Web Resources for SARS-CoV-2 Genomic Database, Annotation, Analysis and Variant Tracking.

The SARS-CoV-2 genomic data continue to grow, providing valuable information for researchers and public health officials. Genomic analysis of these data sheds light on the transmission and evolution of the virus. To aid in SARS-CoV-2 genomic analysis, many web resources have been developed to store, collate, analyze, and visualize the genomic data. This review summarizes web resources used for the SARS-CoV-2 genomic epidemiology, covering data management and sharing, genomic annotation, analysis, and variant tracking. The challenges and further expectations for these web resources are also discussed. Finally, we highlight the importance and need for continued development and improvement of related web resources to effectively track the spread and understand the evolution of the virus.

Tracing the Origin of Genotype II African Swine Fever Virus in China by Genomic Epidemiology Analysis

The pandemic spread of African swine fever (ASF) has caused serious effects on the global pig industry. Virus genome sequencing and genomic epidemiology analysis play an important role in tracking the outbreaks of the disease and tracing the transmission of the virus. Here we obtained the full-length genome sequence of African swine fever virus (ASFV) in the first outbreak of ASF in China on August 3rd, 2018 and compared it with other published genotype II ASFV genomes including 9 genomes collected in China from September 2018 to October 2020. Phylogenetic analysis on genomic sequences revealed that genotype II ASFV has evolved into different genetic clusters with temporal and spatial correlation since being introduced into Europe and then Asia. There was a strong support for the monophyletic grouping of all the ASFV genome sequences from China and other Asian countries, which shared a common ancestor with those from the Central or Eastern Europe. An evolutionary rate of 1.312 × 10−5 nucleotide substitutions per site per year was estimated for genotype II ASFV genomes. Eight single nucleotide variations which located in MGF110-1L, MGF110-7L, MGF360-10L, MGF505-5R, MGF505-9R, K145R, NP419L, and I267L were identified as anchor mutations that defined genetic clusters of genotype II ASFV in Europe and Asia. This study expanded our knowledge of the molecular epidemiology of ASFV and provided valuable information for effective control of the disease.

Adapting the GACT-X Aligner to Accelerate Minimap2 in an FPGA Cloud Instance

Featured ApplicationFast long-read assembly to reference in AWS cloud FPGA instances.In genomic analysis, long reads are an emerging type of data processed by assembly algorithms to recover the complete genome sample. They are, on average, one or two orders of magnitude longer than short reads from the previous generation, which provides important advantages in information quality. However, longer sequences bring new challenges to computer processing, undermining the performance of assembly algorithms developed for short reads. This issue is amplified by the exponential growth of genetic data generation and by the slowdown of transistor technology progress, illustrated by Moore's Law. Minimap2 is the current state-of-the-art long-read assembler and takes dozens of CPU hours to assemble a human genome with clinical standard coverage. One of its bottlenecks, the alignment stage, has not been successfully accelerated on FPGAs in the literature. GACT-X is an alignment algorithm developed for FPGA implementation, suitable for any size input sequence. In this work, GACT-X was adapted to work as the aligner of Minimap2, and these are integrated and implemented in an FPGA cloud platform. The measurements for accuracy and speed-up are presented for three different datasets in different combinations of numbers of kernels and threads. The integrated solution's performance limitations due to data transfer are also analyzed and discussed.

Updated analysis to reject the laboratory-engineering hypothesis of SARS-CoV-2.

A clear understanding of the origin of SARS-CoV-2 is important for future pandemic preparedness. Here, I provided an updated analysis of the type IIS endonuclease maps in genomes of alphacoronavirus, betacoronavirus, and SARS-CoV-2. Scenarios to engineer SARS-CoV-2 in the laboratory and the associated workload was also discussed. The analysis clearly shows that the endonuclease fingerprint does not indicate a synthetic origin of SARS-CoV-2 and engineering a SARS-CoV-2 virus in the laboratory is extremely challenging both scientifically and financially. On the contrary, current scientific evidence does support the animal origin of SARS-CoV-2.

An imported human case with the SARS-CoV-2 omicron subvariant BA.2.75 in Yunnan province, China.

The Omicron variants spread rapidly worldwide after being initially detected in South Africa in November 2021. It showed increased transmissibility and immune evasion with far more amino acid mutations in the Spike (S) protein than the previously circulating variant of concern (VOC). Notably, on 15 July 2022, we monitored the first VOC/Omicron subvariant BA.2.75 in China from an imported case. Moreover, nowadays, this subvariant still is predominant in India. It has nine additional mutations in the S protein compared to BA.2, three of which (W152R, G446S, and R493Q reversion) might contribute to higher transmissibility and immune escape. This subvariant could cause wider spread and pose a threat to the global situation. Our timely reporting and continuous genomic analysis are essential to fully elucidate the characteristics of the subvariant BA.2.75 in the future.

Healthcare-Associated COVID-19 across Five Pandemic Waves: Prediction Models and Genomic Analyses.

BACKGROUND: Healthcare-associated SARS-CoV-2 infections need to be explored further. Our study is an analysis of hospital-acquired infections (HAIs) and ambulatory healthcare workers (aHCWs) with SARS-CoV-2 across the pandemic in a Belgian university hospital. METHODS: We compared HAIs with community-associated infections (CAIs) to identify the factors associated with having an HAI. We then performed a genomic cluster analysis of HAIs and aHCWs. We used this alongside the European Centre for Disease Control (ECDC) case source classifications of an HAI. RESULTS: Between March 2020 and March 2022, 269 patients had an HAI. A lower BMI, a worse frailty index, lower C-reactive protein (CRP), and a higher thrombocyte count as well as death and length of stay were significantly associated with having an HAI. Using those variables to predict HAIs versus CAIs, we obtained a positive predictive value (PPV) of 83.6% and a negative predictive value (NPV) of 82.2%; the area under the ROC was 0.89. Genomic cluster analyses and representations on epicurves and minimal spanning trees delivered further insights into HAI dynamics across different pandemic waves. The genomic data were also compared with the clinical ECDC definitions for HAIs; we found that 90.0% of the 'definite', 87.8% of the 'probable', and 70.3% of the 'indeterminate' HAIs belonged to one of the twenty-two COVID-19 genomic clusters we identified. CONCLUSIONS: We propose a novel prediction model for HAIs. In addition, we show that the management of nosocomial outbreaks will benefit from genome sequencing analyses.

Tracking SARS-CoV2 variants and strains: an overview of Nigeria Centre for Disease Control's first 596 sequences, November,2021

Introduction/ Background: There are 249,851,155 cases of COVID-19 globally as of 6th November 2021. SARS-CoV-2, accounts for 5,053,813 deaths worldwide. In Nigeria 212,511 cases and 2,902 deaths were recorded at the same time point. his report describes the first 596 SARS-CoV-2 genomes sequenced at the National Reference Laboratory (NRL) of NCDC. Methods: Samples sequenced include positive samples from baseline surveillance and in-bound travellers from several states in-country. Isolates were obtained from nasopharyngeal and oropharyngeal swabs and Library preparation was done using ARTIC NEB SARSCoV- 2 or the NEBNext FS Library preparation kits and sequencing on Oxford Nanopore MinION or Illumina MiSeq. Sequence analysis was done using ARTIC bioinformatics pipeline for MinION and Illumina Basespace DRAGEN COVID Lineage app for MiSeq sequence data respectively Results: Of the 596 sequences, 51.8% were Delta variants, 17.4% Eta variants, and 1.0% Alpha variants. The sequences represented mostly the second and third waves of the COVID-19 pandemic in Nigeria, mostly driven by the Eta and Delta variants respectively. The first wave was driven by D614G, L452R and Y1155F spike mutations, while the second wave was characterized by the Eta variant and the Third wave was driven by Delta variants. Impact: Genomic surveillance has been recognised as a major element for pandemic response and has become a necessity for public health. To monitor local transmission and importation of SARS-CoV-2 variants in Nigeria, whole genome sequencing of SARS-CoV-2 was carried out as part of the response to the ongoing COVID-19 pandemic. Conclusion: There were multiple introductions of SARS-CoV-2 variants into Nigeria despite all the measures in place at various points of entry. The importance of timely detection of circulating variants of SARS-CoV-2 for effective preparedness and response activities cannot be overemphasised. Sequencing helped inform rational public health advisory and response.

Affordable analysis of genomes ‘key to tackling diseases’

Speed read A project is aiding resource-limited scientists to analyse deadly microbes’ genetic materials Large collections can now be analysed for as little as US$10 per genome Affordable genomic analysis is key to tackling infectious diseases [NAIROBI] A project equipping researchers with cheap and accessible methods for studying genetic materials of large collections of bacteria that cause diseases could be critical in tackling future global health challenges, scientists say. According to researchers, large-scale bacterial genome analyses have been possible in only a few sequencing centres globally until now and the cost had been as much as US$100 per genome. See PDF] “Our project has provided the best understanding of the Salmonella variants responsible for bloodstream infections in African countries including Democratic Republic of Congo, Gambia, Mali, Malawi, Kenya, Senegal and Uganda in recent years — information that will be invaluable for evaluating the impact of the [Salmonella] vaccine rollout,” Hinton explained.

In Silico Study and Excito-Repellent Activity of Vitex negundo L. Essential Oil against Anopheles gambiae

(1) Background: Essential oil from Vitex negundo is known to have repellent and insecticidal properties toward the Anopheles gambiae and this is linked to its monoterpene and sesquiterpene content. In this work, an effort is made to delineate the constitution of V. negundo essential oil (VNEO) and their interaction with odorant-binding proteins (OBPs) of A. gambiae and hence access its repellent efficiency as cost-effective and safer malaria vector control alternatives. (2) Methods: Anopheles species authentication was performed by genomic DNA analysis and was subjected to behavioral analysis. GC-MS profiling was used to identify individual components of VNEO. Anopheles OBPs were obtained from the RCSB protein data bank and used for docking studies. Determination of ligand efficiency metrics and QSAR studies were performed using Hyper Chem Professional 8.0.3, and molecular dynamics simulations were performed using the Desmond module. (3) Results: GC-MS analysis of VNEO showed 28 compounds (monoterpenes, 80.16%;sesquiterpenes, 7.63%;and unknown constituents, 10.88%). The ligand efficiency metrics of all four ligands against the OBP 7 were within acceptable ranges. β-selinene (−12.2 kcal/mol), β-caryophellene (−9.5 kcal/mol), sulcatone (−10.9 kcal/mol), and α-ylangene (−9.3 kcal/mol) showed the strongest binding affinities for the target proteins. The most stable hydrophobic interactions were observed between β-selinene (Phe111 and Phe120), Sulcatone (Phe54 and Phe120), and α-ylangene (Phe111), while only sulcatone (Tyr49) presented H-bond interactions in the simulated environment. (4) Conclusions: Sulcatone and β-caryophyllene presented the best log p values, 6.45 and 5.20, respectively. These lead phytocompounds can be used in their purest as repellent supplement or as a natural anti-mosquito agent in product formulations.

The Clinical and Genomic Epidemiology of Rhinovirus in Homeless Shelters-King County, Washington.

BACKGROUND: Rhinovirus (RV) is a common cause of respiratory illness in all people, including those experiencing homelessness. RV epidemiology in homeless shelters is unknown. METHODS: We analyzed data from a cross-sectional homeless shelter study in King County, Washington, October 2019-May 2021. Shelter residents or guardians aged ≥3 months reporting acute respiratory illness completed questionnaires and submitted nasal swabs. After 1 April 2020, enrollment expanded to residents and staff regardless of symptoms. Samples were tested by multiplex RT-PCR for respiratory viruses. A subset of RV-positive samples was sequenced. RESULTS: There were 1066 RV-positive samples with RV present every month of the study period. RV was the most common virus before and during the coronavirus disease 2019 (COVID-19) pandemic (43% and 77% of virus-positive samples, respectively). Participants from family shelters had the highest prevalence of RV. Among 131 sequenced samples, 33 RV serotypes were identified with each serotype detected for ≤4 months. CONCLUSIONS: RV infections persisted through community mitigation measures and were most prevalent in shelters housing families. Sequencing showed a diversity of circulating RV serotypes, each detected over short periods of time. Community-based surveillance in congregate settings is important to characterize respiratory viral infections during and after the COVID-19 pandemic. CLINICAL TRIALS REGISTRATION: NCT04141917.

Early detection and improved genomic surveillance of SARS-CoV-2 variants from deep sequencing data.

A key task of genomic surveillance of infectious viral diseases lies in the early detection of dangerous variants. Unexpected help to this end is provided by the analysis of deep sequencing data of viral samples, which are typically discarded after creating consensus sequences. Such analysis allows one to detect intra-host low-frequency mutations, which are a footprint of mutational processes underlying the origination of new variants. Their timely identification may improve public-health decision-making with respect to traditional approaches exploiting consensus sequences. We present the analysis of 220,788 high-quality deep sequencing SARS-CoV-2 samples, showing that many spike and nucleocapsid mutations of interest associated to the most circulating variants, including Beta, Delta, and Omicron, might have been intercepted several months in advance. Furthermore, we show that a refined genomic surveillance system leveraging deep sequencing data might allow one to pinpoint emerging mutation patterns, providing an automated data-driven support to virologists and epidemiologists.

Computational drug repurposing against SARS-CoV-2 reveals plasma membrane cholesterol depletion as key factor of antiviral drug activity

Comparing SARS-CoV-2 infection-induced gene expression signatures to drug treatment-induced gene expression signatures is a promising bioinformatic tool to repurpose existing drugs against SARS-CoV-2. The general hypothesis of signature-based drug repurposing is that drugs with inverse similarity to a disease signature can reverse disease phenotype and thus be effective against it. However, in the case of viral infection diseases, like SARS-CoV-2, infected cells also activate adaptive, antiviral pathways, so that the relationship between effective drug and disease signature can be more ambiguous. To address this question, we analysed gene expression data from in vitro SARS-CoV-2 infected cell lines, and gene expression signatures of drugs showing anti-SARS-CoV-2 activity. Our extensive functional genomic analysis showed that both infection and treatment with in vitro effective drugs leads to activation of antiviral pathways like NFkB and JAK-STAT. Based on the similarity—and not inverse similarity—between drug and infection-induced gene expression signatures, we were able to predict the in vitro antiviral activity of drugs. We also identified SREBF1/2, key regulators of lipid metabolising enzymes, as the most activated transcription factors by several in vitro effective antiviral drugs. Using a fluorescently labeled cholesterol sensor, we showed that these drugs decrease the cholesterol levels of plasma-membrane. Supplementing drug-treated cells with cholesterol reversed the in vitro antiviral effect, suggesting the depleting plasma-membrane cholesterol plays a key role in virus inhibitory mechanism. Our results can help to more effectively repurpose approved drugs against SARS-CoV-2, and also highlights key mechanisms behind their antiviral effect.

Variants of concern responsible for SARS-CoV-2 vaccine breakthrough infections from India.

Emerging reports of SARS-CoV-2 breakthrough infections entail methodical genomic surveillance for determining the efficacy of vaccines. This study elaborates genomic analysis of isolates from breakthrough infections following vaccination with AZD1222/Covishield and BBV152/Covaxin. Variants of concern B.1.617.2 and B.1.1.7 responsible for cases surge in April-May 2021 in Delhi, were the predominant lineages among breakthrough infections.

Genomic, immunological, and clinical analysis of COVID-19 vaccine breakthrough infections in Beijing, China.

As the coronavirus disease 2019 (COVID-19) pandemic is still ongoing and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants are circulating worldwide, an increasing number of breakthrough infections are being detected despite the good efficacy of COVID-19 vaccines. Data on 88 COVID-19 breakthrough cases (breakthrough infections group) and 41 unvaccinated cases (unvaccinated group) from June 1 to August 22, 2021, were extracted from a cloud database established at Beijing Ditan Hospital to evaluate the clinical, immunological, and genomic characteristics of COVID-19 breakthrough infections. Among these 129 COVID-19 cases, 33 whole genomes were successfully sequenced, of which 23 were Delta variants, including 15 from the breakthrough infections group. Asymptomatic and mild cases predominated in both groups, but two patients developed severe disease in the unvaccinated group. The median time of viral shedding in the breakthrough infections group was significantly lower than that in the unvaccinated group (p = 0.003). In the breakthrough infections group, the IgG titers showed a significantly increasing trend (p = 0.007), and the CD4 + T lymphocyte count was significantly elevated (p = 0.018). For people infected with the Delta variant in the two groups, no significant difference was observed in either the quantitative reverse-transcription polymerase chain reaction results or viral shedding time. In conclusion, among vaccinated patients, the cases of COVID-19 vaccine breakthrough infections were mainly asymptomatic and mild, IgG titers were significantly increased and rose rapidly, and the viral shedding time was shorter.

Genomic chronicle of SARS-CoV-2: a mutational analysis with over 1 million genome sequences.

Use of information technologies to analyse big data on SARS-CoV-2 genome provides an insight for tracking variations and examining the evolution of the virus. Nevertheless, storing, processing, alignment and analyses of these numerous genomes are still a challenge. In this study, over 1 million SARS-CoV-2 genomes have been analysed to show distribution and relationship of variations that could enlighten development and evolution of the virus. In all genomes analysed in this study, a total of over 215M SNVs have been detected and average number of SNV per isolate was found to be 21.83. Single nucleotide variant (SNV) average is observed to reach 31.25 just in March 2021. The average variation number of isolates is increasing and compromising with total case numbers around the world. Remarkably, cytosine deamination, which is one of the most important biochemical processes in the evolutionary development of coronaviruses, accounts for 46% of all SNVs seen in SARS-CoV-2 genomes within 16 months. This study is one of the most comprehensive SARS-CoV-2 genomic analysis study in terms of number of genomes analysed in an academic publication so far, and reported results could be useful in monitoring the development of SARS-CoV-2.

Design of Nucleic Acid Biosensors Based on CRISPR/Cas Systems and Reporter Split Proteins.

Highly sensitive, specific, rapid, and easy-to-use diagnostic methods for the detection of nucleic acids of pathogens are required for the diagnosis of many human, animal, and plant diseases and environmental monitoring. The approaches based on the use of the natural ability of bacterial CRISPR/Cas9 systems to recognize DNA sequences with a high specificity under isothermal conditions are an alternative to the polymerase chain reaction method, which requires expensive laboratory equipment. The development of the methods for signal registration with the formation of a DNA/RNA/Cas9 protein complex is a separate bioengineering task. In this work, a design was developed and the applicability of a biosensor system based on the binding of two dCas9 proteins with target DNA sequences (without their cutting) and detection of their colocalization using reporter systems based on split enzymes was studied. Using the methods of molecular modeling, possible mutual positions of two dCas9 proteins at a detectable locus of genomic DNA, allowing the split enzyme domains attached to them to interact in an optimal way, were determined. The optimal distances on DNA between binding sites of dCas9 proteins in different orientations were determined, and the dependence of the complex structure on the distance between the binding sites of dCas9 proteins was modeled. Using the methods of bioinformatics, the genomes of a number of viruses (including SARS-CoV-2) were analyzed, and the presence of genomic loci unique to the species, allowing the possibility of landing pairs of dCas9 proteins in optimal positions, was demonstrated. The possibility of a combined use of dCas9 proteins from different bacteria to expand the spectrum of detected loci was analyzed. The results of the work indicate a fundamental possibility of the creation of highly specific nucleic acid biosensors based on a combination of CRISPR/Cas9 technologies and split enzymes.

Phylogenetic estimates of SARS-CoV-2 introductions into Washington State.

BACKGROUND: The first confirmed case of SARS-CoV-2 in North America was identified in Washington state on January 21, 2020. We aimed to quantify the number and temporal trends of out-of-state introductions of SARS-CoV-2 into Washington. METHODS: We conducted a molecular epidemiologic analysis of 11,422 publicly available whole genome SARS-CoV-2 sequences from GISAID sampled between December 2019 and September 2020. We used maximum parsimony ancestral state reconstruction methods on time-calibrated phylogenies to enumerate introductions/exports, their likely geographic source (US, non-US, and between eastern and western Washington), and estimated date of introduction. To incorporate phylogenetic uncertainty into our estimates, we conducted 5,000 replicate analyses by generating 25 random time-stratified samples of non-Washington reference sequences, 20 random polytomy resolutions, and 10 random resolutions of the reconstructed ancestral state. FINDINGS: We estimated a minimum 287 introductions (range 244-320) into Washington and 204 exported lineages (range 188-227) of SARS-CoV-2 out of Washington. Introductions began in mid-January and peaked on March 29, 2020. Lineages with the Spike D614G variant accounted for the majority (88%) of introductions. Overall, 61% (range 55-65%) of introductions into Washington likely originated from a source elsewhere within the US, while the remaining 39% (range 35-45%) likely originated from outside of the US. Intra-state transmission accounted for 65% and 28% of introductions into eastern and western Washington, respectively. INTERPRETATION: The SARS-CoV-2 epidemic in Washington was continually seeded by a large number of introductions. Our findings highlight the importance of genomic surveillance to monitor for emerging variants due to high levels of inter- and intra-state transmission of SARS-CoV-2. FUNDING SOURCE: None.

Epidemiology and Treatment Options for COVID-19: A Review.

The Coronavirus disease 19 (COVID-19) is a highly transmittable and pathogenic viral infection caused by severe acute respiratory syndrome Coronavirus 2 (SARS-CoV-2), which emerged in Wuhan, China and spread around the world. As of 19 June 2020 data from the World Health Organization (WHO) have shown that more than 8457305 confirmed cases have been identified in more than 200 countries, with the number of cases cutting across all continents. On 30th January 2020, the WHO declared COVID-19 as the sixth public health emergency of international concern. Genomic analysis revealed that SARS-CoV-2 is phylogenetically related to severe acute respiratory syndrome-like (SARS-like) bat viruses; therefore, bats could be the possible primary reservoir. The intermediate source of origin and transfer to humans is not known, however, the rapid human-to-human transfer has been confirmed widely via droplets or direct contact, and infection has been estimated to have mean incubation period of 6.4 days. Currently, controlling infection to prevent the spread of SARS-CoV-2 is the primary intervention being used. However, public health authorities should keep monitoring the situation closely, as the more we can learn about this novel virus and its associated outbreak, the better we can respond.

Possible Bat Origin of Severe Acute Respiratory Syndrome Coronavirus 2.

We showed that severe acute respiratory syndrome coronavirus 2 is probably a novel recombinant virus. Its genome is closest to that of severe acute respiratory syndrome-related coronaviruses from horseshoe bats, and its receptor-binding domain is closest to that of pangolin viruses. Its origin and direct ancestral viruses have not been identified.