Molecular genetics and genomics of the ABO blood group system

The A and B oligosaccharide antigens of the ABO blood group system are produced from the common precursor, H substance, by enzymatic reactions catalyzed by A and B glycosyltransferases (AT and BT) encoded by functional A and B alleles at the ABO genetic locus, respectively. In 1990, my research team cloned human A, B, and O allelic cDNAs. We then demonstrated this central dogma of ABO and opened a new era of molecular genetics. We identified four amino acid substitutions between AT and BT and inactivating mutations in the O alleles, clarifying the allelic basis of ABO. We became the first to achieve successful ABO genotyping, discriminating between AA and AO genotypes and between BB and BO, which was impossible using immunohematological/serological methods. We also identified mutations in several subgroup alleles and also in the cis-AB and B(A) alleles that specify the expression of the A and B antigens by single alleles. Later, other scientists interested in the ABO system characterized many additional ABO alleles. However, the situation has changed drastically in the last decade, due to rapid advances in next-generation sequencing (NGS) technology, which has allowed the sequencing of several thousand genes and even the entire genome in individual experiments. Genome sequencing has revealed not only the exome but also transcription/translation regulatory elements. RNA sequencing determines which genes and spliced transcripts are expressed. Because more than 500,000 human genomes have been sequenced and deposited in sequence databases, bioinformaticians can retrieve and analyze this data without generating it. Now, in this era of genomics, we can harness the vast sequence information to unravel the molecular mechanisms responsible for important biological phenomena associated with the ABO polymorphism. Two examples are presented in this review: the delineation of the ABO gene evolution in a variety of species and the association of single nucleotide variant (SNV) sites in the ABO gene with diseases and biological parameters through genome-wide association studies (GWAS).Copyright © Annals of Blood. All rights reserved.

Design of a Laboratory Developed Assay to Aid in the Detection of Sars-Cov-2 Virus Rna in Oropharyngeal and Nasopharyngeal Swabs Adapted from the Cdc Protocol

Intro: SARS-CoV-2 is a single-strand enveloped RNA virus belonging to the family Coronaviridae. It was first recognized in late 2019 as causing COVID-19, and later declared a pandemic. The development of this assay aided in the detection of positive cases early in the pandemic which in turn facilitated the isolation of infected individuals to minimize the spread. Method(s): The SARS-CoV-2 RNA detection by real time RT-PCR is a molecular in vitro diagnostic test that aids in the detection and diagnosis of SARS-CoV-2 in nasopharyngeal and oropharyngeal specimens. This test is based on nucleic acid extraction and amplification technology and uses oligonucleotide primers and dual-labeled hydrolysis probes. RNA is isolated and purified from specimens using the Abbott m2000sp. This technology uses magnetic particles to capture and purify the RNA. The bound RNA is eluted and transferred to a 96 deep-well plate and is ready for amplification. The master mix is prepared manually and is added to a PCR plate together with the extracted RNA. The RNA is reverse transcribed to cDNA and subsequently amplified in the Abbott m2000rt. In this process, the probe anneals to a specific target sequence located between the forward and reverse primers. During the extension step of the PCR cycle, the 5' nuclease activity of Taq polymerase degrades the probe, causing the reporter dye molecules to be cleaved from their respective probes, increasing the fluorescence intensity. Fluorescence intensity is monitored at each PCR cycle on the Abbott m2000rt instrument. Finding(s): The clinical evaluation was performed by testing patient samples in a blinded fashion. The performance of SARS-CoV-2 Assay was established using 60 clinical specimens. The positive and negative percent agreements were analyzed by comparing the SARS-CoV-2 Assay results to Seegene's AllplexTM 2019-nCoV which showed 100% concordance. Conclusion(s): This assay demonstrated accuracy and reproducibility for the detection of SARS-CoV-2.Copyright © 2023

A New CURE in Molecular Biology: Testing a Novel Pyrrolidine Compound to Determine Mechanism of Action in an Upper-Division Molecular Biology Course

The COVID-19 pandemic shut down forced introductory biology and chemistry laboratory courses online at DePauw University from March 2020-June 2021, leaving multiple classes of students without the opportunity to learn basic laboratory skills that are essential for the molecular biology laboratory. In an effort to provide students with both basic laboratory skills and advanced molecular biology skills, a new course-based undergraduate research experience (CURE) was developed for the 2022-23 academic year. In collaboration with Dr. Jeff Hansen in the Chemistry and Biochemistry department, novel compounds with potential anti-tumor properties were identified. The CURE in Molecular Biology was designed to have students use Saccharomyces cerevisiae as a model system to evaluate possible cellular pathways affected by the compound, including: cytoskeleton and cell migration, nucleotide biosynthesis, glucose metabolism, apoptosis, and cell cycle regulation. Students learned techniques DNA isolation and PCR, transformation, RNA isolation, cDNA synthesis, qPCR, and Western Blotting, while contributing to an active research project. At the conclusion of the project, students were surveyed about their comfort with molecular techniques and data analysis.Copyright © 2023 The American Society for Biochemistry and Molecular Biology, Inc.

Development of PCR diagnostic method for Trichomonas foetus infection based on 18S rRNA.

To establish a PCR detection method for Trichomonas foetus, the primers were designed and synthesized according to the 18S rRNA gene sequence of T. foetus published by GenBank. The positive recombinant plasmid pUCm-T-TF18S of T. foetus was used as the template, and the genomic DNA of Giardia felis, Coccidia +e-lis, feline parvovirus and cDNA of feline coronavirus were used as the control for PCR detection to analyze the specificity of this method. The positive T. foetus recombinant plasmid was serial to 8 different concentrations with a gap of 10 folds, and PCR was performed to analyze the sensitivity of this method. The pUCm-T-TF18S plasmids stored at -20 " for 3, 6, 9 and 12 months were detected by PCR to analyze the stability of the method. Twenty cat fecal samples were tested using this established PCR assay and compared with those of microscopic examination. The results showed that the recombinant plasmid pUCm-T- TF18S gave specific bands after PCR amplification. The sequencing results showed that the length of the product sequence was 1 264 bp, and the BLAST sequence comparison analysis showed 99.53% sequence identity, which is consistent with that of T. foetus from cats (GenBank registration number M81842.1). The PCR method for detection of T. foetus had no cross-reactivities with C. felis, G. felis, feline coronavirus and feline parvovirus;the minimum detectable template concentration is 4.52 X 105 copies/xl;The target band of T. foetus DNA can still be detected after being stored in the refrigerator at -20 " for 12 months. This method detected 16 positive samples of T. foetus nucleic acid from 20 cat fecal samples, which is more accurate and sensitive than the results from traditional microscopy (13 samples). It is suggested that the PCR method for the detection of T. foetus is highly specific, sensitive and stable, and can be used for clinical detection and epidemiological investigation of T. foetus.Copyright © 2022, National Institute of Parasitic Diseases. All rights reserved.

Assessment of different laboratory tests for the diagnosis of novel coronavirus infections

Rapid diagnosis of coronavirus disease 2019 (COVID-19)-infected patients is urgent in making decisions on public health measures. There are different types of diagnostic tests, such as quantitative PCR assay, antibody, and antigen-based and CRISPR-based tests, which detect genetic materials, viral proteins, or human antibodies in clinical samples. However, the proper test should be highly sensitive, quick, and affordable to address this life-threatening situation. This review article highlights the advantages and disadvantages of each test and compares its different features, such as sensitivity, specificity, and limit of detection to reach a reliable conclusion. Moreover, the FDA- authorized kits and studies' approaches toward these have been compared to provide a better perspective to the researchers.Copyright © 2022 Lippincott Williams and Wilkins. All rights reserved.

OPTIMIZATION OF MOLECULAR METHODS FOR SARS-CoV-2 QUALITATIVE DETECTION AND GENOTYPING IN RESPIRATORY SPECIMENS FROM PATIENTS WITH LIVER DISEASE

Introduction and Objectives: SARS-CoV-2 active infection diagnosis is currently performed through RT-qPCR. Despite the fact that PCR-based assays can provide results relatively fast, these techniques require capable professionals, specific equipment and adequate infrastructure. In order to facilitate COVID-19 diagnosis in remote areas, an alternative to RT-qPCR would be loop-mediated isothermal (RT-LAMP) amplification. SARS-CoV-2 variant genotyping through high-throughput sequencing (HTS) allows SARS-CoV-2 genomic surveillance, especially for patients with a higher vulnerability. This study aimed to optimize RT-LAMP and HTS methods for SARS-CoV-2 RNA detection and genotyping, respectively, in respiratory samples from patients with liver disease. Material(s) and Method(s): A total of 142 respiratory secretions were obtained from individuals with SARS-CoV-2 RNA detectable by RT-qPCR (N1 Ct <= 30), divided into groups with (n=18) or without (n=124) liver disease. The study also enrolled 55 individuals who had SARS-CoV-2 RNA undetectable at RT-qPCR. For RT-LAMP methodology, primers were used for ORF1 gene amplification. As for HTS genotyping, the steps of cDNA synthesis, complete SARS-CoV-2 genome PCR amplification, preparation of genomic libraries and sequencing in MinION device were performed for 26 swab samples. Result(s): Samples with viral RNA detectable by RT-qPCR had a mean Ct value of 24.3 +/- 3.75. Referring to RT-LAMP, it was observed a sensitivity of 71.1% (101/142). When considering RT-qPCR mean Ct value, RT-LAMP sensitivity was 88.9% (16/18), associated with a mean Ct of 23.3 +/- 3.5 for patients with COVID and hepatitis. A specificity of 100% (55/55) was observed since all negative swabs tested by RT-qPCR were negative at RT-LAMP. Through sequencing by MinION, SARS-CoV-2 lineages gamma (7/26;27%), zeta (1/26;3.9%), delta (6/26;23%) and omicron (12/26;46.1%) were genotyped and detected by RT-LAMP. Conclusion(s): RT-LAMP demonstrated high sensitivity for molecular detection of SARS-CoV-2 RNA for patients with high viral load. Besides, RT-LAMP was capable of detecting all SARS-CoV-2 lineages genotyped by MinION in both groups.Copyright © 2023

A beginner's guide to RT-PCR, qPCR and RT-qPCR

The development of the polymerase chain reaction (PCR), for which Kary Mullis received the 1992 Novel Prize in Chemistry, revolutionized molecular biology. At around the time that prize was awarded, research was being carried out by Russel Higuchi which led to the discovery that PCR can be monitored using fluorescent probes, facilitating quantitative real-time PCR (qPCR). In addition, the earlier discovery of reverse transcriptase (in 1970) laid the groundwork for the development of RT-PCR (used in molecular cloning). The latter can be coupled to qPCR, termed RT-qPCR, allowing analysis of gene expression through messenger RNA (mRNA) quantitation. These techniques and their applications have transformed life science research and clinical diagnosis.Copyright © The Authors.

Biomarkers of COVID-19 and technologies to combat SARS-CoV-2.

Due to the unprecedented public health crisis caused by COVID-19, our first contribution to the newly launching journal, Advances in Biomarker Sciences and Technology, has abruptly diverted to focus on the current pandemic. As the number of new COVID-19 cases and deaths continue to rise steadily around the world, the common goal of healthcare providers, scientists, and government officials worldwide has been to identify the best way to detect the novel coronavirus, named SARS-CoV-2, and to treat the viral infection - COVID-19. Accurate detection, timely diagnosis, effective treatment, and future prevention are the vital keys to management of COVID-19, and can help curb the viral spread. Traditionally, biomarkers play a pivotal role in the early detection of disease etiology, diagnosis, treatment and prognosis. To assist myriad ongoing investigations and innovations, we developed this current article to overview known and emerging biomarkers for SARS-CoV-2 detection, COVID-19 diagnostics, treatment and prognosis, and ongoing work to identify and develop more biomarkers for new drugs and vaccines. Moreover, biomarkers of socio-psychological stress, the high-technology quest for new virtual drug screening, and digital applications are described.

A Brief Review of Graphene-Based Biosensors Developed for Rapid Detection of COVID-19 Biomarkers.

The prevalence of mutated species of COVID-19 antigens has provided a strong impetus for identifying a cost-effective, rapid and facile strategy for identifying the viral loads in public places. The ever-changing genetic make-up of SARS-CoV-2 posts a significant challenfge for the research community to identify a robust mechanism to target, bind and confirm the presence of a viral load before it spreads. Synthetic DNA constructs are a novel strategy to design complementary DNA sequences specific for antigens of interest as in this review's case SARS-CoV-2 antigens. Small molecules, complementary DNA and protein-DNA complexes have been known to target analytes in minimal concentrations. This phenomenon can be exploited by nanomaterials which have unique electronic properties such as ballistic conduction. Graphene is one such candidate for designing a device with a very low LOD in the order of zeptomolar and attomolar concentrations. Surface modification will be the significant aspect of the device which needs to have a high degree of sensitivity at the same time as providing a rapid signaling mechanism.

Rapid Detection of Attomolar SARS-CoV-2 Nucleic Acids in All-Dielectric Metasurface Biosensors.

Worldwide infection due to SARS-CoV-2 revealed that short-time and extremely high-sensitivity detection of nucleic acids is a crucial technique for human beings. Polymerase chain reactions have been mainly used for the SARS-CoV-2 detection over the years. However, an advancement in quantification of the detection and shortening runtime is important for present and future use. Here, we report a rapid detection scheme that is a combination of nucleic acid amplification and a highly efficient fluorescence biosensor, that is, a metasurface biosensor composed of a pair of an all-dielectric metasurface and a microfluidic transparent chip. In the present scheme, we show a series of proof-of-concept experimental results that the metasurface biosensors detected amplicons originating from attomolar SARS-CoV-2 nucleic acids and that the amplification was implemented within 1 h. Furthermore, this detection capability substantially satisfies an official requirement of 100 RNA copies/140 µL, which is a criterion for the reliable infection tests.

Feasibility and accuracy verification of respiratory virus detection by mask virus extraction

OBJECTIVE: To explore a new method for detecting respiratory viruses by extracting residual virus on mask, and verify its reliability and sensitivity. METHODS: The novel coronavirus analogs-s La Sota strains of chicken Newcastle disease virus and H120 strains of infectious bronchitis virus with different diluted concentrations were sprayed onto surgical masks and N95 masks through a respiratory simulator, and they were left standing at room temperature for 2 hours and 12 hours, respectively. The cDNA and its amplification cycle(CT) values of the nucleoocapsid protein(N) of chicken Newcastle disease virus and the nucleoprotein(NP) genes of infectious bronchitis virus were detected by ordinary polymerase chain reaction(PCR) and quantitative real-time PCR(qRT-PCR). The minimum detectable virus concentration and viral content in masks under different retention times were compared. RESULTS: The gene bands of the Newcastle disease virus La Sota strains and the infectious bronchitis virus H120 strains were detected on the masks stored for different times, and the total RNA of the virus had good amplification curves in the range of 10 pg-10 ng. The mean CT values of N gene and NP gene of the residual virus on the general medical surgical mask and N95 masks placed for 2 h were 22.547+or-0.342,23.698+or-0.501 and 22.855+or-0.308,24.036+or-0.338, respectively. However, only part of them could be detected after 12 h. respectively, and there was no significant difference in CT values between the two masks during the same period of time(P2 h=0.452, P12 h=0.355). The minimum detectable concentration of virus in the masks was 1:800, and the number of residual viruses on the mask that can be detected was 6.75x10~3. CONCLUSION: The method of screening coronavirus by detecting virus residues on masks within 2 hours was feasible and suitable for medical surgical masks and N95 masks, which can be used for preliminary screening of respiratory viruses.

Genomic surveillance of SARS-CoV-2 in Kenya: March 2020-October 2021

Introduction/ Background: By end of October 2021, the Ministry of Health had confirmed over 250 thousand SARS-CoV-2 cases in Kenya following identification of the initial cases in March 2020. We setup a genome surveillance platform in Kenya to track introductions, local evolution and transmission of SARS-CoV-2 within the country and the region. Methods: Samples were collected from designated diagnostic centres across 47 Kenyan counties. Viral RNA was extracted from the Nasal and oropharyngeal swabs from RT-PCR confirmed cases followed by viral amplification of recovered cDNA using the ARTIC nCoV-2019 primer set and thereafter library preparation and sequencing using the Oxford Nanopore MinION platform. The raw signal files were base-called and processed to obtain consensus sequences followed by SARSCoV- 2 lineage assignment and phylogenetics analysis. Results: Phylogenetics and epidemiological analysis of 4,200 sequences provided insight on introduction of SARSCoV- 2 in Kenya. The first (March-September 2020), second (October 2020-February 2021) waves of infections were dominated by B-like lineages. The third wave (March-June 2021) coincided with introduction of Alpha and Beta variants (December 2020), merging into the fourth wave (June-October 2021), the Delta variant in April 2021. Ancestral reconstruction identified multiple introductions of the basal lineages (37<n<69) and Variants of Concern (Beta (n=14), Alpha (n=83), Delta (n=92)). We observed rapid replacement of ancestral lineages leading to dominance of the Delta variant that comprised the fourth wave of infections. Impact: Our genomic surveillance platform has improved monitoring of the diversity of circulating variants of concern (VOCs) and revealed transitions across the country in the dominance VOCs detected between late 2020 to October 2021. This output had fed into national decision-making through regular policy briefs. Conclusion: The Delta variant is the dominant variant of concern across the country. Genomic surveillance of SARSCoV- 2 should focus on identifying the emergence of local mutations with the potential to confer additional transmissibility and antigenic drift, particularly in the background of inadequate vaccine coverage and waning natural immunity.

Characterization of SARS-CoV-2 using the Ion AmpliSeq SARS-CoV-2 research panel

Background: The rapid spread of COVID-19 has resulted in an urgent need for effective diagnostic and therapeutic strategies against SARS-CoV-2. Next-generation sequencing (NGS) is a powerful tool in the identification and characterization of this pathogen and genomic information may aid in understanding the mechanisms of therapeutic resistance, vaccine escape, virulence, and pathogenicity. The Ion AmpliSeq SARS-CoV-2 Research Panel is a targeted NGS solution that facilitates sequence analysis of the SARS-CoV-2 genome. Paired with a bioinformatics assembly and variant calling pipelines, this assay allows for accurate characterization of the dominant SARS-CoV-2 variant. This assay's performance was analytically validated for the detection of mutations (substitutions, insertions, and deletions) in RNA derived from nasopharyngeal (NP) swabs. Method: The Ion AmpliSeq SARS-CoV-2 Research panel consists of two primer pair pools generating 237 amplicons specific to the SARS-CoV-2 virus. Reverse transcription of the RNA was performed using the SuperScript VILO cDNA Synthesis kit. Library preparation was then completed using the Ion AmpliSeq Library Kit Plus kit. The final library was quantified, normalized, pooled, and sequenced. Raw sequencing data was aligned to the AmpliSeq SARS-CoV-2 Research panel, using the MN908947.3 reference genome. Variants were called using the Torrent Variant Caller and annotated using the COVID19AnnotateSnpEff plugin. The reference-guided iterative assembler IRMA was used to produce a single consensus sequence consisting of the reference genome sequence modified to include sequence variations supported by the reads. The Pangolin COVID-19 lineage assigner software tool was used to assign SARS-CoV-2 lineage. Analytical validation was completed using controls (Twist Biosciences, BEI Resources, ATCC) and RNA derived from NP swabs. Accuracy and specificity were examined by evaluating the correctness of calling true negative variants compared to false positive and all other variant calls, respectively. Precision and limit of detection (LoD) were examined by evaluating the concordance of variants across replicate samples. Limit of Blank (LoB) was calculated as the 95th percentile of reads per amplicon in the negative samples. Results: Accuracy of base calling, specificity, and precision were 100% for SNVs, insertions, and deletions above 25% allele frequency. LoD was determined to be 576 viral copies/mL. LoB was determined to be 202 reads per amplicon. Pangolin lineage assignment was 100% for all samples. Conclusions: This panel accurately characterizes SARS-CoV-2 variants, allowing for accurate consensus sequence generation, mutation annotation, and lineage assignment.

Rapid and Highly Sensitive Detection of Target DNA Related to COVID-19 Virus With a Fluorescent Bio-conjugated Probe via a FRET Mechanism.

A novel cyanine 3 (Cy3)-based bio-conjugated sensor has been developed to detect target DNA or extracted RNA from COVID -19 samples using the fluorescence resonance energy transfer (FRET) experiment. A special sequence of the COVID -19 genome was selected as a complementary DNA (target DNA) part. The opposite chain of this target sequence was designed in 2 parts; one part was attached to the Cy3 organic dye (capture DNA or Cy3- DNA), and the other part was attached to the BHQ2 molecule (quencher DNA or BHQ2- DNA). The Cy3 molecule acts as a donor pair, and BHQ2 acts as an acceptor pair in the FRET experiment. The capture DNA and quencher DNA can form a sandwiched complex in the presence of target DNA. The formation of the entitled sandwiched hybrid causes the decrement of emission intensity of the Cy3 donor in bio-conjugated Cy3-DNA via energy transfer from Cy3 (as a donor) to BHQ2 (as an acceptor). Indeed, in the presence of non-complementary DNA, the pairing of DNA strands does not occur, the FRET phenomenon does not exist, and therefore fluorescence intensity of Cy3 does not decrease. Moreover, this biosensor was successfully applied to analyze real samples containing extracted RNA of COVID -19 prepared for the reverse transcriptase-polymerase chain reaction (RT-PCR) test, and the results were promising.

ORF1 REGION of SARS-C V-2 GENOMIC RNA AS A PROMISING TARGET for siRNA-BASED THERAPY

Background: A promising approach to tackle the Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) could be small interfering (si)RNAs. However, it is unclear so far, which viral replication steps can be efficiently inhibited with siRNAs. Here we report the first-ever in-depth analysis of RNAi-accessible SARS-CoV-2 replication steps. Methods: siRNAs were designed against four genomic regions of SARS-CoV-2. Initial screening of siRNA activity was performed with a dual luciferase reporter assay. Efficacy of siRNAs to terminate various viral replication steps was analyzed by infecting VeroE6 cells with wildtype SARS-CoV-2 or a GFP expressing recombinant SARS-CoV-2 and monitoring viral spread in real-time by time-lapse fluorescence microscopy. Positive and negative sense viral RNA transcripts were distinctly quantified via sense specific cDNA synthesis and reverse-transcriptase quantitative PCR. Finally, the antiviral activity of the siRNAs was primarily evaluated in a highly relevant model, SARS-CoV-2 infected human lung explants. Results: When applied in a prophylactic fashion, siRNAs were able to target genomic RNA (gRNA) of SARS-CoV-2 after cell entry, terminating replication before start of transcription, thereby preventing cytopathic effects. Surprisingly, siRNAs were not active against intermediate negative sense transcripts formed during replication. Targeting sequences that are commonly shared by all viral transcripts indeed allowed a simultaneous suppression of gRNA and subgenomic (sg)RNAs by a single siRNA. However, siRNAs that targeted ORF1 which is solely part of gRNA, presented an enhanced antiviral activity. We show that the reason for this was that siRNAs that targeted the common regions of transcripts were outcompeted by the highly abundant sgRNAs. Based on these findings, we developed a chemically stabilized siRNA, which targets a highly conserved region of ORF1, and which inhibited SARS-CoV-2 replication by >90% ex vivo in explants of the human lung. Conclusion: Our work strongly encourages the development of siRNA-based therapies for COVID-19 and suggests that early therapy start, or prophylactic application, together with targeting ORF1, might be key for high antiviral efficacy.

Hybridoma technology: is it still useful?

The isolation of single monoclonal antibodies (mAbs) against a given antigen was only possible with the introduction of the hybridoma technology, which is based on the fusion of specific B lymphocytes with myeloma cells. Since then, several mAbs were described for therapeutic, diagnostic, and research purposes. Despite being an old technique with low complexity, hybridoma-based strategies have limitations that include the low efficiency on B lymphocyte-myeloma cell fusion step, and the need to use experimental animals. In face of that, several methods have been developed to improve mAb generation, ranging from changes in hybridoma technique to the advent of completely new technologies, such as the antibody phage display and the single B cell antibody ones. In this review, we discuss the hybridoma technology along with emerging mAb isolation approaches, taking into account their advantages and limitations. Finally, we explore the usefulness of the hybridoma technology nowadays.

FNCAS9 editor linked uniform detection assay (FELUDA)

The present invention describes a method for Tusing a bacterial CRISPR Cas Ribonucleoprotein complex for detecting single nucleotide variants in RNA or DNA or more broadly, any DNA or RNA fragment, without the need for sequencing. The principle ofdiscrimination is derived from the natural property of the enzyme being used for the invention, Francisellanovicida Cas9 (FnCas9) which shows very low binding affinity to mismatched substrates. DNA is isolated either from blood, saliva, or any other biological sources like bacteria and amplified if required. For virus infected patients, samples are collected as a nasal swab and inactivated. Total RNA isolated from the sample is converted to cDNA using the reverse transcriptase enzyme. The DNA (when test material is DNA) or cDNA (when test material is RNA, like for COVID-19) is subjected to Polymerase Chain reaction, amplifying using specific primers and tagging the amplified DNA products with a ligand of choice. The detection mix consists of labelled PCR products, sgRNA-fnCAS9 complex. The detection complex can be visualized using a wide array of technologies like lateral flow, gel based cleavage assay, fluorescence based detection, in both low, medium or plate based high-throughput format. Science behind this technology will be discussed in the presentation.

SARS-CoV2 Reinfections in a University Teaching Hospital

Background. The consequences of SARS-CoV2 reinfections for patients, healthcare workers and society are unclear. We reviewed the clinical, laboratory, and epidemiological characteristics of patients re-infected with genetically distinct strains of SARS-CoV2 identified by Whole Virus Genome Sequencing (WvGS). Methods. Cases were selected based on a positive SARS-CoV-2 Reverse Transcriptase Polymerase Chain Reaction (RT-PCR) test, clinical resolution, a negative interim test and a subsequent positive nasopharyngeal swab. Positive samples were prepared for sequencing by cDNA synthesis, tiled-PCR following the ARTIC protocol and amplicon sequencing using Illumina MiSeq platform. Raw reads were mapped to the reference sequence using bowtie and Samtools was used for variants calling and to generate the consensus sequences. Comparative sequence analysis was conducted by phylogenetic inference maximum likelihood method with RAxML using the multiple sequence aligned by MAFFT. Clades and variants were assigned respectively using Nextstrain and Pangolin COVID-19 lineage assigner (Figure 1). The clinical, radiological and laboratory data were collected from patient medical notes and laboratory information system. Results. Two cases of SARS-CoV-2 reinfection were detected by RT-PCR (patient 1 and 2). CT values and strain variants are presented in Table 1. The time between detection of the first and second infection was 67 and 270 days respectively. WvGS confirmed that the second episodes were due to a genetically distinct strain of SARS CoV2. These reflected the dominant contemporaneous variants in circulation. Both patients were immunocompromised from co-morbidities and medications. First and subsequent infections were minimally symptomatic. Both cases were associated with known hospital outbreaks. They passed away within 2 weeks of the second infection of unrelated causes. Conclusion. Two patients in this study were diagnosed with a SARS-CoV-2 reinfection confirmed by WvGS. A common factor in these cases was immunocompromise. Where a previously infected patient test shows a new positive or an unexpected reduction in CT value is observed, we recommend individual risk assessment to determine the timing of discontinuation of isolation and infection control precautions.

LUNG ACE2 AND TMPRSS2 GENE EXPRESSION VARIES WITH ALLERGEN EXPOSURES IN MURINE MODELS OF ASTHMA

Introduction: The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) requires angiotensin-converting enzyme 2 (ACE2) and the transmembrane protease, serine 2 (TMPRSS2) for cell entry. Prior studies have reported that allergen exposure can downregulate ACE2 expression. Here, we sought to determine if exposure to distinct combinations of allergens results in the differential expression of ACE2 and TMPRSS2 in the mouse lung. Methods: We utilized three established murine models of asthma: 1. Alum/Ovalbumin (OVA) model;2. House dust mite (HDM)/OVA model;3. Mixed-allergen (MA) model using OVA, HDM, Aspergillus fumigatus and Alternaria alternata. Phosphate-buffered saline (PBS) treated mice were used as controls. Lung RNA was extracted using the RNeasy Mini Kit (Qiagen) according to the manufacturer’s protocol, and complementary DNA was synthesized. Quantitative PCR (qPCR) was performed 24 hours after the last challenge utilizing validated primers for ACE2 and TMPRSS2. Analysis was performed using one-way ANOVA. Results: Here we report that ACE2 mRNA expression was lower in the MA and Alum/OVA-treated mice compared to the controls (p-value < 0.0001). No difference was seen in the ACE2 mRNA expression between HDM/OVA and PBS-treated mice. Furthermore, HDM/OVA-treated mice expressed higher levels of TMPRSS2 mRNA compared to controls (p-value < 0.01). No difference was seen in the TMPRSS2 mRNA expression between the MA or Alum/OVA, and the PBS-treated mice. Conclusion: The exposure to distinct combinations of allergens results in unique patterns of ACE2 and TMPRSS2 gene expression in the mouse lung. Further studies are required to evaluate the effects of allergen exposure with the susceptibility to SARS-CoV-2 infection.

Investigation of patient and viral characteristics associated with SARS-CoV-2 vaccine breakthrough infections in Atlanta, GA

Purpose of Study Despite the tremendous success of SARSCoV- 2 vaccines, breakthrough infections occur and are being recognized with increasing frequency. It is unclear whether breakthrough infections are the result of host and/or viral factors. We examined clinical and viral genomic data from patients with SARS-CoV-2 infection after vaccination to elucidate factors contributing to breakthrough. Methods Used This study was conducted in the Emory Healthcare (EHC) System. Patients with vaccine breakthrough infection, defined as a positive PCR test ≥14 days after the final dose of an FDA approved vaccine, were identified by both routine surveillance and notification by treating clinicians. Vaccination status was obtained from the Georgia Registry of Immunization Transactions and Services records by the Georgia Emerging Infections Program. Clinical information was derived from electronic medical records and was compared to data from 2-3 matched controls per case. Residual SARS-CoV-2 positive nasopharyngeal (NP) samples were collected and underwent RNA extraction. SARSCoV- 2 genome sequencing was performed using random-primer cDNA synthesis, Nextera XT library preparation, and Illumina sequencing. Summary of Results Forty vaccine breakthrough cases were identified between March 22 and July 16, 2021. The median time from final vaccine dose to positive COVID-19 test was 91 days (range 15-163). Compared to 94 controls, vaccine breakthrough cases were significantly older (median 57.5 years vs 42.0 years, p<.0001). Individuals over 60 accounted for half of all breakthrough cases, and individuals over 40 accounted for 80%. Immunosuppressed individuals represented 37.5% of breakthrough cases compared to 25% of unvaccinated controls. Rates of symptomatic infection and severe disease leading to hospitalization were similar between cases and controls. There was no difference in SARS-CoV-2 RT-PCR cycle threshold (Ct) between cases (n=32, median Ct=20.7, interquartile range (IQR)- 10.3) and controls (n=94, median Ct=24.0, IQR= 7.0;p=0.34). SARS-CoV-2 genome sequences from 24 cases were compared to 116 baseline surveillance sequences from unvaccinated EHC patients. There was no distinct phylogenetic clustering of vaccine breakthrough cases, and their sequences belonged to the predominant lineage of the time. From March 22-June 19, B.1.1.7 (alpha) accounted for 78% of breakthrough infections and 77% of surveillance sequences. From June 20-July 16, B.1.617.2 (delta) accounted for 86% of breakthrough infections and 72% of surveillance sequences. No spike mutations or deletions were associated with vaccine breakthrough infections. Conclusions Overall, our findings suggest that host factors, such as older age and immunosuppression, play a more important role than viral factors in SARS-CoV-2 vaccine breakthrough infections. Further studies are needed to understand the potential impacts of waning immunity or poor immunogenicity in individuals who experience vaccine breakthrough infections.