SARS-CoV-2 Variants BA.2.86 and EG.5.1 Alongside Scrub Typhus and Nipah in India During the Ongoing Cricket World Cup 2023: Threat Perceptions and Countermeasures

The United States (US), the United Kingdom (UK), and China witnessed rising cases of coronavirus disease 2019 (COVID-19) in 2023. Concerns about severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) novel strains amid the sudden surge of COVID cases are growing. Recently, BA.2.86 (Pirola) poses a much greater risk due to its higher transmission rate and spreading across regions. Pirola variant has mutations that set it apart from all earlier known SARS-CoV-2 variants. This variant was designated a variant of interest by the World Health Organization (WHO). Another SARS-CoV-2 variant named "Eris" (EG.5.1) was detected in India and started picking up in the US and the UK. The WHO listed EG.5.1 (variant) as a variant under monitoring. Therefore, it is important to remain vigilant. Further, multiple Nipah virus infections and scrub typhus cases are spreading among humans in India currently. In this situation, the 13th edition of the International Cricket Council (ICC) Men's Cricket World Cup is being held in India this year. With global reach, this big sporting carnival attracts millions of cricket fans from several countries. In light of the multiple public health concerns encountered currently, this gala global sports event needs additional preventive measures.

Associations of SARS-CoV-2 cycle threshold values with age, gender, sample collection setting, and pandemic period

Cycle threshold (Ct) values in COVID-19 reverse-transcription polymerase chain reaction (RT-PCR) tests estimate the viral load in biological samples. Studies have investigated variables associated with SARS-CoV-2 viral load, aiming to identify factors associated with higher transmissibility. Using the results from tests performed between May/2020-July/2022 obtained from the database of a referent hospital in Sao Paulo, Brazil, we investigated associations between Ct values and patient's age, gender, sample collection setting and pandemic period according to the predominant SARS-CoV-2 variant locally. We also examined variations in Ct values, COVID-19 incidence, mortality, and vaccination coverage over time. The study sample included 42,741 tests. Gender was not significantly associated with Ct values. Age, sample collection setting and the pandemic period were significantly associated with Ct values even after adjustment to the multivariable model. Results showed lower Ct values in older groups, during the Gamma and Delta periods, and in samples collected in emergency units; and higher Ct values in children under 10 years old, home-based tests, during the Omicron period. We found evidence of a linear trend in the association between age and Ct values, with Ct values decreasing as age increases. We found no clear temporal associations between Ct values and local indicators of COVID-19 incidence, mortality, or vaccination between February/2020-November/2022. Our findings suggest that SARS-CoV-2 Ct values, a proxy for viral load and transmissibility, can be influenced by demographic and epidemiological variables.

Vestibular Dysfunction Secondary to Reactivation of the Neurotropic Virus VZV After COVID-19: A Case Study

BACKGROUND The novel coronavirus COVID-19 infection, caused by the SARS-CoV-2 virus, was declared a global pandemic by the World Health Organization (WHO) in March 2020. As of April 14, 2021, the virus has impacted the lives of over 138 million lives globally, with hundreds of thousands more impacted each day. COVID-19 has resulted in a multitude of clinical manifestations such as respiratory pathology, cardiovascular complications, and neurological dysfunction, and recent evidence points to potential changes in vestibular function secondary to COVID-19 infection. CASE REPORT We present the case of a 67-year-old female patient presenting with vertigo, hearing loss, tinnitus, aural dullness, dizziness, and imbalance following a diagnosis of shingles after contracting COVID-19. Results of a comprehensive balance evaluation were suggestive of a right peripheral vestibulopathy, otolith dysfunction, and a right-sided sensorineural hearing loss. The patient's subjective and objective data may support the claim that COVID-19 can lead to an increase in cases of vestibular dysfunction after reactivation of neurotropic viruses. CONCLUSIONS Our study and others suggest the possibility of vestibular deficits following the reactivation of VZV following a period of immunosuppression in conjunction with the lowered cell-mediated immunity caused by COVID-19. Additionally, vestibular interventions such as advanced vestibular treatment could be used to improve vestibular function in a linear manner.

Distinct Clinical and Laboratory Features of COVID-19 in Children During the Pre-Delta, Delta and Omicron Wave

BACKGROUND

The SARS-CoV-2 variants of concern exhibit distinct features in terms of transmissibility and virulence. This study compared the clinical characteristics of COVID-19 in children during pre-Delta, Delta and Omicron waves.

METHODS

Medical records of 1163 children <19 years of age with COVID-19 admitted to a designated hospital in Seoul, South Korea, were analyzed. Clinical and laboratory findings during the pre-Delta (March 1, 2020, to June 30, 2021; 330 children), Delta (July 1, 2021, to December 31, 2021; 527 children) and Omicron (January 1, 2022, to May 10, 2022; 306 children) waves were compared.

RESULTS

Children during the Delta wave were older and had a higher proportion of fever ≥5 days and pneumonia than children during the pre-Delta and Omicron waves. The Omicron wave was characterized by younger age and a higher proportion of fever ≥39.0 °C, febrile seizure and croup. More children <2 years of age and adolescents aged 10 to <19 years experienced neutropenia and lymphopenia, respectively, during the Delta wave. Children aged 2 to <10 years had a higher incidence of leukopenia and lymphopenia during the Omicron wave.

CONCLUSIONS

Distinct features of COVID-19 were observed in children during the Delta and Omicron surges. Continuous scrutiny of the manifestations of variants of concern is needed for appropriate public health response and management.

COVID-19 Diagnosis and SARS-CoV-2 Strain Identification by a Rapid, Multiplexed, Point-of-Care Antibody Microarray

Antigen tests to detect SARS-CoV-2 have emerged as a promising rapid diagnostic method for COVID-19, but they are unable to differentiate between variants of concern (VOCs). Here, we report a rapid point-of-care test (POC-T), termed CoVariant-SPOT, that uses a set of antibodies that are either tolerant or intolerant to spike protein mutations to identify the likely SARS-CoV-2 strain concurrent with COVID-19 diagnosis using antibodies targeting the nucleocapsid protein. All reagents are incorporated into a portable, multiplexed, and sensitive diagnostic platform built upon a nonfouling polymer brush. To validate CoVariant-SPOT, we tested recombinant SARS-CoV-2 proteins, inactivated viruses, and nasopharyngeal swab samples from COVID-19 positive and negative individuals and showed that CoVariant-SPOT can readily distinguish between two VOCs: Delta and Omicron. We believe that CoVariant-SPOT can serve as a valuable adjunct to next-generation sequencing to rapidly identify variants using a scalable and deployable POC-T, thereby enhancing community surveillance efforts worldwide and informing treatment selection.

Role of FokI rs.2228570 and Tru9I rs.757343 Polymorphisms in the Mortality of Patients Infected with Different Variants of SARS-CoV-2

Background and aim

Low vitamin D levels are associated with the severity of coronavirus disease 19 (COVID-19). Vitamin D receptor gene polymorphisms, such as Tru9I rs.757343 and FokI rs.2228570, have been suggested to be potential risk factors for severe COVID-19 outcomes. This study investigated how Tru9I rs.757343 and FokI rs.2228570 polymorphisms influenced the mortality rate of COVID-19 in relation to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants.

Methods

The polymerase chain reaction-restriction fragment length polymorphism assay was used to genotype Tru9I rs.757343 and FokI rs.2228570 genotypes in 1,734 recovered and 1,450 deceased patients.

Results

Our results demonstrated that the high mortality rate was correlated with FokI rs.2228570 TT genotype in all three variants but was much higher in the Omicron BA.5 variant than in the Alpha and Delta variants. Furthermore, in patients infected with the Delta variant, FokI rs.2228570 CT genotype was more highly correlated with the mortality rate compared to other variants. Thus, a high mortality rate was correlated with the Tru9I rs.757343 AA genotype in the Omicron BA.5 variant, whereas this relationship was not observed in the other two variants. The T-A haplotype was related to COVID-19 mortality in all three variants, but its effect was more pronounced in the Alpha variant. Moreover, the T-G haplotype was significantly associated with all three variants.

Conclusion

Our findings showed that the effects of Tru9I rs.757343 and FokI rs.2228570 polymorphisms were related to SARS-CoV-2 variants. However, further studies are still required to validate our findings.

Simultaneous Detection of Omicron and Other SARS-CoV-2 Variants by Multiplex PCR MassARRAY Technology

The rapid emergence of SARS-CoV-2 variants with high severity and transmutability adds further urgency for rapid and multiplex molecular testing to identify the variants. A nucleotide matrix-assisted laser-desorption-ionization time-of-flight mass spectrophotometry (MALDI-TOF MS)-based assay was developed (called point mutation array, PMA) to identify four major SARS-CoV-2 variants of concern (VOCs) including Alpha, Beta, Delta, and Omicron (namely PMA-ABDO) and differentiate Omicron subvariant (namely PMA-Omicron). PMA-ABDO and PMA-Omicron consist of 24 and 28 mutation sites of the spike gene. Both PMA panels specifically identified VOCs with as low as 10 viral copies/ µl. The panel has shown a 100% concordant with the Next Generation Sequencing (NGS) results testing on 256 clinical specimens with real-time PCR cycle threshold (Ct) values less than 26. It showed a higher sensitivity over NGS; 25/28 samples were positive by PMA but not NGS in the clinical samples with PCR Ct higher than 26. Due to the mass of nucleotide used to differentiate between wild-type and mutation strains, the co-infection or recombination of multiple variants can be determined by the PMA method. This method is flexible in adding a new primer set to identify a new emerging mutation site among the current circulating VOCs and the turnaround time is less than 8 hours. However, the spike gene sequencing or NGS retains the advantage of detecting newly emerged variants.

A Retrospective Population Study of 385 191 Positive Real-Time Reverse Transcription-Polymerase Chain Reaction Tests For SARS-CoV-2 from a Single Laboratory in Katowice, Poland from April 2020 to July 2022

BACKGROUND This retrospective population study identified 385 191 positive real-time reverse transcription-polymerase chain reaction (RT-PCR) tests for the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) from a single laboratory in Katowice, Poland, from April 2020 to July 2022. MATERIAL AND METHODS The material was nasopharyngeal, nasopharyngeal swab or bronchial lavage, and bronchoalveolar lavage (BAL) to confirm or exclude SARS-CoV-2 infection with the RT-PCR technique. Personal data are use according to the Provisions on the Protection of Personal Data by the Gyn-Centrum laboratory. RESULTS In 9 months of 2020, the number of SARS-CoV-2 results was 88 986; in 2021, it was 168 439, and in the first 7 months of 2022, it was 12 786. In 2020, the highest number of positive results was recorded in the third quarter (83 094 cases); 2021, in the 1st, 2nd, and 4th quarters (58 712; 37 720; and 71 753 cases, respectively), and in 2022, in the 1st quarter (127 613 cases) of the year. A positive result was observed more often in women and people aged 30-39, followed by those 40-49 years. Patients aged 10-19 years comprised the smallest population of SARS-CoV-2-positive cases. CONCLUSIONS In the Polish population studied, from April 2020 to July 2022, the detection rates of SARS-CoV-2 positivity were significantly higher for women than for men and in the 30-49 age group for both sexes. Also, the infection detection rate of 385 191 out of 1 332 659 patient samples, or 28.9%, supports that the Polish society adhered to public health recommendations for infection control during the COVID-19 pandemic.

Comparison of clinical characteristics of wild-type SARS-CoV-2 and Omicron

OBJECTIVE

This study aimed to investigate the effect of mutations by comparing wild-type SARS-CoV-2 and Omicron regarding clinical features in patients with COVID-19. It also aimed to assess whether SARS-CoV-2 cycle threshold value could predict COVID-19 severity.

METHODS

A total of 960 wild-type and 411 Omicron variant patients with positive results in SARS-CoV-2 real-time reverse transcriptase polymerase chain reaction test from oropharyngeal and/or nasopharyngeal samples during their hospital admissions were included in this retrospective study. The reference symptoms of the patients were obtained from the hospital database. The correlation between chest computed tomography findings and the "cycle threshold" of patients with wild-type SARS-CoV-2 was assessed.

RESULTS

Cough, fever, shortness of breath, loss of taste and smell, and diarrhea were found to be statistically significantly higher (p=0.001; 0.001; 0.001; 0.001; and 0.006; respectively) in the wild-type cohort, while in the Omicron cohort, sore throat and headache were found to be statistically significantly higher (p=0.001 and 0.003, respectively). An inverse relationship was found between chest computed tomography findings and viral load.

CONCLUSION

This study revealed that the Omicron variant tended to infect predominantly the upper respiratory tract and showed decreased lung infectivity, and the disease progressed with a milder clinical course. Therefore, the study showed that the tropism of the virus was changed and the viral phenotype was affected. It was also found that SARS-CoV-2 viral load did not predict COVID-19 severity in patients with wild-type SARS-CoV-2.

Molecular basis of SARS-CoV-2 Omicron variant evasion from shared neutralizing antibody response

A detailed understanding of the molecular features of the neutralizing epitopes developed by viral escape mutants is important for predicting and developing vaccines or therapeutic antibodies against continuously emerging SARS-CoV-2 variants. Here, we report three human monoclonal antibodies (mAbs) generated from COVID-19 recovered individuals during first wave of pandemic in India. These mAbs had publicly shared near germline gene usage and potently neutralized Alpha and Delta, but poorly neutralized Beta and completely failed to neutralize Omicron BA.1 SARS-CoV-2 variants. Structural analysis of these three mAbs in complex with trimeric spike protein showed that all three mAbs are involved in bivalent spike binding with two mAbs targeting class-1 and one targeting class-4 Receptor Binding Domain (RBD) epitope. Comparison of immunogenetic makeup, structure, and function of these three mAbs with our recently reported class-3 RBD binding mAb that potently neutralized all SARS-CoV-2 variants revealed precise antibody footprint, specific molecular interactions associated with the most potent multi-variant binding / neutralization efficacy. This knowledge has timely significance for understanding how a combination of certain mutations affect the binding or neutralization of an antibody and thus have implications for predicting structural features of emerging SARS-CoV-2 escape variants and to develop vaccines or therapeutic antibodies against these.

SARS-CoV-2 B.1.1.7 infection of Syrian hamster does not cause more severe disease and is protected by naturally acquired immunity

Epidemiological studies have revealed the emergence of multiple SARS-CoV-2 variants of concern (VOC), including the lineage B.1.1.7 that is rapidly replacing old variants. The B.1.1.7 variant has been linked to increased morbidity rates, transmissibility, and potentially mortality (1). To assess viral fitness in vivo and to address whether the B.1.1.7 variant is capable of immune escape, we conducted infection and re-infection studies in naïve and convalescent Syrian hamsters (>10 months old). Hamsters infected by either a B.1.1.7 variant or a B.1 (G614) variant exhibited comparable viral loads and pathology. Convalescent hamsters that were previously infected by the original D614 variant were protected from disease following B.1.1.7 challenge with no observable clinical signs or lung pathology. Altogether, our study did not find that the B.1.1.7 variant significantly differs from the B.1 variant in pathogenicity in hamsters and that natural infection-induced immunity confers protection against a secondary challenge by the B1.1.7 variant.

Stay-At-Home Orders Are Associated With Emergence of Novel SARS-CoV-2 Variants

Background While public health strategies to contain the current coronavirus disease 2019 (COVID-19) pandemic are primarily focused on social distancing and isolation, emerging evidence suggest that in some regions social isolation failed to lead to further decrease in the number of COVID-19 deaths in the long run. This apparent paradox was particularly observed in the northern region of Brazil, in the state of Amazonas. We hypothesized that the emergence of new severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) mutations, leading to more transmissible and pathogenic variants, could explain the lack of further reductions in COVID-19 new cases and related deaths in some regions. Our objective is to determine if social isolation is associated with the emergence of new SARS-CoV-2 variants, particularly the P.1 lineage and E484K mutants, in Brazil and in the state of Amazonas. Materials and methods We assessed the prevailing SARS-CoV-2 genomes present in Brazil available on the GISAID (Global Initiative on Sharing All Influenza Data) database collected between June 1, 2020, and January 31, 2021. Data regarding demographics, lineage, and prevalence of P.1 lineage and E484K mutations were obtained. Social isolation was measured using the Social Isolation Index (SII), which quantifies the percentage of individuals that stayed within a distance of 450 meters from their homes on a given day, between February 1, 2020, and January 24, 2021. The number of daily COVID-19 deaths was obtained from the Brazilian Ministry of Health (OpenDataSUS, 2021) between March 12, 2020, and January 10, 2021. SII was correlated with the prevalence P.1 lineage and E484K mutations in the eight following weeks. All univariate associations were estimated using the Spearman Correlation Index. 3D surfaces were employed to reflect the relationship between time, social isolation, and prevalence of genomic variants simultaneously. Results A total of 773 and 77 samples were obtained in Brazil and in the Amazonas state, respectively. In the state of Amazonas, SII on a given week was positively, significantly, and moderately or strongly (r > 0.6) correlated with the prevalence of both P.1 lineage and other E484K variants in the six following weeks after the SII on a given week. Conversely, in overall Brazil, correlations between SII and P.1 lineage and E484K variants were weaker and shorter, or negative, respectively. When SII was below 40%, P.1 lineage or E484K variants were not detected in the following weeks. When SII was above 40%, apparently exponential positive correlations between SII and prevalence of both P.1 lineage and E484K variants were observed. Conclusion The results of this study indicate that SII above 40% is associated with the emergence of SARS-CoV-2 E484K variants and P.1 lineage in the state of Amazonas, which was not observed in overall Brazil.