Corrigendum: Identification and analysis of SARS-CoV-2 alpha variants in the largest Taiwan COVID-19 outbreak in 2021.

[This corrects the article DOI: 10.3389/fmed.2022.869818.].

Observational cohort study of the clinical outcomes associated with B.1.1.7/SGTF among hospitalized COVID-19 patients in Lebanon.

Background: The B.1.1.7 SARS-CoV-2 variant results in spike gene target failure (SGTF) in reverse transcription-quantitative polymerase chain reaction (RT-PCR) assays. Few studies have been published on the clinical impact of B.1.1.7/SGTF. Aims: To assess the incidence of B.1.1.7/SGTF and its associated clinical characteristics among hospitalized COVID-19 patients. Methods: This observational, single-centre, cohort study was conducted between December 2020 and February 2021 and included 387 hospitalized COVID-19 patients. The Kaplan-Meier method was used for survival analysis, and logistic regression to identify risk factors associated with B.1.1.7/SGTF. Results: By February 2021, B.1.1.7/SGTF (88%) dominated the SARS-CoV-2 PCR results in a Lebanese hospital. Of the 387 eligible COVID-19 patients confirmed by SARS-CoV-2 RT-PCR, 154 (40%) were non-SGTF and 233 (60%) were B.1.1.1.7/SGTF; this was associated with a higher mortality rate among female patients [22/51 (43%) vs 7/37 (19%); P = 0.0170]. Among patients in the B.1.1.7/SGTF group, most were aged ≥ 65 years [162/233 (70%) vs 74/154 (48%); P < 0.0001]. Independent predictors of B.1.1.7/SGTF infection were hypertension (OR = 0.415; CI: 0.242-0.711; P = 0.0010), age ≥ 65 years (OR = 0.379; CI: 0.231-0.622; P < 0.0001), smoking (OR = 1.698; CI: 1.023-2.819; P = 0.0410), and cardiovascular disease (OR = 3.812; CI: 2.215-6.389; P < 0.0001). Only non-SGTF patients experienced multi-organ failure [5/154 (4%) vs 0/233 (0%); P = 0.0096]. Conclusion: There was a clear difference between the clinical features associated with B.1.1.7/SGTF and non-SGTF lineages. Tracking viral evolution and its clinical impact is crucial for proper understanding and management of the COVID-19 pandemic.

A Comparison of Nasal Mucociliary Clearance Time in COVID-19 and Variant COVID-19 Patients

Objective: The aim of this study was to compare nasal mucociliary clearance times in coronavirus disease 2019 and variant coronavirus disease 2019 patients and a control group. Methods: The study was conducted in Karaman Training and Research Hospital between April 2021 and June 2021. Three groups were formed. Group 1 included 41 coronavirus disease 2019 patients, group 2 included 41 patients diagnosed with variant coronavirus disease 2019, and group 3 included 42 patients from the ear, nose, and throat polyclinic with no nasal symptoms. The primary outcome was nasal mucociliary clearance time and sinonasal outcome test-22 scores. Results: The mean nasal mucociliary clearance time was 12.87 +/- 2.46 minutes in group 1, 14.02 +/- 2.95 minutes in group 2, and 8.57 +/- 1.25 minutes in group 3. Nasal mucociliary clearance time was significantly different between groups 1 and 3 and between groups 2 and 3 but not between groups 1 and 2 (P =.07). The nasal mucociliary clearance times of group 2 were determined to be higher than those of group 1. The mean sinonasal outcome test-22 score was 24.70 +/- 6.65 in group 1 and 23.92 +/- 7.01 in group 2, with no significant difference determined between the groups (P >.05). Conclusion: Nasal mucociliary clearance time was higher in coronavirus disease 2019 and variant coronavirus disease 2019 patients than in the control group. There is a need for further studies to be able to understand the underlying pathophysiology of prolonged nasal mucociliary clearance time.

First confirmation of importation and transmission in Spain of the newly identified SARS-CoV-2 B.1.1.7 variant.

INTRODUCTION: A newly identified SARS-CoV-2 variant, VOC202012/01 originating lineage B.1.1.7, recently emerged in the United Kingdom. The rapid spread in the UK of this new variant has caused other countries to be vigilant. MATERIAL AND METHODS: We based our initial screening of B.1.1.7 on the dropout of the S gene signal in the TaqPath assay, caused by the 69/70 deletion. Subsequently, we confirmed the B.1.1.7 candidates by whole genome sequencing. RESULTS: We describe the first three imported cases of this variant from London to Madrid, subsequent post-arrival household transmission to three relatives, and the two first cases without epidemiological links to UK. One case required hospitalization. In all cases, drop-out of gene S was correctly associated to the B.1.1.7 variant, as all the corresponding sequences carried the 17 lineage-marker mutations. CONCLUSION: The first identifications of the SARS-CoV-2 B.1.1.7 variant in Spain indicate the role of independent introductions from the UK coexisting with post-arrival transmission in the community, since the early steps of this new variant in our country.

Virus-Specific Stem Cell Memory CD8+ T Cells May Indicate a Long-Term Protection against Evolving SARS-CoV-2.

Immune memory to SARS-CoV-2 is key for establishing herd immunity and limiting the spread of the virus. The duration and qualities of T-cell-mediated protection in the settings of constantly evolving pathogens remain an open question. We conducted a cross-sectional study of SARS-CoV-2-specific CD4+ and CD8+ T-cell responses at several time points over 18 months (30-750 days) post mild/moderate infection with the aim to identify suitable methods and biomarkers for evaluation of long-term T-cell memory in peripheral blood. Included were 107 samples from 95 donors infected during the periods 03/2020-07/2021 and 09/2021-03/2022, coinciding with the prevalence of B.1.1.7 (alpha) and B.1.617.2 (delta) variants in Bulgaria. SARS-CoV-2-specific IFNγ+ T cells were measured in ELISpot in parallel with flow cytometry detection of AIM+ total and stem cell-like memory (TSCM) CD4+ and CD8+ T cells after in vitro stimulation with peptide pools corresponding to the original and delta variants. We show that, unlike IFNγ+ T cells, AIM+ virus-specific CD4+ and CD8+ TSCM are more adequate markers of T cell memory, even beyond 18 months post-infection. In the settings of circulating and evolving viruses, CD8+ TSCM is remarkably stable, back-differentiated into effectors, and delivers immediate protection, regardless of the initial priming strain.

In Silico Analysis of SARS-CoV-2 Spike Proteins of Different Field Variants.

Coronaviruses belong to the group of RNA family of viruses that trigger diseases in birds, humans, and mammals, which can cause respiratory tract infections. The COVID-19 pandemic has badly affected every part of the world. Our study aimed to explore the genome of SARS-CoV-2, followed by in silico analysis of its proteins. Different nucleotide and protein variants of SARS-CoV-2 were retrieved from NCBI. Contigs and consensus sequences were developed to identify these variants using SnapGene. Data of the variants that significantly differed from each other was run through Predict Protein software to understand the changes produced in the protein structure. The SOPMA web server was used to predict the secondary structure of the proteins. Tertiary structure details of the selected proteins were analyzed using the web server SWISS-MODEL. Sequencing results showed numerous single nucleotide polymorphisms in the surface glycoprotein, nucleocapsid, ORF1a, and ORF1ab polyprotein while the envelope, membrane, ORF3a, ORF6, ORF7a, ORF8, and ORF10 genes had no or few SNPs. Contigs were used to identify variations in the Alpha and Delta variants of SARS-CoV-2 with the reference strain (Wuhan). Some of the secondary structures of the SARS-CoV-2 proteins were predicted by using Sopma software and were further compared with reference strains of SARS-CoV-2 (Wuhan) proteins. The tertiary structure details of only spike proteins were analyzed through the SWISS-MODEL and Ramachandran plots. Through the Swiss-model, a comparison of the tertiary structure model of the SARS-CoV-2 spike protein of the Alpha and Delta variants was made with the reference strain (Wuhan). Alpha and Delta variants of the SARS-CoV-2 isolates submitted in GISAID from Pakistan with changes in structural and nonstructural proteins were compared with the reference strain, and 3D structure mapping of the spike glycoprotein and mutations in the amino acids were seen. The surprisingly increased rate of SARS-CoV-2 transmission has forced numerous countries to impose a total lockdown due to an unusual occurrence. In this research, we employed in silico computational tools to analyze the SARS-CoV-2 genomes worldwide to detect vital variations in structural proteins and dynamic changes in all SARS-CoV-2 proteins, mainly spike proteins, produced due to many mutations. Our analysis revealed substantial differences in the functionality, immunological, physicochemical, and structural variations in the SARS-CoV-2 isolates. However, the real impact of these SNPs can only be determined further by experiments. Our results can aid in vivo and in vitro experiments in the future.

Tracing COVID-19 Trails in Wastewater: A Systematic Review of SARS-CoV-2 Surveillance with Viral Variants

The emergence of new variants of SARS-CoV-2 associated with varying infectivity, pathogenicity, diagnosis, and effectiveness against treatments challenged the overall management of the COVID-19 pandemic. Wastewater surveillance (WWS), i.e., monitoring COVID-19 infections in communities through detecting viruses in wastewater, was applied to track the emergence and spread of SARS-CoV-2 variants globally. However, there is a lack of comprehensive understanding of the use and effectiveness of WWS for new SARS-CoV-2 variants. Here we systematically reviewed published articles reporting monitoring of different SARS-CoV-2 variants in wastewater by following the PRISMA guidelines and provided the current state of the art of this study area. A total of 80 WWS studies were found that reported different monitoring variants of SARS-CoV-2 until November 2022. Most of these studies (66 out of the total 80, 82.5%) were conducted in Europe and North America, i.e., resource-rich countries. There was a high variation in WWS sampling strategy around the world, with composite sampling (50/66 total studies, 76%) as the primary method in resource-rich countries. In contrast, grab sampling was more common (8/14 total studies, 57%) in resource-limited countries. Among detection methods, the reverse transcriptase polymerase chain reaction (RT-PCR)-based sequencing method and quantitative RT-PCR method were commonly used for monitoring SARS-CoV-2 variants in wastewater. Among different variants, the B1.1.7 (Alpha) variant that appeared earlier in the pandemic was the most reported (48/80 total studies), followed by B.1.617.2 (Delta), B.1.351 (Beta), P.1 (Gamma), and others in wastewater. All variants reported in WWS studies followed the same pattern as the clinical reporting within the same timeline, demonstrating that WWS tracked all variants in a timely way when the variants emerged. Thus, wastewater monitoring may be utilized to identify the presence or absence of SARS-CoV-2 and follow the development and transmission of existing and emerging variants. Routine wastewater monitoring is a powerful infectious disease surveillance tool when implemented globally.

RT-qPCR based determination of SARS-CoV-2 in health care workers, Cologne, Germany - A pre-delta/pre-omicron proof of principle field study

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), causing coronavirus disease 2019 (COVID-19), and SARS-CoV-2 variants pose an increased risk to global health. Therefore, monitoring of SARS-CoV-2 variants of concern (VOCs) is of high importance for the implementation of disease control methods, for timely public health decisions, and the development of vaccines against SARS-CoV-2 variants. In this study, which was performed before the delta and omicron variants of concern became dominant, a total of 111 SARS-CoV-2 positive samples from our hospital staff in Cologne, Germany, collected from March 2020 to May 2021 were analysed for VOCs. For determination of VOCs, mutation genotyping analysis (MGA) using mutation-specific simple (MSS) probes based on quantitative reverse transcription-polymerase chain reaction (RT-qPCR) of ten spike protein variants (SPVs) was performed. The MGA focuses on the detection of the spike protein mutation (SPM) of SPVs belonging to VOCs. By successful determination of SPV, the work concludes that 24.66 % of the samples belong to VOC B.1.1.7 and 1.37 % of the samples belong to VOC B.1.351. Based on these results, MGA proves to be a suitable alternative to sequencing technologies as it is a rapid, cost-effective, widely available, and feasible method that allows high sample throughput for the determination of circulating and monitored SARS-CoV-2 VOCs. With focus on the novel variants such as SARS-CoV-2 omicron BA.4 and BA.5 similar approaches could be used for a rapid initial screening, while, however, due to the increasing number of single nucleotide polymorphisms that determine the variants of concern in depth screening becomes more cost efficient by next generation sequencing.Copyright © 2022 AEPress, s.r.o.. All rights reserved.

Insights from comparison of the clinical presentation and outcomes of patients hospitalized with COVID-19 in an Italian internal medicine ward during first and third wave.

Background: The reasons of variability of clinical presentation of coronavirus disease-19 (COVID-19) across different pandemic waves are not fully understood, and may include individual risk profile, SARS-CoV-2 lineage and seasonal variations of viral spread. The objective of this retrospective study was to compare the characteristics and outcomes of patients admitted with confirmed coronavirus disease-19 (COVID-19) in the same season during the first (March 2020) and the third pandemic wave (March 2021, dominance of SARS-CoV-2 B.1.1.7 lineage) in an internal medicine ward of a large teaching hospital in Italy. Materials and methods: Data of 769 unvaccinated patients (399 from the first and 370 from the third wave) were collected from clinical records, including symptom type and duration, extension of lung abnormalities on chest computed tomography (CT) and PaO2/FiO2 ratio on admission arterial blood gas analysis. Results: Third wave patients were in average younger (median 65, interquartile range [IQR] 55-75, vs. 72, IQR 61-81 years old, p < 0.001), with less comorbidities and better pulmonary (CT visual score median 25, IQR 15-40, vs. 30, IQR 15-50, age- and sex-adjusted p = 0.017) and respiratory involvement (PaO2/FiO2 median 288, IQR 237-338, vs. 233, IQR 121-326 mmHg, age- and sex-adjusted p < 0.001) than first wave patients. Hospital mortality was lower (19% vs. 36%, p < 0.001), but not for subjects over 75 years old (46 vs. 49%). Age, number of chronic illnesses, PCT levels, CT visual score [Odds Ratio (OR) 1.022, 95% confidence interval (CI) 1.009-1.036, p < 0.001] and PaO2/FiO2 (OR 0.991, 95% CI 0.988-0.994, p < 0.001), but not the pandemic wave, were associated with mortality on stepwise multivariate logistic regression analysis. Conclusion: Despite the higher virulence of B.1.1.7 lineage, we detected milder clinical presentation and improved mortality in patients hospitalized during the third COVID-19 wave, with involvement of younger subjects. The reasons of this discrepancy are unclear, but could involve the population effect of vaccination campaigns, that were being conducted primarily in older frail subjects during the third wave.

Detection of SARS-CoV-2 Genome for over 100 Days after COVID-19 Onset.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of coronavirus disease 2019 (COVID-19), is spreading globally. Generally, the viral genome becomes undetectable within a couple of weeks after infection. Herein, we report a case of long-term detection of the SARS-CoV-2 genome in the same individual for 106 days. Whole genome sequencing was performed on specimens taken at the onset of the disease and 2 months after onset, and the B.1.1.7 lineage was detected in both samples. A comparison of the full-length sequences revealed a single-base difference and no amino acid mutations. This is the first case in Japan where the virus was detected over a long period, and the full-length sequences were compared.

New Postmortem Perspective on Emerging SARS-CoV-2 Variants of Concern, Germany.

We performed autopsies on persons in Germany who died from COVID-19 and observed higher nasopharyngeal SARS-CoV-2 viral loads for variants of concern (VOC) compared with non-VOC lineages. Pulmonary inflammation and damage appeared higher in non-VOC than VOC lineages until adjusted for vaccination status, suggesting COVID-19 vaccination may mitigate pulmonary damage.

Severe acute respiratory syndrome coronavirus-2 Alpha variant (B.1.1.7), original wild-type severe acute respiratory syndrome coronavirus 2, and cytomegalovirus co-infection in a young adult with acute lymphoblastic leukemia, case report, and review of the possible cytomegalovirus reactivation mechanisms.

BACKGROUND: Like other viral infections, severe acute respiratory syndrome coronavirus-2 infection could affect different human body systems, including host immune responses. Three years after its pandemic, we learn more about this novel coronavirus. As we expected, different co-infections with various organisms, such as viruses, bacteria, and even fungi, have been reported. However, concurrent infection with two severe acute respiratory syndrome coronavirus-2 strains and cytomegalovirus is extremely unusual. We have only a rudimentary understanding of such co-infections and their long-term consequences for patients with cancer. CASE PRESENTATION: An 18-year-old young Iranian adult with acute lymphoblastic leukemia presented with abdominal pain, diarrhea, nausea, and vomiting following a recent history of severe acute respiratory syndrome coronavirus-2 infection. The patient never experienced respiratory symptoms, and the chest imaging study was normal on admission. His primary laboratory investigation revealed prerenal azotemia and severe abnormal liver function tests (blood urea nitrogen 32 mg/dL, creatinine 1.75 mg/dL, prothrombin time 66 s, partial thromboplastin time 44.5 s, international normalized ratio 5.14, total bilirubin 2.9 mg/dL, and direct bilirubin 2.59 mg/dL). Cytomegalovirus disease was diagnosed by polymerase chain reaction in his blood and stool samples. The patient's gastrointestinal signs and symptoms improved shortly after receiving intravenous ganciclovir treatment. His gastrointestinal symptoms continued intermittently for weeks despite maintenance valganciclovir prescription, necessitating frequent hospitalizations. The patient was complicated by the recurrence of gastrointestinal symptoms during the sixth hospitalization, even though he had no respiratory symptoms, and the nasopharyngeal test revealed severe acute respiratory syndrome coronavirus-2 Wuhan strain for the first time. Remdesivir and valganciclovir were administrated due to persistent enteritis and evidence of intestinal tissue invasion by severe acute respiratory syndrome coronavirus 2 and cytomegalovirus on multiple intestinal biopsies, which led to partial clinical responses. Cytomegalovirus and severe acute respiratory syndrome coronavirus-2 fecal shedding continued for more than 6 months despite repeated antiviral therapy, and the Wuhan and Alpha strains were also detected in his nasopharyngeal samples through repeated sampling (confirmed by four nasopharyngeal sampling and multiple stool specimens and several intestinal biopsies). Finally, during the Delta-variant (B.1.617.2) outbreak in Iran, the patient was admitted again with febrile neutropenia and decreased level of consciousness, necessitating respiratory support and mechanical ventilation. During the Delta-variant peak, the patient's nasopharyngeal sample once more tested positive for severe acute respiratory syndrome coronavirus 2. The patient died a few days later from cardiopulmonary arrest. CONCLUSION: The coronavirus disease 2019 pandemic has encountered patients with cancer with critical diagnostic and treatment challenges. Patients who are immunocompromised may co-infect with multiple severe acute respiratory syndrome coronavirus-2 strains and cytomegalovirus, and even with timely diagnosis and treatment, the prognosis may be poor.

The importance of LDH/Albumin, LDH/Lymphocyte, and LDH/Platelet ratios in the evaluation of COVID-19 B.1.1.7 variant

Objectives: The aim is to investigate the usefulness of lactate dehydrogenase (LDH)/Albumin, LDH/Lymphocyte and LDH/Platelet ratios on the prognosis of coronavirus disease (COVID-19) Alpha (B.1.1.7) variant pneumonia. Method(s): A total of 113 patients who were diagnosed with COVID-19 pneumonia and 60 healthy control group were included in this study. The cases were divided into 2 as classic COVID-19 group, and COVID-19 B.1.1.7 variant group. Complete blood count (CBC) and biochemical parameters of the patients were analyzed retrospectively. Patients with COVID-19 B.1.1.7 variant group were also grouped according to the length of stay in the hospital and the days of hospitalization. Result(s): LDH/Albumin, LDH/Platelet, and LDH/Lymphocyte ratios were found to be higher in COVID-19 B.1.1.7 variant group when compared to the control group (p<0.001). The ferritin, neutrophils/lymphocyte (NLR) ratio, procalcitonin (PCT) and LDH/Albumin had the highest area under the curve (AUC) values in the COVID-19 B.1.1.7 variant group (0.950, 0.802, 0.759, and 0.742, respectively). Albumin, Lymphocytes and hemoglobin values were significantly higher in the COVID-19 B.1.1.7 variant group than in the classic COVID-19 group (p<0.05). Conclusion(s): LDH/Albumin and LDH/Lymphocyte ratios may be useful for clinicians in predicting the risk of progression to pneumonia in COVID-19 B.1.1.7 variant patients. Copyright © 2022 the author(s), published by De Gruyter.

South African (501Y.V2) and the United Kingdom (B.1.1.7) SARS-CoV-2 spike (S) protein variants demonstrate a higher binding affinity to ACE2.

INTRODUCTION: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), affects the lower respiratory tract by binding to angiotensin-converting enzyme 2 (ACE2) via its S-protein. Recent emerging SARS-CoV-2 variants from the United Kingdom (B.1.1.7) and South Africa (501Y.V2) are spreading worldwide at an alarming rate. The new variants have manifested amino acid substitution K417N, E484K and N501Y on the RBD domain that binds to ACE2. As such, these mutations may influence the binding of the S-protein to ACE2 and affect viral entry into the host cell. Methods In this study, we modelled the amino acids substitutions on the S-protein and utilised HADDOCK server to assess the S-protein RBD domain binding with ACE2. Additionally, we calculated the binding affinity of ACE2 to S-protein WT, B.1.1.7 and 501Y.V2 variants using Molecular Mechanics-Generalized Born Surface Area (MM/GBSA). Results We demonstrate that the S-protein of both variants possesses higher binding affinity to ACE2 than WT, with the South African 501Y.V2 is a more infective strain than the B.1.1.7 that originated in the United Kingdom. Conclusion The South African 501Y.V2 variant presents three amino acid substitutions that changed the H-bonding network resulting in a higher affinity to ACE2, indicating that the 501Y.V2 strain is more infective than the B.1.1.7 strain.

Clinical and laboratory features of COVID-19 patients infected with SARS-CoV-2 variant B.1.1.7 versus those infected with other SARS-CoV-2 strains: A retrospective observational study

Objective: To investigate the clinical symptoms of coronavirus disease 2019 (COVID-19) patients with and without B.1.1.7 mutation. Method(s): This retrospective observational study included COVID-19 patients who were divided into two groups, the mutation and the non-mutation group. Demographics characteristics, clinical characteristics, laboratory parameters, and mortality rates were recorded and compared between the two groups. Result(s): A total of 196 patients were included in the study. The relationship between the mutant virus status and sex, age, comorbidity, survival status, and disease severity was not significant (P>0.05). No significant differences were found in duration of hospitalization between the mutation and the non-mutation group (P>0.05). However, there was a statistically significant difference between patients with and without mutant viruses in hemoglobin, mean platelet volume, procalcitonin, low density lipoprotein, ironbinding capacity, potassium, calcium, C-reactive protein, folate, creatine kinase myocardial band, D-dimer, and international normalized ratio (P<0.05). Conclusion(s): No significant difference is found in mortality rate, disease severity or duration of hospitalization between the patients with and without variant B.1.1.7. Careful monitoring of COVID-19 patients is required for all variants. Copyright ©2022 Journal of Acute Disease Produced by Wolters Kluwer-Medknow.

SARS-CoV-2 B.1.214.1, B.1.214.2 and B.1.620 are predominant lineages between December 2020 and July 2021 in the Republic of Congo.

Background: : SARS-CoV-2 variants have been emerging and are shown to increase transmissibility, pathogenicity, and decreased vaccine efficacies. The objective of this study was to determine the distribution, prevalence, and dynamics of SARS-CoV-2 variants circulating in Brazzaville, the Republic of Congo (ROC). Methods: : Between December 2020 and July 2021, a total of n=600 oropharyngeal specimens collected in the community were tested for COVID-19. Of the samples tested, 317 (53%) were SARS-CoV-2 positive. All samples that had a threshold of Ct <30 (n=182) were sequenced by next-generation sequencing (NGS), and all complete sequenced genomes were submitted to GISAID; lineages were assigned using pangolin nomenclature and a phylogenetic tree was reconstructed. In addition, the global prevalence of the predominant lineages was analysed using data from GISAID and Outbreak databases. Results: : A total of 15 lineages circulated with B.1.214.2 (26%), B.1.214.1 (19%) and B.1.620 (18%) being predominant. The variants of concern (VOC) alpha (B.1.1.7) (6%) and for the first time in June delta (B.1.617.2) (4%) were observed. In addition, the B.1.214.1 lineage first reported from ROC was observed to be spreading locally and regionally. Phylogenetic analysis suggests that the B.1.620 variant (VUM) under observation may have originated from either Cameroon or the Central African Republic. SARS-CoV-2 lineages were heterogeneous, with the densely populated districts of Poto-Poto and Moungali likely the epicenter of spread. Conclusion: : Longitudinal monitoring and molecular surveillance across time and space are critical to understanding viral phylodynamics, which could have important implications for transmissibility and impact infection prevention and control measures.

Generation of Novel Severe Acute Respiratory Syndrome Coronavirus 2 Variants on the B.1.1.7 Lineage in 3 Patients With Advanced Human Immunodeficiency Virus-1 Disease.

The emergence of new severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants is of public health concern in case of vaccine escape. Described are 3 patients with advanced human immunodeficiency virus (HIV)-1 and chronic SARS-CoV-2 infection in whom there is evidence of selection and persistence of novel mutations that are associated with increased transmissibility and immune escape.

First confirmation of importation and transmission in Spain of the newly identified SARS-CoV-2 B.1.1.7 variant.

INTRODUCTION: A newly identified SARS-CoV-2 variant, VOC202012/01 originating lineage B.1.1.7, recently emerged in the United Kingdom. The rapid spread in the UK of this new variant has caused other countries to be vigilant. MATERIAL AND METHODS: We based our initial screening of B.1.1.7 on the dropout of the S gene signal in the TaqPath assay, caused by the 69/70 deletion. Subsequently, we confirmed the B.1.1.7 candidates by whole genome sequencing. RESULTS: We describe the first three imported cases of this variant from London to Madrid, subsequent post-arrival household transmission to three relatives, and the two first cases without epidemiological links to UK. One case required hospitalization. In all cases, drop-out of gene S was correctly associated to the B.1.1.7 variant, as all the corresponding sequences carried the 17 lineage-marker mutations. CONCLUSION: The first identifications of the SARS-CoV-2 B.1.1.7 variant in Spain indicate the role of independent introductions from the UK coexisting with post-arrival transmission in the community, since the early steps of this new variant in our country.

A Spotlight on Novel Coronavirus (COVID - 19) with Various Types of Strains

Deadly COVID-19 viruses have raised a pandemic situation in the year 2019, causing serious and contagious respiratory infections in humans. SARS-CoV-2 (Severe Acute Respiratory Syndrome Coronavirus 2) is the main causative agent for this disease outbreak. The pandemic created a critical impact on the global economy. The emergence of SARS-CoV-2 in late 2019 was followed by a period of relative evolutionary stasis that lasted about 11 months. Since, late 2020, SARS-CoV-2 evolution has been characterized by the emergence of sets of mutations. This resulted so far, in over 2.7 million deaths and near about 122 million infection cases. Most mutations in the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) genome are either deleterious and swiftly purged or relatively neutral. As far as the concern is the variants it impacts the virus characteristics, including antigenicity and transmissibility in response to the modification of the human immune profile. In recent days, COVID-19 affected cases are rapidly increasing and it became difficult to inhibit this virus as they are continuously mutated in the host cell forming various new strains like B.1.1.7, B.1.351, P.1, P.2, B.1.1.529, etc. These monitoring, surveillance of variation, and sequencing efforts within the SARS-CoV-2 genome enabled the rapid identification of the first some of Variants of Concern (VOCs) in late 2020, where genome changes became the most observable impact on virus biology and disease transmission. In this review article, we tried to focus and spot the light on the genetic diversification of various strains, their nature, similarities and dissimilarities, mechanism of action, and the prophylactic interventions which could prevent this life-threatening disease in the long run.