylogenetic relationships of these strains with the published SARS-CoV-2 reference genome, SARS-CoV, variants of concern (VOC) of SARS-CoV-2, and some closely related coronaviruses. These insights have important implications for future research efforts aimed at identifying within-host diversity, understanding the evolution and spread of these viruses, as well as the development of effective treatments and vaccines against them.

Key mutations on spike protein altering ACE2 receptor utilization and potentially expanding host range of emerging SARS-CoV-2 variants.

Increasing evidence supports inter-species transmission of SARS-CoV-2 variants from humans to domestic or wild animals during the ongoing COVID-19 pandemic, which is posing great challenges to epidemic control. Clarifying the host range of emerging SARS-CoV-2 variants will provide instructive information for the containment of viral spillover. The spike protein (S) of SARS-CoV-2 is the key determinant of receptor utilization, and therefore amino acid mutations on S will probably alter viral host range. Here, to evaluate the impact of S mutations, we tested 27 pseudoviruses of SARS-CoV-2 carrying different spike mutants by infecting Hela cells expressing different angiotensin-converting enzyme 2 (ACE2) orthologs from 20 animals. Of these 27 pseudoviruses, 20 bear single mutation and the other 7 were cloned from emerging SARS-CoV-2 variants, including D614G, Alpha (B.1.1.7), Beta (B.1.351), Gamma (P.1), Delta (B.1.617.2), Lambda (B.1.429), and Mu (B.1.621). Using pseudoviral reporter assay, we identified that the substitutions of T478I and N501Y enabled the pseudovirus to utilize chicken ACE2, indicating potential infectivity to avian species. Furthermore, the S mutants of real SARS-CoV-2 variants comprising N501Y showed significantly acquired abilities to infect cells expressing mouse ACE2, indicating a critical role of N501Y in expanding SARS-CoV-2 host range. In addition, A262S and T478I significantly enhanced the utilization of various mammal ACE2. In summary, our results indicated that T478I and N501Y substitutions were two S mutations important for receptor adaption of SARS-CoV-2, potentially contributing to the spillover of the virus to many other animal hosts. Therefore, more attention should be paid to SARS-CoV-2 variants with these two mutations.

Density-based detection of cell transition states to construct disparate and bifurcating trajectories.

Tree- and linear-shaped cell differentiation trajectories have been widely observed in developmental biologies and can be also inferred through computational methods from single-cell RNA-sequencing datasets. However, trajectories with complicated topologies such as loops, disparate lineages and bifurcating hierarchy remain difficult to infer accurately. Here, we introduce a density-based trajectory inference method capable of constructing diverse shapes of topological patterns including the most intriguing bifurcations. The novelty of our method is a step to exploit overlapping probability distributions to identify transition states of cells for determining connectability between cell clusters, and another step to infer a stable trajectory through a base-topology guided iterative fitting. Our method precisely re-constructed various benchmark reference trajectories. As a case study to demonstrate practical usefulness, our method was tested on single-cell RNA sequencing profiles of blood cells of SARS-CoV-2-infected patients. We not only re-discovered the linear trajectory bridging the transition from IgM plasmablast cells to developing neutrophils, and also found a previously-undiscovered lineage which can be rigorously supported by differentially expressed gene analysis.

Comparative studies on the high-performance compression of SARS-CoV-2 genome collections.

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is fast mutating worldwide. The mutated strains have been timely sequenced by worldwide labs, accumulating a huge amount of viral genome sequences open to public for biomedicine research such as mRNA vaccine design and drug recommendation. It is inefficient to transmit the millions of genome sequences without compression. In this study, we benchmark the performance of reference-free and reference-based compression algorithms on SARS-CoV-2 genome collections extracted from NCBI. Experimental results show that reference-based two-level compression is the most suitable approach to the compression, achieving the best compression ratio 1019.33-fold for compressing 132 372 genomes and 949.73-fold for compressing 416 238 genomes. This enormous file size reduction and efficient decompression have enabled a 5-min download and decompression of $10^5$ SARS-CoV-2 genomes. As compression on datasets containing such big numbers of genomes has been explored seldom before, our comparative analysis of the state-of-the-art compression algorithms provides practical guidance for the selection of compression tools and their parameters such as reference genomes to compress viral genome databases with similar characteristics. We also suggested a genome clustering approach using multiple references for a better compression. It is anticipated that the increased availability of SARS-CoV-2 genome datasets will make biomedicine research more productive.

Innate Immunity Evasion Strategies of Highly Pathogenic Coronaviruses: SARS-CoV, MERS-CoV, and SARS-CoV-2.

In the past two decades, coronavirus (CoV) has emerged frequently in the population. Three CoVs (SARS-CoV, MERS-CoV, SARS-CoV-2) have been identified as highly pathogenic human coronaviruses (HP-hCoVs). Particularly, the ongoing COVID-19 pandemic caused by SARS-CoV-2 warns that HP-hCoVs present a high risk to human health. Like other viruses, HP-hCoVs interact with their host cells in sophisticated manners for infection and pathogenesis. Here, we reviewed the current knowledge about the interference of HP-hCoVs in multiple cellular processes and their impacts on viral infection. HP-hCoVs employed various strategies to suppress and evade from immune response, including shielding viral RNA from recognition by pattern recognition receptors (PRRs), impairing IFN-I production, blocking the downstream pathways of IFN-I, and other evasion strategies. This summary provides a comprehensive view of the interplay between HP-hCoVs and the host cells, which is helpful to understand the mechanism of viral pathogenesis and develop antiviral therapies.

Single-cell multi-omics sequencing: application trends, COVID-19, data analysis issues and prospects.

Single-cell sequencing is a biotechnology to sequence one layer of genomic information for individual cells in a tissue sample. For example, single-cell DNA sequencing is to sequence the DNA from every single cell. Increasing in complexity, single-cell multi-omics sequencing, or single-cell multimodal omics sequencing, is to profile in parallel multiple layers of omics information from a single cell. In practice, single-cell multi-omics sequencing actually detects multiple traits such as DNA, RNA, methylation information and/or protein profiles from the same cell for many individuals in a tissue sample. Multi-omics sequencing has been widely applied to systematically unravel interplay mechanisms of key components and pathways in cell. This survey overviews recent developments in single-cell multi-omics sequencing, and their applications to understand complex diseases in particular the COVID-19 pandemic. We also summarize machine learning and bioinformatics techniques used in the analysis of the intercorrelated multilayer heterogeneous data. We observed that variational inference and graph-based learning are popular approaches, and Seurat V3 is a commonly used tool to transfer the missing variables and labels. We also discussed two intensively studied issues relating to data consistency and diversity and commented on currently cared issues surrounding the error correction of data pairs and data imputation methods. The survey is concluded with some open questions and opportunities for this extraordinary field.

Infectious disease mRNA vaccines and a review on epitope prediction for vaccine design.

Messenger RNA (mRNA) vaccines have recently emerged as a new type of vaccine technology, showing strong potential to combat the COVID-19 pandemic. In addition to SARS-CoV-2 which caused the pandemic, mRNA vaccines have been developed and tested to prevent infectious diseases caused by other viruses such as Zika virus, the dengue virus, the respiratory syncytial virus, influenza H7N9 and Flavivirus. Interestingly, mRNA vaccines may also be useful for preventing non-infectious diseases such as diabetes and cancer. This review summarises the current progresses of mRNA vaccines designed for a range of diseases including COVID-19. As epitope study is a primary component in the in silico design of mRNA vaccines, we also survey on advanced bioinformatics and machine learning algorithms which have been used for epitope prediction, and review on user-friendly software tools available for this purpose. Finally, we discuss some of the unanswered concerns about mRNA vaccines, such as unknown long-term side effects, and present with our perspectives on future developments in this exciting area.

CURRENT TAX READING

[...]only 50 percent of a decline in natural resource revenues is eligible for stabilization, compared with 95 percent for a decline in non-resource revenues. R.B. David Green, Jonathan Rhys Kesselman, and Lindsay Tedds, "Considerations for Basic Income as a Covid-19 Response" (2020) 13:11 SPP Briefing Papers [University of Calgary School of Public Policy] 1-15 (http://dx.doi.org/10.11575/sppp.v13i0.70353) Discussions of basic income have been prominent since the government introduced, in March 2019, the Canada Emergency Response Benefit (CERB) in order to cushion the income shock that befell many workers as businesses shut down because of the COVID-19 lockdown. During the same period, members of the BC expert panel on basic income were in the midst of their research and deliberations about whether a basic income was a suitable policy instrument for the province to use in its poverty reduction strategy. Should it be delivered through the income tax system, like refundable tax credits and the CERB?

The 442th amino acid residue of the spike protein is critical for the adaptation to bat hosts for SARS-related coronaviruses.

Bats carry diverse severe acute respiratory syndrome-related coronaviruses (SARSr-CoVs). The suspected interspecies transmission of SARSr-CoVs from bats to humans has caused two severe CoV pandemics, the SARS pandemic in 2003 and the recent COVID-19 pandemic. The receptor utilization of SARSr-CoV plays the key role in determining the host range and the interspecies transmission ability of the virus. Both SARS-CoV and SARS-CoV-2 use angiotensin-converting enzyme 2 (ACE2) as their receptor. Previous studies showed that WIV1 strain, the first living coronavirus isolated from bat using ACE2 as its receptor, is the prototype of SARS-CoV. The receptor-binding domain (RBD) in the spike protein (S) of SARS-CoV and WIV1 is responsible for ACE2 binding and medicates the viral entry. Comparing to SARS-CoV, WIV1 has three distinct amino acid residues (442, 472, and 487) in its RBD. This study aimed at exploring whether these three residues could alter the receptor utilization of SARSr-CoVs. We replaced the three residues in SARS-CoV (BJ01 strain) S with their counterparts in WIV1 S, and then evaluated the change of their utilization of bat, civet, and human ACE2s using a lentivirus-based pseudovirus infection system. To further validate the S-ACE2 interactions, the binding affinity between the RBDs of these S proteins and the three ACE2s were verified by flow cytometry. The results showed that the single amino acid substitution Y442S in the RBD of BJ01 S enhanced its utilization of bat ACE2 and its binding affinity to bat ACE2. On the contrary, the reverse substitution in WIV1 S (S442Y) significantly attenuated the pseudovirus utilization of bat, civet and human ACE2s for cell entry, and reduced its binding affinity with the three ACE2s. These results suggest that the S442 is critical for WIV1 adapting to bats as its natural hosts. These findings will enhance our understanding of host adaptations and cross-species infections of coronaviruses, contributing to the prediction and prevention of coronavirus epidemics.

CURRENT TAX READING

The United States has introduced the Families First Coronavirus Responses Act (FFCRA), which includes paid sick leave, tax credits for paid sick leave, free COVID-19 testing, and a supplemental nutritional assistance program;and the Coronavirus Aid, Relief, and Economic Security (CARES) Act, which includes a monthly US $1,200 support payment to individuals (known as "recovery rebates"), and COVID-19 -related loss carryback rules for businesses. Because the three priorities may come to be in tension with one another and because these policy decisions must be made during a pandemic, it is necessary to consider innovative and wide-ranging policy solutions. The authors consider that this act's tax relief measures-which include mandatory paid sick leave or family leave for workers, and tax credits for the employers that provide those wages-have responded to the three policy priorities: providing social insurance for workers, preventing widespread market distress and the collapse of many businesses, and encouraging good spatio-behavioural practices. According to the authors of this paper, many Americans may not have filed their 2019 returns, and it is likely that about 15 percent of electronic payments by the IRS went to closed bank accounts or accounts not controlled by the taxpayer.

Coronavirus, Telecommuting, and the 'Employer Convenience' Rule/OECD Secretariat Analysis of Tax Treaties and the Impact of the COVID-19 Crisis

The articles Coronavirus, Telecommuting, and the 'Employer Convenience' Rule by Edward A. Zelinsky and OECD Secretariat Analysis of Tax Treaties and the Impact of the COVID-19 Crisis from the Organization for Economic Co-operation and Development are discussed. During the COVID-19 pandemic, most non-essential workers have been unable to work at their employer's physical premises and have thus become telecommuters, working from home. Cross-border telecommuting raises interjurisdictional tax issues. Zelinsky discusses the implications of New York State income tax for telecommuting employees who are employed in the state while living outside it because of the pandemic.

Receptor utilization of angiotensin-converting enzyme 2 (ACE2) indicates a narrower host range of SARS-CoV-2 than that of SARS-CoV.

Coronavirus (CoV) pandemics have become a huge threat to the public health worldwide in the recent decades. Typically, severe acute respiratory syndrome CoV (SARS-CoV) caused SARS pandemic in 2003 and SARS-CoV-2 caused the ongoing COVID-19 pandemic. Both viruses are most likely originated from bats. Thus, direct or indirect inter-species transmission from bats to humans is required for the viruses to cause pandemics. Receptor utilization is a key factor determining the host range of viruses which is critical to the inter-species transmission. Angiotensin-converting enzyme 2 (ACE2) is the receptor of both SARS-CoV and SARS-CoV-2, but only ACE2s of certain animals can be utilized by the viruses. Here, we employed pseudovirus cell-entry assay to evaluate the receptor-utilizing capability of ACE2s of 20 animals by the two viruses and found that SARS-CoV-2 utilized less ACE2s than SARS-CoV, indicating a narrower host range of SARS-CoV-2. Especially, SARS-CoV-2 tended not to use murine or non-mammal ACE2s. Meanwhile, pangolin-CoV, another SARS-related coronavirus highly homologous to SARS-CoV-2 in its genome, yet showed similar ACE2 utilization profile with SARS-CoV rather than SARS-CoV-2. Nevertheless, the actual susceptibility of these animals to the coronaviruses should be further verified by in vivo studies. To clarify the mechanism underlying the receptor utilization, we compared the amino acid sequences of the 20 ACE2s and found 5 amino acid residues potentially critical for ACE2 utilization, including the N-terminal 20th and 42nd amino acid residues that might determine the different receptor utilization of SARS-CoV, SARS-CoV-2 and pangolin-CoV. Our studies enhance the understanding of receptor utilization of pandemic coronaviruses, potentially contributing to the virus tracing, intermediate host screening and epidemic prevention for pathogenic coronaviruses.

Predicting the angiotensin converting enzyme 2 (ACE2) utilizing capability as the receptor of SARS-CoV-2.

SARS-CoV-2, the newly identified human coronavirus causing severe pneumonia pandemic, was probably originated from Chinese horseshoe bats. However, direct transmission of the virus from bats to humans is unlikely due to lack of direct contact, implying the existence of unknown intermediate hosts. Angiotensin converting enzyme 2 (ACE2) is the receptor of SARS-CoV-2, but only ACE2s of certain species can be utilized by SARS-CoV-2. Here, we evaluated and ranked the receptor-utilizing capability of ACE2s from various species by phylogenetic clustering and sequence alignment with the currently known ACE2s utilized by SARS-CoV-2. As a result, we predicted that SARS-CoV-2 tends to utilize ACE2s of various mammals, except murines, and some birds, such as pigeon. This prediction may help to screen the intermediate hosts of SARS-CoV-2.

The ORF6, ORF8 and nucleocapsid proteins of SARS-CoV-2 inhibit type I interferon signaling pathway.

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a novel human coronavirus causing the pandemic of severe pneumonia (Coronavirus Disease 2019, COVID-19). SARS-CoV-2 is highly pathogenic in human, having posed immeasurable public health challenges to the world. Innate immune response is critical for the host defense against viral infection and the dysregulation of the host innate immune responses probably aggravates SARS-CoV-2 infection, contributing to the high morbidity and lethality of COVID-19. It has been reported that some coronavirus proteins play an important role in modulating innate immunity of the host, but few studies have been conducted on SARS-CoV-2. In this study, we screened the viral proteins of SARS-CoV-2 and found that the viral ORF6, ORF8 and nucleocapsid proteins were potential inhibitors of type I interferon signaling pathway, a key component for antiviral response of host innate immune. All the three proteins showed strong inhibition on type I interferon (IFN-ß) and NF-κB-responsive promoter, further examination revealed that these proteins were able to inhibit the interferon-stimulated response element (ISRE) after infection with Sendai virus, while only ORF6 and ORF8 proteins were able to inhibit the ISRE after treatment with interferon beta. These findings would be helpful for the further study of the detailed signaling pathway and unveil the key molecular player that may be targeted.

The epidemic of 2019-novel-coronavirus (2019-nCoV) pneumonia and insights for emerging infectious diseases in the future.

At the end of December 2019, a novel coronavirus, 2019-nCoV, caused an outbreak of pneumonia spreading from Wuhan, Hubei province, to the whole country of China, which has posed great threats to public health and attracted enormous attention around the world. To date, there are no clinically approved vaccines or antiviral drugs available for these human coronavirus infections. Intensive research on the novel emerging human infectious coronaviruses is urgently needed to elucidate their route of transmission and pathogenic mechanisms, and to identify potential drug targets, which would promote the development of effective preventive and therapeutic countermeasures. Herein, we describe the epidemic and etiological characteristics of 2019-nCoV, discuss its essential biological features, including tropism and receptor usage, summarize approaches for disease prevention and treatment, and speculate on the transmission route of 2019-nCoV.