Haplotype distribution of SARS-CoV-2 variants in low and high vaccination rate countries during ongoing global COVID-19 pandemic in early 2021

A retrospective study suggests 55 days of persistence of SARS-CoV-2 during the first wave of the pandemic in Santiago de Chile

Background

As the COVID-19 pandemic persists, infections continue to surge globally. Presently, the most effective strategies to curb the disease and prevent outbreaks involve fostering immunity, promptly identifying positive cases, and ensuring their timely isolation. Notably, there are instances where the SARS-CoV-2 virus remains infectious even after patients have completed their quarantine.

Objective

Understanding viral persistence post-quarantine is crucial as it could account for localized infection outbreaks. Therefore, studying and documenting such instances is vital for shaping future public health policies.

Design

This study delves into a unique case of SARS-CoV-2 persistence in a 60-year-old female healthcare worker with a medical history of hypertension and hypothyroidism. The research spans 55 days, marking the duration between her initial and subsequent diagnosis during Chile's first COVID-19 wave, with the analysis conducted using RT-qPCR.

Results

Genomic sequencing-based phylogenetic analysis revealed that the SARS-CoV-2 detected in both Nasopharyngeal swab samples (NPSs) was consistent with the 20B clade of the Nextstrain classification, even after a 55-day interval.

Conclusion

This research underscores the need for heightened vigilance concerning cases of viral persistence. Such instances, albeit rare, might be pivotal in understanding sporadic infection outbreaks that occur post-quarantine.

Genome analysis of SARS-CoV-2 isolates from a population reveals the rapid selective sweep of a haplotype carrying many pre-existing and new mutations

To understand the mechanism underlying the evolution of SARS-CoV-2 in a population, we sequenced 92 viral genomes from Assam, India. Analysis of these and database sequences revealed a complete selective sweep of a haplotype in Assam carrying 13 pre-existing variants, including a high leap in frequency of a variant on ORF8, which is involved in immune evasion. A comparative study between sequences of same lineage and similar time frames in and outside Assam showed that 10 of the 13 pre-existing variants had a frequency ranging from 96 to 99%, and the remaining 3 had a low frequency outside Assam. Using a phylogenetic approach to infer sequential occurrences of variants we found that the variant Phe120del on ORF8, which had a low frequency (1.75%) outside Assam, is at the base of the phylogenetic tree of variants and became totally fixed (100%) in Assam population. Based on this observation, we inferred that the variant on ORF8 had a selective advantage, so it carried the haplotype to reach the100% frequency. The haplotype also carried 32 pre-existing variants at a frequency from 1.00 to 80.00% outside Assam. Those of these variants that are more closely linked to the S-protein locus, which often carries advantageous mutations and is tightly linked to the ORF8 locus, retained higher frequencies, while the less tightly linked variants showed lower frequencies, likely due to recombination among co- circulating variants in Assam. The ratios of non-synonymous substitutions to synonymous substitutions suggested that some genes such as those coding for the S-protein and non-structural proteins underwent positive selection while others were subject to purifying selection during their evolution in Assam. Furthermore, we observed negative correlation of the Ct value of qRT-PCR of the patients with abundant ORF6 transcripts, suggesting that ORF6 can be used as a marker for estimating viral titer. In conclusion, our in-depth analysis of SARS-CoV-2 genomes in a regional population reveals the mechanism and dynamics of viral evolution.

Molecular characterisation and tracking of severe acute respiratory syndrome coronavirus 2 in Thailand, 2020-2022

The global COVID-19 pandemic, caused by the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), was first detected in China in December 2019. To date, there have been approximately 3.4 million reported cases of COVID-19 and over 24,000 deaths in Thailand. In this study, we investigated the molecular characteristics and evolution of SARS-CoV-2 in Thailand from 2020 to 2022. Two hundred sixty-eight SARS-CoV-2 isolates, collected mostly in Bangkok from COVID-19 patients, were characterised by partial genome sequencing. Moreover, the viruses in 5,627 positive SARS-CoV-2 samples were identified as viral variants - B.1.1.7 (Alpha), B.1.617.2 (Delta), B.1.1.529 (Omicron/BA.1), or B.1.1.529 (Omicron/BA.2) - by multiplex real-time reverse transcription polymerase chain reaction (RT-PCR) assays. The results revealed that B.1.36.16 caused the predominant outbreak in the second wave (December 2020-January 2021), B.1.1.7 (Alpha) in the third wave (April-June 2021), B.1.617.2 (Delta) in the fourth wave (July-December 2021), and B.1.1.529 (Omicron) in the fifth wave (January-March 2022). The evolutionary rate of the viral genome was 2.60 × 10^-3 (95% highest posterior density [HPD], 1.72 × 10^-3 to 3.62 × 10^-3) nucleotide substitutions per site per year. Continued molecular surveillance of SARS-CoV-2 is crucial for monitoring emerging variants with the potential to cause new COVID-19 outbreaks.

Factors Affecting Perceived Effectiveness of Government Response towards COVID-19 Vaccination in Occidental Mindoro, Philippines

The COVID-19 pandemic has caused several developing countries to fall behind on vaccination at the onset of the pandemic, thus affecting the mobility of easing restrictions and lowering virus transmission. The current study integrated the Protection Motivation Theory (PMT) and extended the Theory of Planned Behavior (TPB) to evaluate factors affecting the perceived effectiveness of government response towards COVID-19 vaccination in Occidental Mindoro. A total of 400 respondents from the municipalities of Occidental Mindoro answered the online questionnaires, which contained 61 questions. This study outlined the relationship between the dependent and independent variables using structural equation modeling (SEM). The results indicated that knowledge of COVID-19 vaccination had significant direct effects on its perceived severity. Subjective standards had significant adverse effects on willingness to follow. In addition, perceived behavioral control was discovered to impact willingness to follow positively. It also showed that perceived government response was significantly affected by adaptive behavior and actual behavior regarding the perceived government response. Meanwhile, it was found that the perceived government response had significant effects on perceived effectiveness. The current study is one of the first to study the factors that affect the perceived effectiveness of government response toward COVID- 19 vaccination.

SARS-CoV-2 variants and vulnerability at the global level

Numerous variants of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic have evolved. Viral variants may evolve with harmful susceptibility to the immunity established with the existing COVID-19 vaccination. These variants are more transmissible, induce relatively extreme illness, have evasive immunological features, decrease neutralization using antibodies from vaccinated persons, and are more susceptible to re-infection. The Centers for Disease Control and Prevention (CDC) has categorized SARS-CoV-2 mutations as variants of interest (VOI), variants of concern (VOC), and variants of high consequence (VOHC). At the moment, four VOC and many variants of interest have been defined and require constant observation. This review article summarizes various variants of SARS-CoV-2 surfaced with special emphasis on VOCs that are spreading across the world, as well as several viral mutational impacts and how these modifications alter the properties of the virus.

Early Genomic, Epidemiological, and Clinical Description of the SARS-CoV-2 Omicron Variant in Mexico City

Omicron is the most mutated SARS-CoV-2 variant-a factor that can affect transmissibility, disease severity, and immune evasiveness. Its genomic surveillance is important in cities with millions of inhabitants and an economic center, such as Mexico City. Results. From 16 November to 31 December 2021, we observed an increase of 88% in Omicron prevalence in Mexico City. We explored the R346K substitution, prevalent in 42% of Omicron variants, known to be associated with immune escape by monoclonal antibodies. In a phylogenetic analysis, we found several independent exchanges between Mexico and the world, and there was an event followed by local transmission that gave rise to most of the Omicron diversity in Mexico City. A haplotype analysis revealed that there was no association between haplotype and vaccination status. Among the 66% of patients who have been vaccinated, no reported comorbidities were associated with Omicron; the presence of odynophagia and the absence of dysgeusia were significant predictor symptoms for Omicron, and the RT-qPCR Ct values were lower for Omicron. Conclusions. Genomic surveillance is key to detecting the emergence and spread of SARS-CoV-2 variants in a timely manner, even weeks before the onset of an infection wave, and can inform public health decisions and detect the spread of any mutation that may affect therapeutic efficacy.