Molecular Epidemiology Analysis of SARS-CoV-2 Strains Circulating in Romania during the First Months of the Pandemic

Colliding Challenges: An Analysis of SARS-CoV-2 Infection in Patients with Pulmonary Tuberculosis versus SARS-CoV-2 Infection Alone

Background and Objectives: The concurrent occurrence of tuberculosis and COVID-19 coinfection poses significant clinical complexities, warranting a nuanced approach to diagnosis, management, and patient care. Materials and Methods: A retrospective, cross-sectional study was conducted on two groups: one comprising 32 patients with pulmonary TB (PTB) and COVID-19 co-infection, and one including 100 patients with COVID-19 alone. Data was collected from medical records, including patient history, clinical parameters, laboratory, imaging results, and patient outcome. Results: A lower BMI emerges as a significant marker suggesting underlying PTB in patients with SARS-CoV-2 co-infection. Type 2 diabetes mellitus increases the risk of death in PTB-SARS-CoV-2 co-infection. Co-infected patients show lymphocytopenia and higher neutrophil levels, CRP, transaminases, and D-dimer levels. Elevated CRP and ALT levels are linked to increased co-infection likelihood. Certain parameters like SpO2, CRP, ALT, AST, and D-dimer effectively differentiate between co-infected and COVID-19 patients. Platelet-to-lymphocyte ratio is notably higher in co-infected individuals. Lesion severity on imaging is significantly associated with co-infection, highlighting imaging's diagnostic importance. Longer hospital stays are linked to co-infection but not significantly to death risk. Conclusions: Certain clinical and biological factors may serve as potential indicators of PTB co-infection in patients with SARS-CoV-2.

Clinical and molecular epidemiology of influenza viruses from Romanian patients hospitalized during the 2019/20 season

Two main mechanisms contribute to the continuous evolution of influenza viruses: accumulation of mutations in the hemagglutinin and neuraminidase genes (antigenic drift) and genetic re-assortments (antigenic shift). Epidemiological surveillance is important in identifying new genetic variants of influenza viruses with potentially increased pathogenicity and transmissibility. In order to characterize the 2019/20 influenza epidemic in Romania, 1042 respiratory samples were collected from consecutive patients hospitalized with acute respiratory infections in the National Institute for Infectious Diseases "Prof. Dr. Matei Balș", Bucharest Romania and tested for influenza A virus, influenza B virus and respiratory syncytial virus (RSV) by real-time PCR. Out of them, 516 cases were positive for influenza, with relatively equal distribution of influenza A and B. Two patients had influenza A and B co-infection and 8 patients had influenza-RSV co-infection. The most severe cases, requiring supplemental oxygen administration or intensive care, and the most deaths were reported in patients aged 65 years and over. Subtyping showed the predominance of A(H3N2) compared to A(H1N1)pdm09 pdm09 (60.4% and 39.6% of all subtyped influenza A isolates, respectively), and the circulation of Victoria B lineage only. Influenza B started to circulate first (week 47/2019), with influenza A appearing slightly later (week 50/2019), followed by continued co-circulation of A and B viruses throughout the season. Sixty-eight samples, selected to cover the entire influenza season and all circulating viral types, were analysed by next generation sequencing (NGS). All A(H1N1)pdm09 sequences identified during this season in Romania were clustered in the 6b1.A clade (sub-clades: 6b1.A.183P -5a and 6b1.A.187A). For most A(H1N1)pdm09 sequences, the dominant epitope was Sb (pepitope = 0.25), reducing the vaccine efficacy by approximately 60%. According to phylogenetic analysis, influenza A(H3N2) strains circulating in this season belonged predominantly to clade 3C.3A, with only few sequences in clade 3C.2A1b. These 3C.2A1b sequences, two of which belonged to vaccinated patients, harbored mutations in antigenic sites leading to potential reduction of vaccine efficacy. Phylogenetic analysis of influenza B, lineage Victoria, sequences showed that the circulating strains belonged to clade V1A3. As compared to the other viral types, fewer mutations were observed in B/Victoria strains, with limited impact on vaccine efficiency based on estimations.

A Global Mutational Profile of SARS-CoV-2: A Systematic Review and Meta-Analysis of 368,316 COVID-19 Patients

Since its first detection in December 2019, more than 232 million cases of COVID-19, including 4.7 million deaths, have been reported by the WHO. The SARS-CoV-2 viral genomes have evolved rapidly worldwide, causing the emergence of new variants. This systematic review and meta-analysis was conducted to provide a global mutational profile of SARS-CoV-2 from December 2019 to October 2020. The review was conducted according to the Preferred Reporting Items for Systematic Reviews and Meta-analysis (PRISMA), and a study protocol was lodged with PROSPERO. Data from 62 eligible studies involving 368,316 SARS-CoV-2 genomes were analyzed. The mutational data analyzed showed most studies detected mutations in the Spike protein (n = 50), Nucleocapsid phosphoprotein (n = 34), ORF1ab gene (n = 29), 5′-UTR (n = 28) and ORF3a (n = 25). Under the random-effects model, pooled prevalence of SARS-CoV-2 variants was estimated at 95.1% (95% CI; 93.3–96.4%; I² = 98.952%; p = 0.000) while subgroup meta-analysis by country showed majority of the studies were conducted ‘Worldwide’ (n = 10), followed by ‘Multiple countries’ (n = 6) and the USA (n = 5). The estimated prevalence indicated a need to continuously monitor the prevalence of new mutations due to their potential influence on disease severity, transmissibility and vaccine effectiveness.

One year into the pandemic: Short-term evolution of SARS-CoV-2 and emergence of new lineages

The COVID-19 pandemic was officially declared on March 11th, 2020. Since the very beginning, the spread of the virus has been tracked nearly in real-time by worldwide genome sequencing efforts. As of March 2021, more than 830,000 SARS-CoV-2 genomes have been uploaded in GISAID and this wealth of data allowed researchers to study the evolution of SARS-CoV-2 during this first pandemic year. In parallel, nomenclatures systems, often with poor consistency among each other, have been developed to designate emerging viral lineages. Despite general fears that the virus might mutate to become more virulent or transmissible, SARS-CoV-2 genetic diversity has remained relatively low during the first ~ 8 months of sustained human-to-human transmission. At the end of 2020/beginning of 2021, though, some alarming events started to raise concerns of possible changes in the evolutionary trajectory of the virus. Specifically, three new viral variants associated with extensive transmission have been described as variants of concern (VOC). These variants were first reported in the UK (B.1.1.7), South Africa (B.1.351) and Brazil (P.1). Their designation as VOCs was determined by an increase of local cases and by the high number of amino acid substitutions harboured by these lineages. This latter feature is reminiscent of viral sequences isolated from immunocompromised patients with long-term infection, suggesting a possible causal link. Here we review the events that led to the identification of these lineages, as well as emerging data concerning their possible implications for viral phenotypes, reinfection risk, vaccine efficiency and epidemic potential. Most of the available evidence is, to date, provisional, but still represents a starting point to uncover the potential threat posed by the VOCs. We also stress that genomic surveillance must be strengthened, especially in the wake of the vaccination campaigns.

Across regions: Are most COVID-19 deaths above or below life expectancy?

Introduction

Life expectancy varies across geographical and political landscapes for a multitude of reasons. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus responsible for the 2020 coronavirus disease (COVID-19) and pandemic, is present in 215 countries, and is described as a pathogen that is most deadly to individuals 65 years and older. However, it is unclear if the majority of COVID-19-related deaths are targeting individuals above or below life expectancy.

Methods

Through seven months of the 2020 COVID-19 pandemic, an association between life expectancy and COVID-19 related deaths was assessed. The reported age of those suffering from COVID-19-related deaths was evaluated across eight countries (United States, Germany, Italy, Hungary, Poland, South Africa, Sweden, and Switzerland), and placed into binary categories depending on whether or not the death occurred above or below the country's life expectancy.

Results

Given this dataset, it was observed that there was a greater proportion of COVID related deaths above life expectancy (M=64.58%, SD=6.46) as opposed to below life expectancy (M=35.41%, SD=6.46), as these differences were significant (95%CI [18.518, 42.881], p<0.001). In contrast, an insignificant trend was observed when examining the relationship between deaths above life expectancy and Gini index (Pearson correlation coefficient r= -0.62, n=8, p=0.09). The disparity, or percent difference in death occurring above versus below life expectancy was greatest in the countries with life expectancies of 80+ (Sweden, Switzerland, Germany).

Conclusions

Considering life expectancy may be an appropriate approach for reporting COVID-19-related deaths, as well as planning responses to localized COVID-19 outbreaks, prioritizing drug treatment, and assessing ICU capacity.

Short Communication:Evidence of Novel SARS-CoV-2 Variants Circulation in Romania

New SARS-CoV-2 variants are constantly emerging and putting a strain on public health systems by spreading faster and potentially evading immune protection through vaccination. One of these strains is the B.1.1.7 variant that has initially been described in the United Kingdom and has subsequently spread to several countries. Monitoring the amplification of the S gene-a major hotspot for molecular evolution-by reverse transcription polymerase chain reaction (RT-PCR) allows rapidly screening for such variants. This report describes the detection of sequence variants in Romania by using this strategy followed by next-generation sequencing of the entire genome for confirmation and further characterization. One B.1.1.7 and three B.1.258 sequences were confirmed. Each of these strains presented additional mutations with possible impact on the replicative capacity. Public health strategies should be devised to ensure molecular monitoring of SARS-CoV-2 evolution during the pandemic and allow adequate and rapid reaction.

High Mortality Rate in Adult COVID-19 Inpatients in Eastern Sudan: A Retrospective Study

AIM

The current pandemic of coronavirus disease 2019 (COVID-19) is caused by severe acute respiratory coronavirus syndrome 2 (SARS-CoV-2). It is a global public health concern that has resulted in the rapid growth in the number of infected patients with significant mortality rates. Hence, we conducted a retrospective study in Gadarif Hospital to evaluate the presenting manifestations, mortality rate, and the risk factors associated with mortality in hospitalized patients.

METHODS

A retrospective study was conducted at Gadarif Hospital in Eastern Sudan. Medical files of the patients admitted during the period between April and July 2020 were reviewed. All the files of the adult patients (aged 18 or above), of both sexes, who had a confirmed COVID-19-positive status via laboratory testing using PCR and who were admitted during this period were reviewed. The data extracted included patients' demographics and initial clinical presentation, symptoms, signs, and the laboratory and radiographic findings. The data were analyzed using SPSS v22.

RESULTS

Eighty-eight patients were admitted with COVID-19. The median (interquartile) age was 62 (55.00-70.00) years old, and 72 (81.8%) of them were males. Most patients (75%) experienced a one-week duration of symptoms. A fever (87.5%), cough (80.68%), and shortness of breath (77.27%) were the most common presenting symptoms. Following a clinical assessment, both the systolic and diastolic blood pressure were found to be normal in most patients, at 92.05% and 89.77%, respectively. An oxygen saturation of less than 90% was seen in 71.59% of patients. The general mortality rate was 37.5% and most deaths occurred during the first 24 h of admission (21/33 [63.64%]). There was no significant difference in the death rate between females and males (5/16 [31.3%] vs 28/72 [38.9%], P = 0.776). There was no significant difference in the body mass index, tobacco use, or education level between the patients who died and those who survived. A logistic regression showed that being older (AOR = 1.05, 95% CI = [1.01, 1.10]) and having a lower PO2 level (AOR = 1.11, 95% CI = [1.04, 1.16]) were associated with mortality.

CONCLUSION

The general mortality rate was 37.5%, and the risk factors that could predict increased mortality in hospitalized COVID-19 positive cases included old age and a lower PO2 level.

Ultrafast Sample Placement on Existing Trees (UShER) Empowers Real-Time Phylogenetics for the SARS-CoV-2 Pandemic

As the SARS-CoV-2 virus spreads through human populations, the unprecedented accumulation of viral genome sequences is ushering a new era of "genomic contact tracing" - that is, using viral genome sequences to trace local transmission dynamics. However, because the viral phylogeny is already so large - and will undoubtedly grow many fold - placing new sequences onto the tree has emerged as a barrier to real-time genomic contact tracing. Here, we resolve this challenge by building an efficient, tree-based data structure encoding the inferred evolutionary history of the virus. We demonstrate that our approach improves the speed of phylogenetic placement of new samples and data visualization by orders of magnitude, making it possible to complete the placements under real-time constraints. Our method also provides the key ingredient for maintaining a fully-updated reference phylogeny. We make these tools available to the research community through the UCSC SARS-CoV-2 Genome Browser to enable rapid cross-referencing of information in new virus sequences with an ever-expanding array of molecular and structural biology data. The methods described here will empower research and genomic contact tracing for laboratories worldwide.

SOFTWARE AVAILABILITY

USHER is available to users through the UCSC Genome Browser at https://genome.ucsc.edu/cgi-bin/hgPhyloPlace . The source code and detailed instructions on how to compile and run UShER are available from https://github.com/yatisht/usher .