scholarly journals The Emergence and Spread of Novel SARS-CoV-2 Variants

2021 ◽  
Vol 9 ◽  
Author(s):  
Huaimin Yi ◽  
Jin Wang ◽  
Jiong Wang ◽  
Yuying Lu ◽  
Yali Zhang ◽  
...  
Keyword(s):  
Immune Response ◽  
Severe Acute Respiratory Syndrome ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Neutralizing Antibodies ◽  
Whole Genome ◽  
Distribution Characteristics ◽  
S Protein ◽  
The World ◽  
Viral Genes

Since severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) began to spread in late 2019, laboratories around the world have widely used whole genome sequencing (WGS) to continuously monitor the changes in the viral genes and discovered multiple subtypes or branches evolved from SARS-CoV-2. Recently, several novel SARS-CoV-2 variants have been found to be more transmissible. They may affect the immune response caused by vaccines and natural infections and reduce the sensitivity to neutralizing antibodies. We analyze the distribution characteristics of prevalent SARS-CoV-2 variants and the frequency of mutant sites based on the data available from GISAID and PANGO by R 4.0.2 and ArcGIS 10.2. Our analysis suggests that B.1.1.7, B.1.351, and P.1 are more easily spreading than other variants, and the key mutations of S protein, including N501Y, E484K, and K417N/T, have high mutant frequencies, which may have become the main genotypes for the spread of SARS-CoV-2.

scholarly journals Vaccine Breakthrough Infections by SARS-CoV-2 Variants after ChAdOx1 nCoV-19 Vaccination in Healthcare Workers

Vaccines ◽  
2021 ◽  
Vol 10 (1) ◽  
pp. 54
Author(s):  
Pratibha Kale ◽  
Ekta Gupta ◽  
Chhagan Bihari ◽  
Niharika Patel ◽  
Sheetalnath Rooge ◽  
...  
Keyword(s):  
Immune Response ◽  
Single Dose ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Humoral Immune Response ◽  
Neutralizing Antibodies ◽  
Healthcare Workers ◽  
Genomic Analysis ◽  
Whole Genome ◽  
Humoral Immune

This study elucidated the clinical, humoral immune response and genomic analysis of vaccine breakthrough (VBT) infections after ChAdOx1 nCoV-19/Covishield vaccine in healthcare workers (HCWs). Amongst 1858 HCWs, 1639 had received either two doses (1346) or a single dose (293) of ChAdOx1 nCoV-19 vaccine. SARS-CoV-2 IgG antibodies and neutralizing antibodies were measured in the vaccinated group and the development of SARS-CoV-2 infection was monitored.Forty-six RT-PCR positive samples from the 203 positive samples were subjected to whole genome sequencing (WGS). Of the 203 (10.92%) infected HCWs, 21.46% (47/219) were non-vaccinated, which was significantly more than 9.52% (156/1639) who were vaccinated and infection was higher in doctors and nurses. Unvaccinated HCWs had 1.57 times higher risk compared to partially vaccinated HCWs and 2.49 times higher risk than those who were fully vaccinated.The partially vaccinated were at higher risk than the fully vaccinated (RR 1.58). Antibody non-response was seen in 3.44% (4/116), low antibody levels in 15.51% (18/116) and medium levels were found in 81.03% (94/116). Fully vaccinated HCWs had a higher antibody response at day 42 than those who were partially vaccinated (8.96 + 4.00 vs. 7.17 + 3.82). Whole genome sequencing of 46 samples revealed that the Delta variant (B.1.617.2) was predominant (69.5%). HCWs who had received two doses of vaccine showed better protection from mild, moderate, or severe infection, with a higher humoral immune response than those who had received a single dose. The genomic analysis revealed the predominance of the Delta variant (B.1.617.2) in the VBT infections.

scholarly journals SARS-CoV-2 B.1.1.7 lineage rapidly spreads and overwhelms R.1 lineage in Japan: serial and stationary observation in a community

2021 ◽  
Author(s):  
Yosuke Hirotsu ◽  
Masao Omata
Keyword(s):  
Severe Acute Respiratory Syndrome ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Genome Analysis ◽  
Whole Genome ◽  
Community Based ◽  
The World ◽  
Viral Lineage

Background The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) circulates in the world and acquires mutations during evolution. To identify the new emergent variants, the surveillance of the variants of concern (VOC) and variants of interest (VOI) is ongoing. This study aimed to determine how the transition of viral lineage occurred by stationary genome analysis in Yamanashi, Japan. Methods We performed the whole genome sequencing using SARS-CoV-2 positive samples (n=325) collected from February 2020 to the end of June 2021. The number of analyzed samples accounted for 15.4% of the total 2,109 samples identified in our community. Viral lineage was defined by the Phylogenetic Assignment of Named Global Outbreak (PANGO) lineages. Results We identified 13 types of viral lineages including R.1, P.1, B.1.1.7 (Alpha) and B.1.617.2 (Delta) These virus lineages had distinct periods of expansion and decline. After the emerging of the R.1 lineage harboring E484K variant (designated VOI in Japan), the prevalent B.1.1.214 lineage were no longer identified. The R.1 lineages were temporarily prevalent afterwards, but the influx of B.1.1.7 lineage (designated VOC) led to a decline in R.1. Currently, B.1.1.7 has become dominant after mid-April, 2021. Conclusion We clearly elucidated the transition and replacement of viral lineage by the community-based analysis. The virus completely replaced by more infectious lineages, therefore, it will be necessary to continue to monitor the VOC and VOI.

scholarly journals Comparative Analysis of Genotyping by Sequencing and Whole-Genome Sequencing Methods in Diversity Studies of Olea europaea L.

Plants ◽  
2021 ◽  
Vol 10 (11) ◽  
pp. 2514
Author(s):  
James Friel ◽  
Aureliano Bombarely ◽  
Carmen Dorca Fornell ◽  
Francisco Luque ◽  
Ana Maria Fernández-Ocaña
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Olea Europaea ◽  
Genetic Relationships ◽  
Germplasm Collection ◽  
Whole Genome ◽  
Population Genetic Analysis ◽  
Olea Europaea L ◽  
The World ◽  
Olea Europaéa

Olive, Olea europaea L., is a tree of great economic and cultural importance in the Mediterranean basin. Thousands of cultivars have been described, of which around 1200 are conserved in the different olive germplasm banks. The genetic characterisation of these cultivars can be performed in different ways. Whole-genome sequencing (WGS) provides more information than the reduced representation methods such as genotype by sequencing (GBS), but at a much higher cost. This may change as the cost of sequencing continues to drop, but, currently, genotyping hundreds of cultivars using WGS is not a realistic goal for most research groups. Our aim is to systematically compare both methodologies applied to olive genotyping and summarise any possible recommendations for the geneticists and molecular breeders of the olive scientific community. In this work, we used a selection of 24 cultivars from an olive core collection from the World Olive Germplasm Collection of the Andalusian Institute of Agricultural and Fisheries Research and Training (WOGBC), which represent the most of the cultivars present in cultivated fields over the world. Our results show that both methodologies deliver similar results in the context of phylogenetic analysis and popular population genetic analysis methods such as clustering. Furthermore, WGS and GBS datasets from different experiments can be merged in a single dataset to perform these analytical methodologies with proper filtering. We also tested the influence of the different olive reference genomes in this type of analysis, finding that they have almost no effect when estimating genetic relationships. This work represents the first comparative study between both sequencing techniques in olive. Our results demonstrate that the use of GBS is a perfectly viable option for replacing WGS and reducing research costs when the goal of the experiment is to characterise the genetic relationship between different accessions. Besides this, we show that it is possible to combine variants from GBS and WGS datasets, allowing the reuse of publicly available data.

scholarly journals Use of whole genome sequencing to investigate a cluster of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) infections in emergency department personnel

2021 ◽  
pp. 1-10
Author(s):  
Ernest R. Chan ◽  
Lucas D. Jones ◽  
Sarah N. Redmond ◽  
Maria E. Navas ◽  
Nataliya M. Kachaluba ◽  
...  
Keyword(s):  
Emergency Department ◽  
Severe Acute Respiratory Syndrome ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Healthcare Personnel ◽  
Whole Genome ◽  
Suspected Outbreak

Abstract Several recent reports have raised concern that infected co-workers may be an important source of SARS-CoV-2 acquisition by healthcare personnel. In a suspected outbreak among emergency department personnel, sequencing of SARS-CoV-2 confirmed transmission among co-workers. The suspected 6-person outbreak included 2 distinct transmission clusters and 1 unrelated infection.

scholarly journals Flight-Associated Transmission of Severe Acute Respiratory Syndrome Coronavirus 2 Corroborated by Whole-Genome Sequencing

2020 ◽  
Vol 26 (12) ◽  
pp. 2872-2880 ◽  
Author(s):  
Hollie Speake ◽  
Anastasia Phillips ◽  
Tracie Chong ◽  
Chisha Sikazwe ◽  
Avram Levy ◽  
...  
Keyword(s):  
Severe Acute Respiratory Syndrome ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Whole Genome

scholarly journals Fast SARS-CoV-2 Variant Detection Using Snapback Primer High-Resolution Melting

Diagnostics ◽  
2021 ◽  
Vol 11 (10) ◽  
pp. 1788
Author(s):  
Joseph C. Lownik ◽  
Jared S. Farrar ◽  
Grayson W. Way ◽  
Angela McKay ◽  
Pavitra Roychoudhury ◽  
...  
Keyword(s):  
High Resolution ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
High Resolution Melting ◽  
Whole Genome ◽  
Current Standard ◽  
The Past ◽  
The World ◽  
Variant Detection ◽  
Sensitive Testing

SARS-CoV-2, the virus responsible for COVID-19, emerged in late 2019 and has since spread throughout the world, infecting over 200 million people. The fast spread of SARS-CoV-2 showcased the need for rapid and sensitive testing methodologies to help track the disease. Over the past 18 months, numerous SARS-CoV-2 variants have emerged. Many of these variants are suggested to be more transmissible as well as less responsive to neutralization by vaccine-induced antibodies. Viral whole-genome sequencing is the current standard for tracking these variants. However, whole-genome sequencing is costly and the technology and expertise are limited to larger reference laboratories. Here, we present the feasibility of a fast, inexpensive methodology using snapback primer-based high-resolution melting to test for >20 high-consequence SARS-CoV-2 spike mutations. This assay can distinguish between multiple variant lineages and be completed in roughly 2 h for less than $10 per sample.

scholarly journals How Do We Find the Source of Foodborne Superbug Outbreaks?

2021 ◽  
Vol 9 ◽  
Author(s):  
Joy Scaria ◽  
Shruti Menon ◽  
Maristela Rovai
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Food Supply ◽  
Supply System ◽  
New Method ◽  
Resistant Bacteria ◽  
Whole Genome ◽  
Testing Methods ◽  
Antibiotic Resistant ◽  
The World

Lately, there have been more foodborne “superbug” outbreaks than ever before, which creates a problem because superbugs are antibiotic-resistant bacteria that are difficult to treat. To reduce such outbreaks, better ways of finding the source of the infection are needed. Superbugs, such as Salmonella are often transmitted through food. The world’s food supply system has become so complex that it is often difficult to find the source of an outbreak with older testing methods. A new method called whole genome sequencing (WGS) has now been developed to track superbug infections. Using WGS, it is now possible to identify the source of an outbreak in one country that may be transmitted through food imported from the opposite side of the world. Good outbreak tracing methods help scientists make better predictions about outbreaks. Finding the source of an outbreak early on can lead to better containment and lower costs.

scholarly journals Bioinformatics approaches to the study of antimicrobial resistance

2021 ◽  
Vol 34 (Suppl 1) ◽  
pp. 15-17
Author(s):  
Alejandro Seoane ◽  
Germán Bou ◽  
Keyword(s):  
Mass Spectrometry ◽  
Antimicrobial Resistance ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Clinical Microbiology ◽  
Whole Genome ◽  
Human Pathology ◽  
The World ◽  
The Creation

Detection and monitoring of antimicrobial resistance are two pillars on which clinical microbiology will be based in the coming decades. The implementation of certain technologies such as whole genome sequencing (WGS) or mass spectrometry and the creation of national and international databases that include and gather data on antimicrobial resistance from around the world has allowed the application of bioinformatics in the study of antimicrobial resistance in microorganisms involved in human pathology.

scholarly journals Coronavirus Disease 2019 (COVID-19) Re-infection by a Phylogenetically Distinct Severe Acute Respiratory Syndrome Coronavirus 2 Strain Confirmed by Whole Genome Sequencing

2020 ◽  
Author(s):  
Kelvin Kai-Wang To ◽  
Ivan Fan-Ngai Hung ◽  
Jonathan Daniel Ip ◽  
Allen Wing-Ho Chu ◽  
Wan-Mui Chan ◽  
...  
Keyword(s):  
Severe Acute Respiratory Syndrome ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Natural Infection ◽  
Acute Infection ◽  
Virus Genome ◽  
First Episode ◽  
Whole Genome ◽  
Viral Genomes ◽  
Viral Shedding

Abstract Background Waning immunity occurs in patients who have recovered from Coronavirus Disease 2019 (COVID-19). However, it remains unclear whether true re-infection occurs. Methods Whole genome sequencing was performed directly on respiratory specimens collected during 2 episodes of COVID-19 in a patient. Comparative genome analysis was conducted to differentiate re-infection from persistent viral shedding. Laboratory results, including RT-PCR Ct values and serum Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) IgG, were analyzed. Results The second episode of asymptomatic infection occurred 142 days after the first symptomatic episode in an apparently immunocompetent patient. During the second episode, there was evidence of acute infection including elevated C-reactive protein and SARS-CoV-2 IgG seroconversion. Viral genomes from first and second episodes belong to different clades/lineages. The virus genome from the first episode contained a a stop codon at position 64 of ORF8, leading to a truncation of 58 amino acids. Another 23 nucleotide and 13 amino acid differences located in 9 different proteins, including positions of B and T cell epitopes, were found between viruses from the first and second episodes. Compared to viral genomes in GISAID, the first virus genome was phylogenetically closely related to strains collected in March/April 2020, while the second virus genome was closely related to strains collected in July/August 2020. Conclusions Epidemiological, clinical, serological, and genomic analyses confirmed that the patient had re-infection instead of persistent viral shedding from first infection. Our results suggest SARS-CoV-2 may continue to circulate among humans despite herd immunity due to natural infection. Further studies of patients with re-infection will shed light on protective immunological correlates for guiding vaccine design.

scholarly journals A Novel Adenovirus Species Associated with an Acute Respiratory Outbreak in a Baboon Colony and Evidence of Coincident Human Infection

mBio ◽  
2013 ◽  
Vol 4 (2) ◽  
Author(s):  
Charles Y. Chiu ◽  
Shigeo Yagi ◽  
Xiaoyan Lu ◽  
Guixia Yu ◽  
Eunice C. Chen ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Neutralizing Antibodies ◽  
Nonhuman Primates ◽  
Respiratory Illness ◽  
Clinical Samples ◽  
Whole Genome ◽  
Primate Research ◽  
Acute Respiratory Illness ◽  
Dna Viruses

ABSTRACTAdenoviruses (AdVs) are DNA viruses that infect many vertebrate hosts, including humans and nonhuman primates. Here we identify a novel AdV species, provisionally named “simian adenovirus C (SAdV-C),” associated with a 1997 outbreak of acute respiratory illness in captive baboons (4 of 9) at a primate research facility in Texas. None of the six AdVs recovered from baboons (BaAdVs) during the outbreak, including the two baboons who died from pneumonia, were typeable. Since clinical samples from the two fatal cases were not available, whole-genome sequencing of nasal isolates from one sick baboon and three asymptomatic baboons during the outbreak was performed. Three AdVs were members of species SAdV-C (BaAdV-2 and BaAdV-4 were genetically identical, and BaAdV-3), while one (BaAdV-1) was a member of the recently described SAdV-B species. BaAdV-3 was the only AdV among the 4 isolated from a sick baboon, and thus was deemed to be the cause of the outbreak. Significant divergence (<58% amino acid identity) was found in one of the fiber proteins of BaAdV-3 relative to BaAdV-2 and -4, suggesting that BaAdV-3 may be a rare SAdV-C recombinant. Neutralizing antibodies to the other 3 AdVs, but not BaAdV-3, were detected in healthy baboons from 1996 to 2003 and staff personnel from 1997. These results implicate a novel adenovirus species (SAdV-C) in an acute respiratory outbreak in a baboon colony and underscore the potential for cross-species transmission of AdVs between humans and nonhuman primates.IMPORTANCEAdenoviruses (AdVs) are DNA viruses that infect many animals, including humans and monkeys. In 1997, an outbreak of acute respiratory illness from AdVs occurred in a baboon colony in Texas. Here we use whole-genome sequencing and antibody testing to investigate new AdVs in baboons (BaAdVs) during the outbreak, one of which, BaAdV-3, came from a sick animal. By sequence analysis, BaAdV-3 may be a recombinant strain that arose from a related BaAdV found in baboons nearby in the colony (who were not sick) and yet another unknown AdV. We also found antibodies to these new BaAdVs in baboons and staff personnel at the facility. Taken together, our findings of a new AdV species as the cause of an acute respiratory outbreak in a baboon colony underscore the ongoing threat from emerging viruses that may carry the potential for cross-species transmission between monkeys and humans.

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