Early genomic, epidemiological, and clinical description of the SARS-CoV-2 Omicron variant in Mexico City

BackgroundOmicron is the most mutated SARS-CoV-2 variant that has emerged, resulting in viral phenotype alterations, which can affect transmissibility, disease severity, and immune evasiveness. Genomic surveillance of a highly transmissible variant is important in cities with millions of inhabitants and an economic center such as Mexico City. In this work, we describe the early effects of the Omicron variant in Mexico City, exploring its genomic profile and clinical description. MethodologyWe sequenced SARS-CoV-2-positive samples in November and December 2021 and we using the public database GISAID. Haplotype and phylogenetic analyses were performed to genomically characterize Omicron. We used the Mexican federal database toexplore the association with clinical information such as symptoms and vaccination status. FindingsThe first case of Omicron was detected on November 16, 2022, and until December 31, 2021, we observed an increase from 88% in sequenced samples. Nineteen nonsynonymous mutations were found in the Omicron RBD, and we further explored the R346K substitution, which was prevalent in 42% of the samples and associated with immune escape by monoclonal antibodies. In the phylogenetic analysis, we found that there were several independent exchanges between Mexico and the world, and there was an event followed by local transmission that gave rise to most of the Omicron diversity in Mexico City. The haplotype analysis allowed us to observe that there was no association between haplotype and vaccination status. Of the patients with clinical data, 66% were vaccinated, none of the reported comorbidities were associated with Omicron, the presence of odynophagia and absence of dysgeusia were significant predictor symptoms for Omicron, and the Ct value on RT-qPCR was lower in Omicron. ConclusionsGenomic surveillance in highly populated and fast-moving urban regions such as Mexico City is key to detecting the emergence and spread of SARS-CoV-2 variants in a timely manner, even weeks before the onset of an infection wave, to detect patterns that can inform public health decisions. It is also necessary to continue sequencing to detect the spread of any mutation that may affect the therapeutic efficacy or guide it.

The evolutionary landscape of SARS-CoV-2 variant B.1.1.519 and its clinical impact in Mexico City

The SARS-CoV-2 pandemic is one of the most concerning health problems around the globe. We report the emergence of SARS-CoV-2 variant B.1.1.519 in Mexico City. This variant represented up to 90% of sequenced cases in February 2021. It is characterized by three amino acid changes in the spike protein: T478K, P681H, and T732A. We report the effective reproduction number of B.1.1.519 and present evidence of its geographical origin based on phylogenetic analysis. We also studied its evolution via haplotype analysis and identified the most recurrent haplotypes. Finally, we studied the clinical impact of B.1.1.519: patients infected with variant B.1.1.519 showed a highly significant adjusted odds ratio (aOR) increase of 1.85 over non-B.1.1.519 patients for developing a severe/critical outcome (P = 0.000296, 1.33-2.6 95% CI) and a 2.35-fold increase for hospitalization (P = 0.005, 1.32-4.34 95% CI). The continuous monitoring of this and other variants will be required to control the ongoing pandemic as it evolves.

Liquid-liquid extraction-programmed temperature vaporizer-gas chromatography-mass spectrometry for the determination of polycyclic aromatic hydrocarbons in saliva samples. Application to the occupational exposure of firefighters.

We present the development and validation of a sensitive method for the reliable determination of sixteen polycyclic aromatic hydrocarbons (PAHs) in saliva samples, which can be used as exposure markers. This method was based on a liquid-liquid extraction and programmed temperature vaporizer-gas chromatography-mass spectrometry analysis (LLE-PTV-GC-MS). Since no matrix effect was found, quantification was performed using external calibration. The detection limits were lower than or equal to 0.057 µg L-1 for all analytes, and repeatability and reproducibility (expressed as relative standard deviation, RSD) were always lower than or equal to 11% and 19%, respectively. The method was used to quantify polycyclic aromatic hydrocarbons in the saliva samples taken from firefighters and unexposed volunteers, detecting the presence of seven of the sixteen analytes analysed. Two of the compounds (fluorene and phenanthrene) were found in the both exposed and unexposed individuals, while the remaining five analytes (naphthalene, acenaphthylene, anthracene, fluoranthene and pyrene) were only detected in samples taken from the firefighters. Good discrimination between the firefighters and the unexposed volunteers was obtained through a principal component analysis.

Urinary volatile fingerprint based on mass spectrometry for the discrimination of patients with lung cancer and controls.

Profile signals of urine samples corresponding to patients with lung cancer and controls were obtained using a non-separative methodology. The method is based on the coupling of a headspace sampler, a programed temperature vaporizer and a mass spectrometer (HS-PTV-MS). With only a centrifugation step as prior sample treatment, the samples were subjected to the headspace generation process and the volatiles generated were introduced into the PTV where they were trapped in the Tenax® packed liner while the solvent was purged. Finally, the analytes were introduced directly, without separation, into the mass spectrometer which allows obtaining the fingerprint of the analyzed sample. The mass spectrum corresponding to the mass/charge ratios (m/z) ranging between 35 and 120amu (amu) contains the information related to the composition of the headspace and is used as the analytical signal for the characterization of the samples. Samples of 14 patients with some type of cancer and 24 healthy volunteers were analyzed and the profile signals were subjected to different chemometric techniques, including support vector machines (SVM), linear discriminant analysis (LDA) and partial least squares- discriminant analysis (PLS-DA), with the aim of differentiating the samples of patients with cancer from those of control. Values of 100% were obtained both in sensitivity and specificity in most cases. This methodology has been used previously, as described later, for the analysis of the fingerprint corresponding to saliva samples of patients and controls. However, up to date, the method has not been used in urine samples with the aim of fast discrimination between patients with cancer and controls. The advantages and disadvantages of using urine versus other types of matrices such as saliva are stated. In view of the results obtained in this work, the use of pattern recognition techniques with data corresponding to HS-PTV-MS profile signals is highly suitable as a first screening step to differentiate samples. In addition, it could be applied to a high number of samples in a relatively short period of time due to its high throughput.

Determination of ketones and ethyl acetate-a preliminary study for the discrimination of patients with lung cancer.

In this work, ten possible volatile biomarkers of lung cancer (acetone, 2-butanone, ethyl acetate, 2-pentanone, 4-methyl-2-pentanone, 2-hexanone, 3-heptanone, 2-heptanone, 3-octanone, and 2-nonanone) have been analyzed to evaluate their different concentration levels in urine samples from lung cancer patients (n = 12) and healthy controls (n = 12). The volatile compounds were generated with a headspace autosampler and analyzed with a gas chromatograph equipped with a programmed temperature vaporizer and mass spectrometry detector (HS-PTV-GC-MS). With the aim of evaluating the aforementioned differences, a Mann-Whitney U test and box-plots were obtained. Very good discrimination between cancer and control groups was achieved for three (ethyl acetate, 3-heptanone, and 3-octanone) of the ten analytes studied. With a view to assigning samples to the group of healthy or ill individuals, the Wilcoxon signed-rank test has been used. In spite of the small number of urine samples assayed, the results may suggest that the studied compounds could be considered useful tools in order to discern samples and they could be employed as a complementary test in a diagnosis. Graphical abstract Classification of samples (lung cancer patients and controls) with the Wilcoxon signed rank test.

Headspace-programmed temperature vaporization-mass spectrometry for the rapid determination of possible volatile biomarkers of lung cancer in urine.

We propose a new method for the rapid determination of five volatile compounds described in the literature as possible biomarkers of lung cancer in urine samples. The method is based on the coupling of a headspace sampler, a programmed temperature vaporizer in solvent-vent injection mode, and a mass spectrometer (HS-PTV-MS). This configuration is known as an electronic nose based on mass spectrometry. Once the method was developed, it was used for the analysis of urine samples from lung cancer patients and healthy individuals. Multivariate calibration models were employed to quantify the biomarker concentrations in the samples. The detection limits ranged between 0.16 and 21 µg/L. For the assignment of the samples to the patient group or the healthy individuals, the Wilcoxon signed-rank test was used, comparing the concentrations obtained with the median of a reference set of healthy individuals. To date, this is the first time that multivariate calibration and non-parametric methods have been combined to classify biological samples from profile signals obtained with an electronic nose. When significant differences in the concentration of one or more biomarkers were found with respect to the reference set, the sample is considered as a positive one and a new analysis was performed using a chromatographic method (HS-PTV-GC/MS) to confirm the result. The main advantage of the proposed HS-PTV-MS methodology is that no prior chromatographic separation and no sample manipulation are required, which allows an increase of the number of samples analyzed per hour and restricts the use of time-consuming techniques to only when necessary. Graphical abstract Schematic diagram of the developed methodology.

Genetic Diversity Strategy for the Management and Use of Rubber Genetic Resources: More than 1,000 Wild and Cultivated Accessions in a 100-Genotype Core Collection.

The rubber tree [Hevea brasiliensis (Willd. ex Adr. de Juss.) Muell. Arg.] is the only plant species worldwide that is cultivated for the commercial production of natural rubber. This study describes the genetic diversity of the Hevea spp. complex that is available in the main ex situ collections of South America, including Amazonian populations that have never been previously described. Genetic data were analyzed to determine the genetic structure of the wild populations, quantify the allelic diversity and suggest the composition of a core collection to capture the maximum genetic diversity within a minimal sample size. A total of 1,117 accessions were genotyped with 13 microsatellite markers. We identified a total of 408 alleles, 319 of which were shared between groups and 89 that were private in different groups of accessions. In a population structure and principal component analysis, the level of clustering reflected a primary division into the following two subgroups: cluster 1, which consisted of varieties from the advanced breeding germplasm that originated from the Wickham and Mato Grosso accessions; and cluster 2, which consisted of the wild germplasm from the Acre, Amazonas, Pará and Rondônia populations and Hevea spp. The analyses revealed a high frequency of gene flow between the groups, with the genetic differentiation coefficient (GST) estimated to be 0.018. Additionally, no distinct separation among the H. brasiliensis accessions and the other species from Amazonas was observed. A core collection of 99 accessions was identified that captured the maximum genetic diversity. Rubber tree breeders can effectively utilize this core collection for cultivar improvement. Furthermore, such a core collection could provide resources for forming an association panel to evaluate traits with agronomic and commercial importance. Our study generated a molecular database that should facilitate the management of the Hevea germplasm and its use for subsequent genetic and genomic breeding.

Headspace generation coupled to gas chromatography-mass spectrometry for the automated determination and quantification of endogenous compounds in urine. Aldehydes as possible markers of oxidative stress.

A methodology for the determination of five aldehydes in urine has been developed based on the coupling of a headspace generation sampler with a gas chromatography-mass spectrometry system equipped with a programmed temperature vaporizer. This instrumental configuration minimizes sample manipulation and allows the determination of these compounds without the need for a derivatization step so that the methodology is largely shortened and simplified. An experimental design was carried out in order to optimize the headspace sampling. Sample matrix effect was eliminated by means of dilution of urine samples. The calibration models displayed good linearity (0.1-10 µg/L) and their validity was checked using ANOVA, and it was observed that they did not exhibit any lack of fit. The LODs obtained ranged between 0.04 and 0.08 µg/L and the LOQs between 0.12 and 0.24 µg/L. The accuracy of the method was evaluated in terms of apparent recoveries which were between 86 and 120%. The method developed was applied to the analysis of 17 samples of urine from different subjects in order to quantify these endogenous compounds.

Microextraction by packed sorbent and salting-out-assisted liquid-liquid extraction for the determination of aromatic amines formed from azo dyes in textiles.

EU legislation prohibits the use of certain azo dyes which, on reduction, form any of 22 aromatic amines listed in Regulation (EC) 1907/2006 at concentrations above the threshold limit of 30 mg Kg(-1). Two different extraction techniques for the determination of aromatic amines formed from azo dyes in textiles in combination with gas chromatography-mass spectrometry (GC-MS) are described. The first one is based on microextraction by packed sorbent (MEPS) and the other approach involves salting-out-assisted liquid-liquid extraction (SALLE). The influence of several parameters on the efficiency of the extraction using MEPS (sorbent material, sample volume, elution solvent, elution volume and washing steps, among others) and SALLE (extraction volume and amount of salt) were investigated. In addition, chromatographic separation was optimized and quadrupole mass spectrometry was evaluated using the synchronous SIM/scan data acquisition mode. The repeatability (n=8, S/N=3) of the methods, calculated as the relative standard deviation (RSD) was below 15 and 11% for all compounds when MEPS and SALLE were used, respectively. Standard additions procedure was used to quantify the aromatic amines in the textil samples. The detection limits in the samples for both methods were lower than the maximum value allowed by legislation. The results obtained in the analysis of textiles revealed the presence of o-anisidine, p-chloroaniline, 4-chloro-o-toluidine, 2-naphthylamine and 3,3'-dimethoxybenzidine in some of them.

In situ derivatization coupled to microextraction by packed sorbentand gas chromatography for the automated determination ofhaloacetic acids in chlorinated water.

A novel analytical method is reported for the determination of monochloroacetic acid, dichloroacetic acid, trichloroacetic acid, monobromoacetic acid, and dibromoacetic acid. These are the five haloacetic acids (HAAs) for which the U.S. Environmental Protection Agency (US EPA) has regulated a maximum contamination level (MCL) of 0.060 mg L−1for the sum of their concentrations in drinking waters. Themethod uses in situ aqueous derivatization, followed by microextraction by packed sorbent (MEPS) priorto gas chromatography­mass spectrometry (GC­MS). The parameters affecting derivatization and extraction were optimized with a view to obtaining maximum sensitivity. The HAAs were derivatized with 2,2,2-trifluroethylamine (TFEA), using N-ethyl-N'-(3-dimethylaminopropyl) carbodiimide (EDC) as a condensation agent. The reaction occurred in aqueous medium and was carried out in 10 min in the vial of anautosampler used to perform microextraction by packed sorbent. The whole process, from the mixing of the reagents for the derivatization, was automated. Precision values varied from 4.2 to 9.8% (as intra-day relative standard deviation, RSD) and 9.4 to 14% (as inter-day RSD). The recoveries from spiked concentrations ranged from 83 to 117%, revealing the accuracy of the method. The detection limits ranged from 0.36 to 1.2 g L−1, such that it is possible to measure the US EPA MCL in drinking waters. The method developed was applied to the analysis of HAAs in drinking and swimming pool water from Salamanca(North West of Spain).

In situ aqueous derivatization as sample preparation technique for gas chromatographic determinations.

The use of derivatization reactions is a common practice in analytical laboratories. Although in many cases it is tedious and time-consuming, it does offer a good alternative for the determination of analytes not compatible to gas chromatography. Many of the reactions reported in the literature occur in organic medium. However, in situ aqueous derivatization reactions, which can be performed directly in aqueous medium, offer important advantages over those mentioned above, such as no need of a previous extraction step and easy automation. Here we review the most recent developments and applications of in situ aqueous derivatization. The discussion focuses on the derivatization reactions used for the determination of alcohols and phenols, carboxylic acids, aldehydes and ketones, nitrogen-containing compounds and thiols in different aqueous matrices, such as environmental, biological and food samples. Several reactions are described for each functional group (acylation, alkylation, esterification, among others) and, in some cases, the same reagents can be used for several functional groups, such that there is an unavoidable overlap between sections. Finally, attention is also focused on the techniques used for the introduction of the derivatives formed in the aqueous medium into the chromatographic system. The implementation of in situ aqueous derivatization coupled to preconcentration techniques has permitted the enhancement of recoveries and improvements in the separation, selectivity and sensitivity of the analytical methods.

Fast analytical methodology based on mass spectrometry for the determination of volatile biomarkers in saliva.

We report a methodology for the rapid determination of biomarkers in saliva. The method is based on direct coupling of a headspace sampler with a mass spectrometer. The saliva samples are subjected to the headspace generation process, and the volatiles generated are introduced directly into the mass spectrometer, thereby obtaining a fingerprint of the sample analyzed. The main advantage of the proposed methodology is that no prior chromatographic separation and no sample manipulation is required. The following model compounds were studied to check the possibilities of the methodology: methyl tert-butyl ether and styrene as biomarkers of exposure and dimethyl disulfide, limonene, and 2-ethyl-1-hexanol as biomarkers of diseases. The method was applied to the determination of biomarkers in 28 saliva samples: 24 of them were from healthy volunteers, and the others were from patients with different types of illness (including different types of cancer). Additionally, a separative analysis by GC/MS was performed for confirmatory purposes, and both methods provided similar results.

Microextraction by packed sorbent for the analysis of pharmaceutical residues in environmental water samples by in situ derivatization-programmed temperature vaporizer-gas chromatography-mass spectrometry.

The present work describes the development and validation of a method for the determination of five non-steroidal anti-inflammatory drugs (NSAIDs: clofibric acid, ibuprofen, naproxen, diclofenac and ketoprofen) in water samples. The fully automated method includes in situ aqueous derivatization followed by analyte enrichment by microextraction by packed sorbent (MEPS) coupled directly to programmed temperature vaporizer-gas chromatography-mass spectrometry (PTV-GC-MS). The MEPS variables, such as sample volume, elution solvent, elution volume, fill and injection speed and washing steps were optimized. It was possible to use the MEPS polymer (silica-C18) 250 times. Ibuprofen-d3 was used as internal standard. The reproducibility of the method, calculated as the relative standard deviation (RSD), was below 10% for all compounds. Detection limits in ultrapure water were between 3.0 and 110 ngL(-1) for ibuprofen and ketoprofen, respectively. External calibration was used in the determination of NSAIDs in several types of water samples, including tap, river, sea and influent and effluent wastewater. The results obtained revealed the presence of ibuprofen and naproxen in the influent wastewater sample and of naproxen in the effluent wastewater sample.

In situ aqueous derivatization and determination of non-steroidal anti-inflammatory drugs by salting-out-assisted liquid-liquid extraction and gas chromatography-mass spectrometry.

A new analytical method for the determination of trace levels of five non-steroidal anti-inflammatory drugs (NSAIDs: clofibric acid, ibuprofen, naproxen, diclofenac and ketoprofen) in water samples is described. The analytical procedure involves in situ aqueous derivatization with N-(3-dimethylaminopropyl)-N'-ethylcarbodiimide hydrochloride (EDC) and 2,2,2-trifluoroethylamine hydrochloride (TFEA) and salting-out liquid-liquid extraction (SALLE), followed by gas chromatography-programmed temperature vaporizer-mass spectrometry (GC-PTV-MS). The influence of several parameters on the efficiency of the derivatization (stirring time, reaction time, reagent concentration and pH), and the extraction (solvent, volume, salts and stirring time) and injection steps (liner, injection volume, liner temperature, injection time, venting time and venting flow) was investigated. The detection limits of the method in water varied from 0.042 µg/L for ibuprofen to 1.2 µg/L for ketoprofen. The relative standard deviations (RSD) values were found to be relatively low (<10% for all compounds). The methodology developed was applied to the determination of NSAIDs in several environmental matrices including tap, river, sea and influent and effluent waste water samples. The results obtained show the presence of ibuprofen and naproxen in the influent waste water sample.

Headspace sampling with in situ carbodiimide-mediated derivatization for the determination of ibuprofen in water samples.

A method using headspace generation and in situ derivatization with water soluble EDC (1-[3-(dimethylamino)propyl]-3-ethylcarbodiimide) and TFEA (2,2,2-trifluoroethylamine) has been optimized for the determination of ibuprofen (2-(p-isobutylphenyl)propionic acid), one of the most common non-steroid anti-inflammatory drug (NSAIDs) residues in surface and wastewater samples. Derivatization was carried out in the vial of the headspace sampler (HS) in only 15 min, after which instrumental measurements were made with gas chromatography-mass spectrometry (GC-MS). As the injection system, a programmed temperature vaporizer (PTV) in the solvent-vent injection mode is proposed in order to increase the sensitivity of the measurements. The effects of the variables affecting HS generation, the derivatization reaction, and the instrumental PTV conditions were studied. A limit of quantification as low as 32 ng/L was achieved, and repeatability values were below 10%. Accuracy of the method was evaluated using spiked ultrapure water at three concentration levels, obtaining apparent recoveries between 96% and 104%. The proposed method was applied to the quantification of ibuprofen in sea water and urban wastewater samples.

Simplified QuEChERS approach for the extraction of chlorinated compounds from soil samples.

A simplified version of the QuEChERS method for the extraction of chlorinated pollutant compounds from soil samples is proposed. The procedure involves simple liquid extraction of the soil sample with ethyl acetate, followed by the addition of anhydrous MgSO(4). Gas chromatography/electron capture detection (ECD) is then used to analyse the extracts without any other sample pretreatment. This new QuEChERS version includes, therefore, fewer treatment stages of the sample, which makes the final procedure simpler, faster, and cheaper and minimizes the creation of errors associated with this step. Three chlorinated compounds (chloroform, 1,2-dichlorobenzene, and hexachlorobenzene) of different volatility and polarity have been selected as target compounds and two different solvents (acetonitrile and ethyl acetate) have been evaluated in order to prove the suitability of the proposed approach for the extraction of these compounds from different soil samples. The suitability of the acetonitrile and ethyl acetate for PTV-GC analysis has also been evaluated. Recoveries between 62 and 93% and reproducibilities between 3.5 and 7.6% have been achieved.

Programmed temperature vaporizer based method for the sensitive determination of trihalomethanes and benzene, toluene, ethylbenzene and xylenes in soils.

A methodology based on the coupling of a headspace autosampler with a GC and a MS detector operating in SIM mode has been developed for the determination of volatile organic compounds (THMs and BTEX) in soils. The GC device used is equipped with a programmable temperature vaporizer (PTV) packed with Tenax-TA to introduce the samples (the injection mode used was solvent vent), and a modular accelerated column heater (MACH) to control column temperature. The proposed measurement procedure reduces the sample pretreatment step to a minimum. Combined use of solvent vent injection mode and mass spectrometry detection allows a highly sensitive method to be proposed, with limits of detection of the order of ng/kg for all the target compounds. Furthermore, the capillary column used allows rapid separations of compounds in less than 4.60 min, affording a very short total analysis cycle time of 9 min.

Determination of naphthalene and total methylnaphthalenes in gasoline using direct injection-mass spectrometry.

A high-speed determination of naphthalene and total methylnaphthalenes using a non-separative method based on direct injection into the mass spectrometer was performed. The results obtained for total methylnaphthalenes were very similar to those provided with fast gas chromatography-mass spectrometry (GC-MS). However, the non-separative method afforded higher concentrations in the determination of naphthalene than those found when fast GC-MS was used. We propose a correction that removes this error very satisfactorily and allows the same results to be obtained with both methodologies. The non-separative method is rapid, simple and - in view of the results - highly suitable for the determination of naphthalene and total methylnaphthalenes in gasoline samples.

Differentiation of types of crude oils in polluted soil samples by headspace-fast gas chromatography-mass spectrometry.

The coupling of a headspace sampler to a fast gas chromatography system with mass spectrometry detection is proposed as a method for the identification of the sources of contamination in soils due to the presence of hydrocarbons derived from petroleum. The samples are subjected to the headspace generation process, with no prior treatment, and the volatiles generated are separated by fast gas chromatography. The total time of the chromatogram per sample is less than six minutes. Chemometric treatments, such as hierarchical cluster analysis (HCA), principal component analysis (PCA), and soft independent modelling of class analogy (SIMCA) were applied to the signals obtained for the different samples. The variables used for the chemometric treatments include m/z ratios characteristic of linear and branched saturated hydrocarbons, alkyl cyclohexanes, benzene, toluene, xylenes, C3-benzenes, naphthalene and methyl-naphthalenes. The results obtained show clear differentiated clusters for the different crude oils and correct predictions when SIMCA is applied, thus allowing the differentiation of types of crude oils contaminating soils in a rapid and reliable manner.

A method for the detection of hydrocarbon pollution in soils by headspace mass spectrometry and pattern recognition techniques.

In the present work, we report a methodology for the rapid detection of soil pollution by hydrocarbons that is based on direct coupling of a headspace sampler with a mass spectrometer. With no prior treatment, the samples are subjected to the headspace generation process and the volatiles generated are introduced directly into the mass spectrometer, thereby obtaining a fingerprint of the sample analyzed. The mass spectrum corresponding to the mass/charge ratios (m/z) ranging between 49 and 160 atomic mass units (amu) contains the information related to the composition of the headspace and is used as the analytical signal for the characterization of the samples. Chemometric treatments, such as hierarchical cluster analysis (HCA), linear discriminant analysis (LDA), and soft independent modeling class analogy (SIMCA) were used to characterize the different types of samples analyzed. The main advantage of the proposed methodology is that no prior chromatographic separation and no sample manipulation are required. The method is rapid, simple, and in view of the results, highly suitable for detecting pollution in soils polluted by hydrocarbons.