Emergence and rapid transmission of SARS-CoV-2 B.1.1.7 in the United States

The highly transmissible B.1.1.7 variant of SARS-CoV-2, first identified in the United Kingdom, has gained a foothold across the world. Using S gene target failure (SGTF) and SARS-CoV-2 genomic sequencing, we investigated the prevalence and dynamics of this variant in the United States (US), tracking it back to its early emergence. We found that, while the fraction of B.1.1.7 varied by state, the variant increased at a logistic rate with a roughly weekly doubling rate and an increased transmission of 40%–50%. We revealed several independent introductions of B.1.1.7 into the US as early as late November 2020, with community transmission spreading it to most states within months. We show that the US is on a similar trajectory as other countries where B.1.1.7 became dominant, requiring immediate and decisive action to minimize COVID-19 morbidity and mortality.

Genomic epidemiology identifies emergence and rapid transmission of SARS-CoV-2 B.1.1.7 in the United States

As of January of 2021, the highly transmissible B.1.1.7 variant of SARS-CoV-2, which was first identified in the United Kingdom (U.K.), has gained a strong foothold across the world. Because of the sudden and rapid rise of B.1.1.7, we investigated the prevalence and growth dynamics of this variant in the United States (U.S.), tracking it back to its early emergence and onward local transmission. We found that the RT-qPCR testing anomaly of S gene target failure (SGTF), first observed in the U.K., was a reliable proxy for B.1.1.7 detection. We sequenced 212 B.1.1.7 SARS-CoV-2 genomes collected from testing facilities in the U.S. from December 2020 to January 2021. We found that while the fraction of B.1.1.7 among SGTF samples varied by state, detection of the variant increased at a logistic rate similar to those observed elsewhere, with a doubling rate of a little over a week and an increased transmission rate of 35-45%. By performing time-aware Bayesian phylodynamic analyses, we revealed several independent introductions of B.1.1.7 into the U.S. as early as late November 2020, with onward community transmission enabling the variant to spread to at least 30 states as of January 2021. Our study shows that the U.S. is on a similar trajectory as other countries where B.1.1.7 rapidly became the dominant SARS-CoV-2 variant, requiring immediate and decisive action to minimize COVID-19 morbidity and mortality.

A continuum of admixture in the Western Hemisphere revealed by the African Diaspora genome

The African Diaspora in the Western Hemisphere represents one of the largest forced migrations in history and had a profound impact on genetic diversity in modern populations. To date, the fine-scale population structure of descendants of the African Diaspora remains largely uncharacterized. Here we present genetic variation from deeply sequenced genomes of 642 individuals from North and South American, Caribbean and West African populations, substantially increasing the lexicon of human genomic variation and suggesting much variation remains to be discovered in African-admixed populations in the Americas. We summarize genetic variation in these populations, quantifying the postcolonial sex-biased European gene flow across multiple regions. Moreover, we refine estimates on the burden of deleterious variants carried across populations and how this varies with African ancestry. Our data are an important resource for empowering disease mapping studies in African-admixed individuals and will facilitate gene discovery for diseases disproportionately affecting individuals of African ancestry.

Genome-wide analysis of the world's sheep breeds reveals high levels of historic mixture and strong recent selection

Genomic structure in a global collection of domesticated sheep reveals a history of artificial selection for horn loss and traits relating to pigmentation, reproduction, and body size.

Through their domestication and subsequent selection, sheep have been adapted to thrive in a diverse range of environments. To characterise the genetic consequence of both domestication and selection, we genotyped 49,034 SNP in 2,819 animals from a diverse collection of 74 sheep breeds. We find the majority of sheep populations contain high SNP diversity and have retained an effective population size much higher than most cattle or dog breeds, suggesting domestication occurred from a broad genetic base. Extensive haplotype sharing and generally low divergence time between breeds reveal frequent genetic exchange has occurred during the development of modern breeds. A scan of the genome for selection signals revealed 31 regions containing genes for coat pigmentation, skeletal morphology, body size, growth, and reproduction. We demonstrate the strongest selection signal has occurred in response to breeding for the absence of horns. The high density map of genetic variability provides an in-depth view of the genetic history for this important livestock species.

During the process of domestication, mankind recruited animals from the wild into a captive environment, changing their morphology, behaviour, and genetics. In the case of sheep, domestication and subsequent selection by their animal handlers over thousands of years has produced a spectrum of breeds specialised for the production of wool, milk, and meat. We sought to use this population history to search for the genes that directly underpin phenotypic variation. We collected DNA from 2,819 sheep, belonging to 74 breeds sampled from around the world, and assessed the genotype of each animal at nearly 50,000 locations across the genome. Our results show that sheep breeds have maintained high levels of genetic diversity, in contrast to other domestic animals such as dogs. We also show that particular regions of the genome contain strong evidence for accelerated change in response to artificial selection. The most prominent example was identified in response to breeding for the absence of horns, a trait now common across many modern breeds. Furthermore, we demonstrate that other genomic regions under selection in sheep contain genes controlling pigmentation, reproduction, and body size.

Allosteric inhibitors of telomerase: oligonucleotide N3'-->P5' phosphoramidates

Telomerase is a ribonucleoprotein responsible for maintaining telomeres in nearly all eukaryotic cells. The enzyme is able to utilize a short segment of its RNA subunit as the template for the reverse transcription of d(TTAGGG) repeats onto the ends of human chromosomes. Transfection with telomerase was shown to confer immortality on several types of human cells. Moreover, telomerase activation appears to be one of the key events required for malignant transformation of normal cells. Inhibition of telomerase activity in transformed cells results in the cessation of cell proliferation in cultures and provides the rationale for the selection of telomerase as a target for anticancer therapy. Using oligonucleotide N3'-->P5' phosphoramidates (NPs) we have identified a region of the human telomerase RNA subunit (hTR) approximately 100 nt downstream from the template region whose structural integrity appears crucial for telomerase enzymatic activity. The oligonucleotides targeted to this segment of hTR are potent and specific inhibitors of telomerase activity in biochemical assays. Mutant telomerase, in which 3 nt of hTR were not complementary to a 15 nt NP, was found to be refractory to inhibition by that oligonucleotide. We also demonstrated that the binding of NP, oligonucleotides to this hTR allosteric site results in a marked decrease in the affinity of a telomerase substrate (single-stranded DNA primer) for the enzyme.

Imidazole fungicides provoke histamine release from mast cells and induce airway contraction

The effects of imidazole fungicides on rat mast cells and on guinea-pig airway smooth muscle contraction were studied. The dose-effect studies on mast cells were performed to prove our hypothesis that imidazole fungicides are potential histamine releasing agents and thus may induce bronchoconstriction in vivo. Indeed, all imidazole fungicides tested (i. e. ketoconazole, miconazole, prochloraz) and an agricultural formulation of prochloraz (i. e. Sportak) were able to elicit histamine release from mast cells in the concentration range of 30-300 microM, although there were marked differences in potency and efficacy. The in vivo experiments clearly showed that inhaled Sportak aerosols induce a significant bronchoconstriction in guinea-pigs. Moreover, after a single 5 min exposure to Sportak aerosols the animals developed airway hyperreactivity against histamine. From the results of our study it may be concluded that certain imidazole fungicides provoke histamine release by a non-immunological mechanism, induce airway constriction in guinea-pigs and hence may be harmful to spray operators who might inhale fungicide aerosols used for plant protection.

Effects of the novel dihydropyridine derivative niguldipine on the cytoplasmic free calcium concentration of mouse thymocytes

Niguldipine, a novel dihydropyridine derivative, was tested for its effects on the cytoplasmic free Ca2+ concentration of mouse thymocytes. In quin-2-loaded cells, a concentration-dependent rise of cytoplasmic Ca2+ can be detected, which requires extracellular Ca2+. The effect of niguldipine reaches a maximum after about 5 min; a similar time course has been observed, when using concanavalin A as a stimulus. Niguldipine provokes influx of Ca2+ into thymocytes, but not of Mn2+. Moreover, the effect of niguldipine exhibits some degree of stereospecificity, since (-)-niguldipine was more effective than its (+)-enantiomer. The action of niguldipine could be reversed by addition of bovine serum albumin, but not by addition of nitrendipine. None of several agents tested (e.g. felodipine, nitrendipine, trifluoperazine, cloxacepride, phenylephrine and ouabain) could mimic the effect of niguldipine at a concentration of 1 microM.

Induction of histamine release and calmodulin antagonism are two distinct properties of compound 48/80

Compound 48/80, a mixture of oligomers, was fractionated by passing it in the presence of Ca2+ over a calmodulin-Sepharose column. The fraction not retained by the gel was shown by mass spectrometry to consist mainly of trimers, tetramers and pentamers. A second fraction consisting of hexamers and heptamers was eluted from the column at high ionic strength in the presence of Ca2+. Finally, in the presence of EGTA at high ionic strength, a third fraction eluted mainly consisting of higher oligomers (hexamers to dodecamers). The different fractions were characterized by testing their influence on calmodulin-sensitive Ca2+-transporting ATPase and their ability to elicit histamine release from mast cells. The third fraction showed the highest potency as calmodulin antagonist, however, the second fraction was the most potent in inducing histamine secretion. This would imply that the ability of compound 48/80 to evoke histamine release and to inhibit the function of calmodulin are distinct properties of the agent which are unrelated.

Smooth muscle expresses a cardiac/slow muscle isoform of the Ca2+-transport ATPase in its endoplasmic reticulum

Smooth muscle expresses in its endoplasmic reticulum an isoform of the Ca2+-transport ATPase that is very similar to or identical with that of the cardiac-muscle/slow-twitch skeletal-muscle form. However, this enzyme differs from that found in fast-twitch skeletal muscle. This conclusion is based on two independent sets of observations, namely immunological observations and phosphorylation experiments. Immunoblot experiments show that two different antibody preparations against the Ca2+-transport ATPase of cardiac-muscle sarcoplasmic reticulum also recognize the endoplasmic-reticulum/sarcoplasmic-reticulum enzyme of the smooth muscle and the slow-twitch skeletal muscle whereas they bind very weakly or not at all to the sarcoplasmic-reticulum Ca2+-transport ATPase of the fast-twitch skeletal muscle. Conversely antibodies directed against the fast-twitch skeletal-muscle isoform of the sarcoplasmic-reticulum Ca2+-transport ATPase do not bind to the cardiac-muscle, smooth-muscle or slow-twitch skeletal-muscle enzymes. The phosphorylated tryptic fragments A and A1 of the sarcoplasmic-reticulum Ca2+-transport ATPases have the same apparent Mr values in cardiac muscle, slow-twitch skeletal muscle and smooth muscle, whereas the corresponding fragments in fast-twitch skeletal muscle have lower apparent Mr values. This analytical procedure is a new and easy technique for discrimination between the isoforms of endoplasmic-reticulum/sarcoplasmic-reticulum Ca2+-transport ATPases.

Calmodulin antagonism: a pharmacological approach for the inhibition of mediator release from mast cells

Several Ca2+ antagonists with either Ca2+-entry blocking or calmodulin (CaM) antagonistic properties and antiallergic drugs were investigated for their effects on mediator release from mast cells induced by different secretagogues (compound 48/80, concanavalin A, antigen-IgE and Ca2+ ionophore A23187) and for their ability to inhibit the function of CaM or phospholipid/Ca2+-dependent protein kinase (C-kinase). The effects of the different agents--with the only exception of cromolyn sodium--on histamine release elicited by compound 48/80 correlated well with their actions on two CaM-dependent enzymes whereas the activity of C-kinase was far less altered, or not altered at all. CaM antagonism of cloxacepride, picumast, oxatomide, fendiline and bepridil correlated not only with the inhibition of exocytosis evoked by compound 48/80 but also with that induced by A23187, concanavalin A and antigen-IgE. This indicates an action of these substances distal to the generation of the Ca2+ signal since the various secretagogues elevate the intracellular Ca2+ concentration by different mechanisms. However, prenylamine and thioridazine inhibited concanavalin A- and antigen-IgE-induced mediator release more potently and more effectively than that elicited by compound 48/80 or A23187. Therefore inhibition of allergic histamine release by these drugs may in part be dependent on an impairment of the Ca2+ signal. Since for each of two agents inhibition of histamine release (evoked by different releasers) parallels that of serotonin release it may be concluded that these mediators are secreted via the same mechanism. The results obtained with agents exhibiting different pharmacological properties but which share one common property, namely antagonism of CaM, strengthen the view that CaM is involved in exocytosis of mediators from mast cells.

Diphenylhydantoin (DPH) blocks HIV-receptor on T-lymphocyte surface

Previous reports have shown the capacity of diphenylhydantoin (DPH) to attach to the membranes of lymphatic cells as a hapten and thus exert an unspecific influence on their ability to express certain recognition molecules. This led us to the hypothesis, that DPH might as well serve to manipulate the t-helper-lymphocytes in a way that the mode of infection of these cells by the HIV might be blocked. In order to verify this hypothesis, we exposed normal control lymphocytes as well as lymphocytes from DPH-treated patients (3 X 100-150 mg DPH/day, Phenhydan, for a minimum of 10 days) to radioactively labeled HIV (125I). Remaining radioactivity was assessed using a gamma-counter and measured 64.000-92.000 counts/min (n = 24, mean 80.000) for the control lymphocytes, while remaining radioactivity for the DPH-treated lymphocytes ranged between 2000 and 7000 counts/min (n = 24, mean 4.000, p less than 0.001). These results and similar experiments obtained with FITC-labeled HIV led us to the conclusion that DPH inhibits HIV recognition of T-lymphocytes and therefore might be used in therapy and prophylaxis of AIDS.

Seminalplasmin. An endogenous calmodulin antagonist

Seminalplasmin, a strongly basic protein isolated from bull semen, was found to antagonize with high potency and extraordinary specificity the function of calmodulin. Calmodulin antagonism is the result of an interaction between the two proteins, which is mainly determined by electrostatic forces. The stimulation of Ca2+-transporting ATPase and phosphodiesterase by calmodulin was half-maximally inhibited at approx. 0.1 microM-seminalplasmin. However, the basal activity of calmodulin-dependent enzymes was not significantly altered by seminalplasmin over the concentration range investigated.

Target sizes of human erythrocyte membrane Ca2+-ATPase and Mg2+-ATPase activities in the presence and absence of calmodulin

We have investigated the subunit structure of Ca2+-transport ATPase in human erythrocyte membranes using radiation inactivation analysis. All inactivation data were linear on a semilog plot down to at least 20% of the control activity. We found a target size for the calmodulin-dependent Ca2+-ATPase activity of 331 kDa, consistent with the presence of this enzyme as a dimer in calmodulin-depleted ghosts. Membranes which had been saturated with calmodulin before irradiation yield a a similar size of 317 kDa, implying that activation of Ca2+-transport ATPase by calmodulin does not involve significant change in oligomeric structure. Basal (calmodulin-independent) Ca2+-ATPase activity corresponded to a size of 290 kDa, suggesting that this activity resides in the same, or similar-sized, complex as the calmodulin-dependent activity. Mg2+-ATPase activity, however, was found to reside in a smaller complex of 224 kDa, which proved to be statistically distinct from the target size of Ca2+-ATPase activity. It would appear that Mg2+-ATPase is a distinct entity whose function is likely unrelated to the Ca2+-transport ATPase.

Comparison of the calmodulin antagonists compound 48/80 and calmidazolium

The two presumed calmodulin antagonists calmidazolium and compound 48/80 were compared for their effects on several calmodulin-dependent and calmodulin-independent enzyme systems. Compound 48/80 and calmidazolium were found to be about equipotent in antagonizing the calmodulin-dependent fraction of brain phosphodiesterase and erythrocyte Ca2+-transporting ATPase. Compound 48/80 combines high potency with high specificity in that: (1) the basal, calmodulin-independent, activity of calmodulin-regulated enzymes was not suppressed; (2) calmodulin-independent enzyme activities, such as Ca2+-transporting ATPases of sarcoplasmic reticulum, Mg2+-dependent ATPases of different tissues and Na+/K+-transporting ATPase of cardiac sarcolemma, were far less altered, or not altered at all, by compound 48/80 as compared with calmidazolium; and (3) antagonism of proteolysis-induced stimulation as opposed to calmodulin-induced activation of erythrocyte Ca2+-transporting ATPase required a 32 times higher concentration of compound 48/80. In all these aspects compound 48/80 was found to be a superior antagonist to calmidazolium since inhibition of calmodulin-independent events by the other agent occurred at considerably lower concentrations. Therefore compound 48/80 is proposed to be a much more specific and useful tool for studying the participation of calmodulin in biological processes than the presently used agents.

Compound 48/80 is a selective and powerful inhibitor of calmodulin-regulated functions

Compound 48/80, a condensation product of N-methyl-p-methoxyphenethylamine with formaldehyde, is composed of a family of cationic amphiphiles differing in the degree of polymerization. Compound 48/80 was found to be a potent inhibitor of the calmodulin-activated fraction of brain phosphodiesterase and red blood cell Ca2+-transport ATPase, with IC50 values of 0.3 and 0.85 micrograms/ml, respectively. However, the basal activity of both enzymes is not at all suppressed by the drug at concentrations up to 300 micrograms/ml. Inhibition of Ca2+ transport into inside-out red blood cell vesicles by compound 48/80 follows a similar pattern in that basal, calmodulin-independent, transport is also not affected by the drug. Kinetic analysis revealed that the stimulation of Ca2+-transport ATPase induced by calmodulin is inhibited by compound 48/80 according to a competitive mechanism. It was demonstrated that the inhibitory constituents of compound 48/80 bind to calmodulin in a Ca2+-dependent fashion. Comparison of the specificity of several anti-calmodulin drugs showed that compound 48/80 is the most specific inhibitor of the calmodulin-dependent fraction of red blood cell Ca2+-transport ATPase that has been described hitherto. In addition, compound 48/80 was found to be a rather specific inhibitor of the calmodulin-induced activation of Ca2+-transport ATPase when compared with the stimulation induced by an anionic amphiphile or by limited proteolysis. Half-maximal inhibition of the activity stimulated by oleic acid or mild tryptic digestion required 8- and 32-times higher concentrations of compound 48/80, respectively, compared with the calmodulin-dependent fraction of the ATPase activity. Moreover, calmodulin-independent systems as rabbit skeletal muscle sarcoplasmic reticulum Ca2+-transport ATPase or calf cardiac sarcolemma (Na+ + K+)-transport ATPase are far less influenced by compound 48/80 as compared with trifluoperazine and calmidazolium. Because of its high specificity compound 48/80 is proposed to be a promising tool for studying calmodulin-dependent processes.

Protein-mediated lipid transfer. The effects of lipid-phase transition and of charged lipids

The protein-mediated phospholipid exchange between small unilamellar vesicles was investigated by fluorescence polarization measurements with diphenylhexatriene as optical probe. Thermotropic phase-transition measurements were taken after mixing two vesicle preparations of distinct and different phase-transition temperatures or having different states of charge. From the heights of each phase-transition step, we were able to follow the lipid-exchange process in the presence, as well as in the absence (natural exchange), of so-called transfer protein isolated from beef liver. A strong enhancement of the lipid transfer was observed at the corresponding lipid-phase-transition temperature, which is explained by the presence of fluctuating fluid and ordered domains co-existing at the lipid-phase-transition temperature. A unidirectional lipid transfer of the neutral component was observed between negatively charged phosphatidic acid and neutral phosphatidylcholine vesicles. Fluorescence polarization measurements showed the disappearance of the phosphatidylcholine phase transition, whereas the phosphatidic acid phase transition broadened and its phase transition temperature became lower.

A simple assay to study protein-mediated lipid exchange by fluorescence polarization

We investigated the protein-mediated phospholipid transfer between small vesicles by fluorescence polarization measurements with diphenylhexatriene as optical probe. Thermotropic-phase-transition curves were taken after mixing two vesicle preparations of lipids exhibiting different gel-to-liquid phase transitions. From the heights of each phase-transition step we were able to follow the lipid transfer process without separating the two vesicle preparations.

A model for the regulation of the calmodulin-dependent enzymes erythrocyte Ca2+-transport ATPase and brain phosphodiesterase by activators and inhibitors

Acidic phospholipids, unsaturated fatty acids and limited proteolysis mimic the activating effect of calmodulin on erythrocyte Ca2+-transport ATPase and on brain cyclic nucleotide phosphodiesterase, as has been reported previously in several studies. Three different antagonists of calmodulin-induced activation of these enzymes were tested for their inhibitory potency on the stimulation produced by the other activators. Trifluoperazine and penfluridol were found to antagonize all the above mentioned types of activation of Ca2+-transport ATPase in the same concentration range. Both inhibitors also can reverse the activation of phosphodiesterase by oleic acid, phosphatidylserine and calmodulin at similar concentrations. However, in contrast with erythrocyte Ca2+-transport ATPase, activation of phosphodiesterase by limited tryptic digestion cannot be antagonized by penfluridol and trifluoperazine. Calmidazolium, formerly referred to as compound R 24571, was found to be a relatively specific inhibitor of calmodulin-induced activation of phosphodiesterase and Ca2+-transport ATPase, since antagonism of the other activators required much higher concentrations of the drug. The results suggest that the investigated drugs exert their inhibitory effect on calmodulin-regulated enzymes not solely via their binding to calmodulin but may also interfere directly with the calmodulin effector enzyme. In addition, a general mechanism of activation and inhibition of calmodulin-dependent enzymes is derived from our results.

Multimers of anionic amphiphiles mimic calmodulin stimulation of cyclic nucleotide phosphodiesterase

Oleic acid, phosphatidylserine and pyrenedecanoic acid were found to activate calmodulin-deficient cyclic nucleotide phosphodiesterase at concentrations above their critical micellar concentration. In contrast with calmodulin these activators do not require the presence of Ca2+ for their action. It is shown that the size of phosphatidylserine vesicles is of crucial importance with respect to the activating potency of phosphatidylserine. Fluorescence measurements with the probe pyrenedecanoic acid revealed that micelles rather than monomers are the active species for stimulation of phosphodiesterase. There are indications that this result also may be applied to the other activators.

Large-scale isolation of human erythrocyte Ca2+-transport ATPase

A rapid procedure for preparing large quantities of purified erythrocyte Ca2+-transport ATPase is presented. The method involves: (1) fast preparation of calmodulin-deficient, essentially haemoglobin-free, erythrocyte membranes by molecular filtration using Pellicon filters; (2) solubilization of membrane proteins by deoxycholate; and (3) a batch procedure using calmodulin-Sepharose 4B gel for purification of Ca2+-transport ATPase.

Calmodulin affinity chromatography yields a functional purified erythrocyte (Ca+ + Mg2+)-dependent adenosine triphosphatase

The (Ca2+ + Mg2+)-dependent ATPase of human erythrocyte membranes was solubilized with deoxycholate and purified by calmodulin affinity chromatography to yield a functional enzyme. The method gave an enzyme purified 207-fold as compared with that of the erythrocyte membranes. The molecular weight of the ATPase was in the range 135 000-150 000, as revealed by a single major band after electrophoresis on dodecyl sulphate/polyacrylamide gels. The isolated enzyme was highly sensitive to calmodulin, since the activity was increased about 9-fold. At 37 degrees C and in the presence of calmodulin the purified ATPase had a specific activity of 10.1 mumol/min per mg of protein. Triton X-100 or deoxycholate stimulated the calmodulin-deficient enzyme in a concentration-dependent fashion whereby the calmodulin-sensitivity was lost. The purification method is suitable for studying the lipid-sensitivity of the ATPase, since the lipids can easily be exchanged without a significant loss of activity. A purification procedure described by Niggli, Penniston & Carafoli [(1979) J. Biol. Chem. 254, 9955-9958] resulted in an enzyme that indeed was pure but was lacking a predominant feature, namely the modulation by calmodulin.

Reconstitution of the Ca2+-transport system of human erythrocytes

The (Ca2+ + Mg2+)-dependent ATPase of human erythrocyte 'ghosts' was solubilized and reconstituted to form membranous vesicles capable of energized Ca2+ accumulation. The erythrocyte 'ghosts' for this purpose were prepared by using isoosmotic freeze-haemolysis in the presence of Tween 20 and proteinase inhibitors to stabilize the preparation. The reconstitution procedure is similar to that developed by Meissner & Fleischer [(1974) J. Biol. Chem. 249, 302-309] for skeletal-muscle sarcoplasmic-reticulum in that: (1) deoxycholate is used for the solubilization of the membrane; (2) controlled dialysis at near room temperature, rather than 0 degree C, is required in order to obtain a functional preparation capable of Ca2+ accumulation; and (3) membrane vesicles can be reassembled with protein/lipid ratio (approx. 60% protein and 40% lipid) similar to that of the original membrane.