SARS-COV-2 VARIANTS AVAILABLE FROM BEI RESOURCES
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Winter 2021
The BEI Resources catalog is a dynamic resource supporting the infectious disease
community with reagents, tools and information to further research. Our quarterly
newsletter features a selection of recent and upcoming reagents and product highlights.
For more information on these and other products available from BEI Resources, please
visit our website at www.BEIResources.org.
For a continually updated list of current and upcoming SARS-CoV-2 reagents available to
BEI Resources registrants, please consult our SARS-CoV-2 landing page.
SARS-CoV-2 Variants Available from BEI Resources
Three fast-spreading SARS-CoV-2 lineages currently in
global circulation, B.1.1.7 (UK), B.1.351 (South Africa) and
P.1 (Brazil), are classified by the U.S. Centers for Disease
Control and Prevention as Variants of Concern as a result
of mutations that may provide fitness advantages such as
increased transmissibility and reduced susceptibility to
therapeutic agents or acquired immunity through immune
evasion.1,2,3 Two mutations in the Spike (S) glycoprotein
receptor-binding domain (RBD) shared by all three
lineages, D614G (substitutes glycine for aspartic acid at
position 614) and N501Y (replaces asparagine with tyrosine at position 501), are associated with
an increased ACE2 binding affinity in humans shown to increase viral transmission rates.2
These variants are further characterized by unique lineage-defining mutation profiles:
B.1.1.7: 17 lineage-defining mutations with 8 in the S protein, including P681H in the furin
cleavage site and a 69-70HV deletion that contributes to conformation change in Spike; 4 in
ORF1ab; 3 in ORF8 and 2 in the nucleocapsid protein.1,4
B.1.351: 8 lineage-defining mutations in the S protein, including K417N, E484K and N501Y in
the RBD and L18F, D80A and 215G in the N-terminal domain. Mutation E484K is suspected of
reduced neutralization by some polyclonal and monoclonal antibodies.1,2
P.1: A descendent of B.1.1.28 containing 17 amino acid substitutions, 4 synonymous
mutations and one 4-nucleotide insertion. Lineage P.1 shares 3 mutations in the RBD of S
protein with B.1.351: K417N, E484K and N501Y.1,3
Isolates from lineages B.1.1.7, B.1.351, B.1.5, B.1.1.298 and B.1.222 are now available on the BEI Resources website. Isolates from lineage P.1 are currently in process. Please refer to the table below for item numbers and isolate descriptions. Other available variants include Scottish variants belonging to lineages B.1.5 (BEI Resources NR-53944) and B.1.222 (BEI Resources NR-53945), which share mutations D614G in the S protein and P323L in NSP12, an RNA-dependent RNA polymerase that is essential to viral replication. Another available variant is lineage B.1.1.298 from Denmark, which is a mink- associated SARS-CoV-2 Cluster 5 virus with the Y453F mutation associated with mink-to-human adaptation, two-nucleotide 69-70 HV deletion in the S protein, I692V near the furin cleavage site of the S protein, S1147 in S2 domain and M1229I in the transmembrane domain of the S protein.4,5 Next-generation sequencing is performed on distributed virus preparations. Please refer to the individual Certificates of Analysis for isolate-specific sequencing analysis and mutation data of in-house produced virus stocks as compared to the reference for the specific isolate and to the coordinates of SARS-CoV-2, Wuhan-Hu-1 (GenBank: MN908947). For a complete list of reported mutations by isolate, please refer to the BEI Resources SARS-CoV-2 Strains and Reagents Information page and follow the links to individual Product Information Sheets and Certificates of Analysis of available isolates. BEI Resources continues to accession SARS-CoV-2 strains for availability to the research community and is currently in the process of accessioning the new variants as they are identified. For a complete, up-to-date list of all SARS-CoV-2 strains and reagents available from BEI Resources, please visit the SARS-CoV-2 Information landing page on our website. BEI Resources Product Description NR-53944 SARS-CoV-2, Isolate hCoV-19/Scotland/CVR837/2020 NR-53945 SARS-CoV-2, Isolate hCoV-19/Scotland/CVR2224/2020 NR-53953 SARS-CoV-2, Isolate hCoV-19/Denmark/DCGC-3024/2020 NR-54000 SARS-CoV-2, Isolate hCoV-19/England/204820464/2020 NR-54008 SARS-CoV-2, Isolate hCoV-19/South Africa/KRISP-EC-K005321/2020 NR-54009 SARS-CoV-2, Isolate hCoV-19/South Africa/KRISP-K005325/2020 NR-54011 SARS-CoV-2, Isolate hCoV-19/USA/CA_CDC_5574/2020 References: 1. “Emerging SARS-CoV-2 Variants.” Centers for Disease Control and Prevention, U.S. Department of Health and Human Services, https://www.cdc.gov/coronavirus/2019-ncov/more/science-and- research/scientific-brief-emerging-variants.html. 2. Tegally, H., et al. “Emergence and Rapid Spread of a New Severe Acute Respiratory Syndrome-Related Coronavirus 2 (SARS-CoV-2) Lineage with Multiple Spike Mutations in South Africa.” medRxiv doi:10.1101/2020.12.21.20248640. 3. Galloway, S. E., et al. “Emergence of SARS-CoV-2 B.1.1.7 Lineage – United States, December 29, 2020- January 12, 2021.” MMWR Morb. Mortal. Wkly. Rep. 70 (2021): 95-99. PubMed: 33476315. 4. Lauring, A. S. and E. B. Hodcroft. “Genetic Variants of SARS-CoV-2-What Do They Mean?” JAMA 2021 Jan 6. doi:10.1001/jama.2020.27124. Online ahead of print. PubMed: 33404586.
5. Lassauniére, R., et al. “SARS-CoV-2 Spike Mutations Arising in Danish Mink and their Spread to Humans.” (2020): https://files.ssi.dk/Mink-cluster-5-short-report_AFO2. Recent Enterovirus Isolates for Acute Flaccid Myelitis Research Enterovirus D68 (EV-D68) is increasingly associated with pediatric acute flaccid myelitis (AFM) in the United States and around the world. The EV-D68 outbreak in the United States in 2018 resulted in 358 confirmed cases of EV-D68- associated acute respiratory infection (ARI) in patients under the age of 17 between July and October.1,2 During the same time period, a spike of 238 cases of AFM was seen in pediatric patients within the same regions.3 Similar temporal associations between EV-D68 and AFM cases have also occurred in outbreaks in other countries. Although a causal relationship between the two diseases remains unconfirmed, EV-D68 is suspected based on data demonstrating an increase in AFM cases concomitant with EV-D68. The presence of enterovirus-binding antibodies in the cerebrospinal fluid of some AFM patients further associates EV-D68 as a possible contributing factor to AFM. Six isolates from the 2018 EV-D68 outbreak in the United States produced in serum-free A549 human lung carcinoma cells are newly available in the BEI Resources enterovirus collection, including three isolates from AFM-confirmed patients. BEI Resources Product Description NR-52015 Enterovirus D68, USA/2018-23087 NR-52016 Enterovirus D68, USA/2018-23088 NR-52017 Enterovirus D68, USA/2018-23089 NR-52353 Enterovirus D68, USA/2018-23201 NR-52354 Enterovirus D68, USA/2018-23263 NR-52356 Enterovirus D68, USA/2018-23209 References: 1. Kujawski, S. A., et al. “Enterovirus D68-Associated Acute Respiratory Illness - New Vaccine Surveillance Network, United States, July-October, 2017 and 2018.” MMWR Morb. Mortal Wkly. Rep. 68 (2019): 277-280. PubMed: 30921299. 2. Kidd, S., et al. “Enterovirus D68-Associated Acute Flaccid Myelitis, United States, 2020.” Emerg. Infect. Dis. 26 (2020): e201630. PubMed: 32833616. 3. Kidd, S., et al. “Vital Signs: Clinical Characteristics of Patients with Confirmed Acute Flaccid Myelitis, United States, 2018.” MMWR Morb. Mortal Wkly. Rep. 69 (2020): 1031-1038. PubMed: 32759919. Four New Species Added to BEI Resources Leishmania Collection Leishmaniasis is a neglected tropical disease caused by Leishmania parasites, which are
transmitted to both humans and animals by female
phlebotomine sandflies. Infections take several forms, with
cutaneous leishmaniasis causing skin lesions in an estimated
700,000-to-1.2 million new cases per year, and the high
mortality visceral leishmaniasis resulting in fevers, weight loss
and enlargement of the spleen or liver.1
Leishmania is divided into two subgenera, Leishmania and
Viannia, with more than 30 known species of Leishmania
further classified as New World (Western hemisphere) and
Old World (Eastern hemisphere) species. Pathogenic species
of both subgenera have been grouped into complexes based on phylogenetic analyses
determined through differences in the natural history of their vertebrate hosts, vector specificity,
clinical manifestations, geographical distribution and, more recently, using molecular approaches
with different genetic markers.2,3
A recent deposit of Leishmania strains by Dr. K. P. Chang of Rosalind Franklin University has
expanded the BEI Resources Leishmania collection by four new species, L. braziliensis, L.
gerbilli, L. infantum and L. turanica. Strains have been sequenced for the nagt gene, allowing for
inter- and/or intra-species discrimination.4 Please refer to the individual product documentation
for more information on the nagt variant of each strain.
BEI Resources Product Description
NR-50600 Leishmania turanica, Strain RHO/CN/99/KMA2
NR-50601 Leishmania gerbilli, Strain RHO/CN/62/20
NR-50603 Leishmania infantum, Strain HOM/TR/03/ADANA #7
NR-50608 Leishmania braziliensis, Strain HOM/BR/75/M2903
References:
1. “Leishmaniasis.” Centers for Disease Control and Prevention, U.S. Department of Health and Human
Services, https://www.cdc.gov/parasites/leishmaniasis.
2. Schönian, G., et al. “Molecular Epidemiology and Population Genetics in Leishmania.” Med. Microbiol.
Immunol. 190 (2001): 61-63. PubMed: 11770112.
3. Marcili, A., et al. “Phylogenetic Relationships of Leishmania Species Based on Trypanosomatid Barcode
(SSU rDNA) and gGAPDH Genes: Taxonomic Revision of Leishmania (L.) infantum chagasi in South
America.” Infect Genet Evol. 25 (2014): 44-51. PubMed: 24747606.
4. Waki, K., et al. “Transmembrane Molecules for Phylogenetic Analyses of Pathogenic Protists: Leishmania-
Specific Informative Sites in Hydrophilic Loops of Trans-Endoplasmic Reticulum N-Acetylglucosamine-1-
Phosphate Transferase.” Eukaryot. Cell 6 (2007): 198-210. PubMed: 17142569.
How are BEI Resources reagents being used by your peers?
Here is a selection of references citing BEI Resources reagents:
Cervantes, J., Yokobori, N. and B.-Y. Hong. “Genetic Identification and Drug-Resistance
Characterization of Mycobacterium tuberculosis Using a Portable Sequencing Device. A
Pilot Study.” Antibiotics (Basel) 9 (2020): 548. PubMed: 32867304.
The authors evaluated the capability of a portable, long-read sequencing instrument (MinION sequencer; Oxford
Nanopore Technologies) to determine the genotype of and drug-resistant mutations present in Mycobacteriumtuberculosis DNA from human sputum with potential applications in endemic regions lacking resources for clinical management of tuberculosis. The instrument was capable of discriminating Mycobacterium tuberculosis DNA from the more abundant host DNA present in sputum samples and confirmed the majority of reported mutations in isolates with published whole genome sequences. BEI Resources NR-14867, Genomic DNA from Mycobacterium tuberculosis, Strain HN878, was used in the evaluation of this sequencing method. Elkashif, A. and M. N. Seleem. “Investigation of Auranofin and Gold-Containing Analogues Antibacterial Activity Against Multidrug-Resistant Neisseria gonorrhoeae.” Sci. Rep. 10 (2020): 5602. PubMed: 32221472. Rising antibiotic resistance in Neisseria gonorrhoeae, the causative agent of gonorrhea, the second most common notifiable disease in the United States, presents the urgent need for new therapeutics to replace or support the current first-line drugs. The FDA-approved, gold-containing compounds auranofin, sodium aurothiomalate and auriothioglucose were evaluated for antibacterial activity against a panel of antibiotic-resistant N. gonorrhoeae clinical isolates alone and in combination with first-line drugs azithromycin and ceftriaxone. While all three compounds inhibited the growth of all isolates in the panel, including azithromycin-resistant strains, auranofin required the lowest minimum inhibitory concentrations and outperformed azithromycin in a time-kill assay by reducing the bacterial count below the limit of detection in half the time. The selectivity of sodium aurothiomalate and auriothioglucose toward N. gonorrhoeae over commensal vaginal Lactobacillus spp. (BEI Resources HM-105, HM-406, HM-638, HM-639, HM- 640, HM-642, HM-643, HM-644) suggests effectiveness in treatment without disrupting the normal microbiota, in contrast with azithromycin. Magni, R., et al. “Evaluation of Pathogen Specific Urinary Peptides in Tick-Borne Illness.” Sci. Rep. 10 (2020): 19340. PubMed: 33168903. Magni, et al. present a mass spectrometry method of characterizing pathogen-specific peptides from the urine of patients with diagnosed, suspected or post-treatment tick-borne illness to determine if symptoms are the result of a persistent active infection or attributed to Post-Treatment Lyme Disease Syndrome. Pre-processing of samples with affinity hydrogel particles concentrates the low-abundance biomarkers, achieving assay sensitivity in the low picograms per mL range, which are verified by parallel reaction monitoring, Western blot analysis and a Babesia model of infection using BEI Resources NR-44070 (Babesia microti, Strain GI). Results indicate that the number of pathogen-specific urinary peptides detected in samples from PTLDS and patients with active tick-borne illness directly correlates with the severity of disease symptoms and correspond to results in the animal model. With further development and validation, this method has the potential for cost-effective application in the diagnosis of tick-borne illnesses. Reynolds, J. L. and S. D. Mahajan. “SARS-CoV2 Alters Blood-Brain Barrier Integrity Contributing to Neuro-Inflammation.” J. Neuroimmune. Pharmacol. (2021): 1-3. doi:10.1007%2Fs11481-020-09975-y. PubMed: 33405097. Although 40% of COVID-19 patients have neurological symptoms, human brain microvascular endothelial cells (BMVEC) and normal human astrocytes that comprise the blood-brain barrier (BBB) are not known to express ACE2, the receptor required for SARS-CoV-2 virus entry. An increase in the basal levels of ACE2 after exposure to SARS- CoV-2 Spike protein in immunofluorescence assays using an ACE2 primary antibody (BEI Resources NR-52481) confirms ACE2 expression by human BMVEC. Treatment of an in vitro BBB model with recombinant SARS-CoV-2 Spike protein (BEI Resources NR-52308) or heat-inactivated SARS-CoV-2 virus (BEI Resources NR-52286), resulting in alteration of BBB integrity measured by tight junction gene expression analysis and trans-endothelial electrical resistance, suggests a loss of integrity of the BBB allowing for neuro-invasion. An increase of pro-inflammatory cytokines in the treated culture supernatant was also measured, consistent with clinical reports among fatal COVID- 19 cases. Together, these data identify a SARS-CoV-2 mechanism for BBB entry and pathogenesis, as well as suggest that anti-cytokine therapeutics may be effective treating COVID-19-related neurological disease. Image Credits: Color-enhanced transmission electron micrograph of SARS-CoV-2 virus particles (NIAID) Transmission electron microscopic (TEM) image of Enterovirus-D68 (CDC/Cynthia S. Goldsmith, Yiting Zhang)
TEM image of Leishmania braziliensis (CDC/Cynthia S. Goldsmith, Luciana Flannery)
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