Analysis of SARS-CoV-2 mutations in Mexico, Belize, and isolated regions of Guatemala and its implication in the diagnosis

Current Updates on Variants of SARS-CoV- 2: Systematic Review

Background

Coronavirus disease 2019 is caused by the severe acute respiratory syndrome coronavirus 2, which has become a pandemic. Severe acute respiratory syndrome coronavirus 2 is an enveloped, unsegmented, positive-sense, single-stranded RNA virus that belongs to the family Coronaviridae.

Aim

The objective of this review is to conduct a qualitative analysis of the current updates on epidemiology, evolution, and vaccine variants for SARS-CoV-2.

Method

The search strategy was done from the database based on the PRISMA criteria for qualitative analysis of this review. Literature on variants of severe acute respiratory syndrome coronavirus 2, published in English in the last 5 years (2019-2023), were included. From 179 a total of 105 articles were reviewed, searched, and retrieved from the electronic databases PubMed. The search was done using keywords like COVID-19, SARS-CoV-2, variants, mutations, and vaccines, and articles were managed using EndNote X8 software. The scope of view for this review was the course of the pandemic by emerging variants and how man is struggling to overcome this sudden pandemic through vaccines. The narrative skeleton was constructed based on the article's scope of view.

Result

From the parent severe acute respiratory syndrome coronavirus 2, many variants emerged during the course of this pandemic. They are mainly categorized into two variants: variants of interest and variants of concern based on the impact on public health. The World Health Organization leveled five variants: Alpha (strain B.1.1.7), Beta (strain B.1.351), Gamma (strain P.1), Delta (strain B.1.617.2), and Omicron (B.1.1.529).

Conclusions

It is crucial to stay informed about the latest developments in the understanding of SARS-CoV-2 variants, as new variants can emerge and impact the course of the pandemic. Health authorities and researchers continuously have to monitor and study these variants to assess their characteristics, transmissibility, severity, and the effectiveness of vaccines against them. One has to always refer to the latest information from reputable health journals or organizations for the most up-to-date and accurate details on COVID-19 variants.

Nucleocapsid single point-mutation associated with drop-out on RT-PCR assay for SARS-CoV-2 detection

BACKGROUND

Since its beginning, the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has been a challenge for clinical and molecular diagnostics, because it has been caused by a novel viral agent. Whole-genome sequencing assisted in the characterization and classification of SARS-CoV-2, and it is an essential tool to genomic surveillance aiming to identify potentials hot spots that could impact on vaccine immune response and on virus diagnosis. We describe two cases of failure at the N2 target of the RT-PCR test Xpert® Xpress SARS-CoV-2.

METHODS

Total nucleic acid from the Nasopharyngeal (NP) and oropharyngeal (OP) swab samples and cell supernatant isolates were obtained. RNA samples were submitted to random amplification. Raw sequencing data were subjected to sequence quality controls, removal of human contaminants by aligning against the HG19 reference genome, taxonomic identification of other pathogens and genome recovery through assembly and manual curation. RT-PCR test Xpert® Xpress SARS-CoV-2 was used for molecular diagnosis of SARS-CoV-2 infection, samples were tested in duplicates.

RESULTS

We identified 27 samples positive for SARS-CoV-2 with a nucleocapsid (N) gene drop out on Cepheid Xpert® Xpress SARS-CoV-2 assay. Sequencing of 2 of 27 samples revealed a single common mutation in the N gene C29197T, potentially involved in the failed detection of N target.

CONCLUSIONS

This study highlights the importance of genomic data to update molecular tests and vaccines.

SARS-CoV-2 Variants of Concern and Clinical Severity in the Mexican Pediatric Population

The emergence of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) variants of concern (VOCs) presents global heterogeneity, and their relative effect on pediatric severity is still limited. In this study, we associate VOCs with pediatric clinical severity outcomes in Mexico. Bioinformatics methods were used to characterize VOCs and single amino acid (aa) mutations in 75,348 SARS-CoV-2 genetic sequences from February 2020 to October 2022. High-predominance VOCs groups were calculated and subsequently associated with 372,989 COVID-19 clinical pediatric outcomes. We identified 21 high-frequency mutations related to Omicron lineages with an increased prevalence in pediatric sequences compared to adults. Alpha and the other lineages had a significant increase in case fatality rate (CFR), intensive critical unit (ICU) admission, and automated mechanical ventilation (AMV). Furthermore, a logistic model with age-adjusted variables estimated an increased risk of hospitalization, ICU/AMV, and death in Gamma and Alpha, in contrast to the other lineages. We found that, regardless of the VOCs lineage, infant patients presented the worst severity prognoses. Our findings improve the understanding of the impact of VOCs on pediatric patients across time, regions, and clinical outcomes. Enhanced understanding of the pediatric severity for VOCs would enable the development and improvement of public health strategies worldwide.

Distribution of intra-host variations and mutations in the genomes of SARS-CoV-2 and their implications on detection and therapeutics

The ongoing circulation of SARS-CoV-2 variants of concern (VOCs) has caused global concerns, because VOCs could escape current vaccines, antiviral drugs, and diagnosis. Analyzing mutations and intra-host diversities in different and widespread VOCs can provide important insights to virus adaptive evolution and validity of vaccines, antiviral drugs, and diagnosis. In this study, by analyzing 1744 high-throughput sequencing data for intra-host single-nucleotide variations (iSNVs) and 3,668,205 genome sequences for mutations in different VOCs, it was found that Omicron variant is still evolving at high speed, especially having high iSNVs frequency in its S and N genes. The efficacies of antibodies or detection primers targeting these two genes are at high risks to be invalid. Instead, highly conserved regions such as NSP8 gene could be better therapeutic and detection targets. Furthermore, mutations in later VOCs could be traced to the minor alleles in the previous variant samples such as Alpha and Delta in different countries. Finally, it was found that mutations C14408T in RdRp and A18163G in NSP14 gene might be associated with the higher genetic diversity in Omicron. Our findings not only contribute to understanding the adaptive evolution of SARS-CoV-2 VOCs, but also provide useful information for both drugs and diagnostic kits development.

Assessment of Jordanian health care professionals' perception towards new COVID-19 variants of concern

BACKGROUND

Healthcare professionals working at the frontline, dealing with COVID-19 patients or their samples, should know about variants of concern (VOCs) and their transmissibility, disease severity, and vaccine efficacy. Healthcare professionals' (HCPs) perceptions towards new VOCs affect their practice and attitudes towards their patients. Moreover, these perceptions might significantly impact their patients' perceptions of new COVID-19 variants and public vaccine acceptability.

METHODS

Online and paper-based questionnaires were distributed among Healthcare professionals in Jordan between August 2021 and October 2021.

RESULTS

Among 423 HCPs who participated in this study, a majority believe that when viruses mutate, they become more transmissible (77.8%), more deadly (61.7%), and pathogenic (64.8%). In addition, half of the respondents, perceived current treatments as partially effective against VOCs and current diagnostics to be efficient. However, all VOCs were perceived as more transmissible, more virulent, and related to higher mortality rates when compared to the original strain. Regarding immunity against VOCs, (57.4%) of respondents believe in partial immunity against re-infection, and most respondents were either unsure about the current vaccines' efficacy or agreed that available vaccines would be ineffective. However, respondents (44.4%) still believe that people previously infected should get vaccinated. Respondents referred to the Ministry of Health as the most reliable source of information (45.6%) and the party responsible for educating the public about COVID-19 VOCs (57.9%). Travel was not a source of worry among respondents. However, they were worried about their families getting the new COVID-19 VOCs from their work. Similar proportions agreed/disagreed on the efficacy of the precautions and infection control measures currently applied by the government for preventing the spread of the new COVID-19 VOCs.

CONCLUSION

Campaigns, workshops, and webinars targeting vaccines are highly recommended among HCPs to increase public acceptance of the vaccine and further booster shots.

Rapid, inexpensive methods for exploring SARS CoV-2 D614G mutation

A common mutation has occurred in the spike protein of severe acute respiratory syndrome coronavirus 2 (SARS CoV-2), known as D614G (A23403G). There are discrepancies in the impact of this mutation on the virus's infectivity. Also, the whole genome sequencings are expensive and time-consuming. This study aims to develop three fast economical assays for prompt identifications of the D614G mutation including Taqman probe-based real-time reverse transcriptase polymerase chain reaction (rRT PCR), an amplification refractory mutation system (ARMS) RT and restriction fragment length polymorphism (RFLP), in nasopharyngeal swab samples. Both rRT and ARMS data showed G614 mutants indicated by the presence of HEX probe and 176 bp, respectively. Additionally, the results of the RFLP data and DNA sequencings confirmed the prevalence of the G614 mutants. These methods will be important, in epidemiological, reinfections and zoonotic aspects, through detecting the G614 mutant in retro-perspective samples to track its origins and future re-emergence of D614 wild type.

Emerging SARS-CoV-2 variants of concern and potential intervention approaches

The major variant of concerns (VOCs) have shared mutations in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike proteins, mostly on the S1 unit and resulted in higher transmissibility rate and affect viral virulence and clinical outcome. The spike protein mutations and other non-structural protein mutations in the VOCs may lead to escape approved vaccinations in certain extend. We will discuss these VOC mutations and discuss the need for combination therapeutic strategies targeting viral cycle and immune host responses.

RT-qPCR Assays for Rapid Detection of the N501Y, 69-70del, K417N, and E484K SARS-CoV-2 Mutations: A Screening Strategy to Identify Variants With Clinical Impact

Background

Several variants of the SARS-CoV-2 have been documented globally during the current COVID-19 pandemic. The N501Y, 69-70del, K417N, and E484K SARS-CoV-2 mutations have been documented among the most relevant due to their potential pathogenic biological effects. This study aimed to design, validate, and propose a fast real-time RT-qPCR assay to detect SARS-CoV-2 mutations with possible clinical and epidemiological relevance in the Mexican population.

Methods

Targeting spike (S) gene mutations of SARS-CoV-2 (N501Y, 69-70del, K417N, and E484K), specific primers, and probes for three specific quantitative reverse transcription PCR (RT-qPCR) assays were designed, and validated using Sanger sequencing. These assays were applied in clinical samples of 1060 COVID-19 patients from Jalisco Mexico.

Results

In silico analyzes showed high specificity of the three assays. Amplicons of samples were confirmed through sequencing. The screening of samples of COVID-19 patients allowed the identification of the E484K mutation in nine individuals and the identification of P.2 Brazilian variant in Mexico.

Conclusion

This work provides low-cost RT-qPCR assays for rapid screening and molecular surveillance of mutations with potential clinical impact. This strategy allowed the detection of E484K mutation and P.2 variant for the first time in samples from the Mexican population.

Antibody response to SARS-CoV-2 infection over six months among Nicaraguan outpatients

New information is emerging about SARS-CoV-2 epidemiology and immunity, but little of this information comes from low- and middle-income countries or from patients receiving care in the outpatient setting. The current study investigated the SARS-CoV-2 infection status and antibody responses in 157 patients seeking care for a respiratory disease suggestive of COVID-19 in private healthcare clinics during the first wave (June-October 2020) of infections in Nicaragua. We examined nasal swabs for the presence of viral RNA via RT-PCR and longitudinally collected sera for the changes in SARS-CoV-2 Spike antibody levels over six months. Among patients with confirmed SARS-CoV-2 infections, we evaluated if clinical symptoms were associated with age, hematological parameters and co-morbidities. The combination of PCR and paired serology identified 60 (38%) of the 157 outpatients as acute COVID-19. While both PCR and serology identified the majority (n = 38, 64%) of the acute infections, a notable number of outpatients were identified by RT-qPCR (n = 13, 22%) or by serology (n = 9, 14%) only. During the longitudinal study, we identified 6 new infections by serology among the 97 non-COVID-19 subjects. In conclusion, this study report that more than one third of the outpatients seeking care for acute respiratory disease during the first epidemic wave of SARS-CoV-2 in Nicaragua had an acute mild COVID-19 infection that correlate with prolonged humoral response. This immune response to the RBD antigen, more likely IgG dependent, significantly increased between the acute to convalescent and decay in the late convalescent but still remained seropositive.

RT-qPCR Assays for Rapid Detection of the N501Y, 69-70del, K417N, and E484K SARS-CoV-2 Mutations: A Screening Strategy to Identify Variants With Clinical Impact

BACKGROUND

Several variants of the SARS-CoV-2 have been documented globally during the current COVID-19 pandemic. The N501Y, 69-70del, K417N, and E484K SARS-CoV-2 mutations have been documented among the most relevant due to their potential pathogenic biological effects. This study aimed to design, validate, and propose a fast real-time RT-qPCR assay to detect SARS-CoV-2 mutations with possible clinical and epidemiological relevance in the Mexican population.

METHODS

Targeting spike (S) gene mutations of SARS-CoV-2 (N501Y, 69-70del, K417N, and E484K), specific primers, and probes for three specific quantitative reverse transcription PCR (RT-qPCR) assays were designed, and validated using Sanger sequencing. These assays were applied in clinical samples of 1060 COVID-19 patients from Jalisco Mexico.

RESULTS

In silico analyzes showed high specificity of the three assays. Amplicons of samples were confirmed through sequencing. The screening of samples of COVID-19 patients allowed the identification of the E484K mutation in nine individuals and the identification of P.2 Brazilian variant in Mexico.

CONCLUSION

This work provides low-cost RT-qPCR assays for rapid screening and molecular surveillance of mutations with potential clinical impact. This strategy allowed the detection of E484K mutation and P.2 variant for the first time in samples from the Mexican population.