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2. SARS-CoV-2 Wastewater Genomic Surveillance: Approaches, Challenges, and Opportunities

Author

Munteanu, Viorel, Saldana, Michael, Ciorba, Dumitru, Bostan, Viorel, Su, Justin Maine, Kasianchuk, Nadiia, Sharma, Nitesh Kumar, Knyazev, Sergey, Gordeev, Victor, Aßmann, Eva, Lobiuc, Andrei, Covasa, Mihai, Crandall, Keith A., Ouyang, Wenhao O., Wu, Nicholas C., Mason, Christopher, Tierney, Braden T, Lucaci, Alexander G, Zelikovsky, Alex, Mohebbi, Fatemeh, Skums, Pavel, Gibas, Cynthia, Schlueter, Jessica, Rzymski, Piotr, Solo-Gabriele, Helena, Hölzer, Martin, Smith, Adam, and Mangul, Serghei

Subjects
Quantitative Biology - Genomics
Abstract

During the SARS-CoV-2 pandemic, wastewater-based genomic surveillance (WWGS) emerged as an efficient viral surveillance tool that takes into account asymptomatic cases and can identify known and novel mutations and offers the opportunity to assign known virus lineages based on the detected mutations profiles. WWGS can also hint towards novel or cryptic lineages, but it is difficult to clearly identify and define novel lineages from wastewater (WW) alone. While WWGS has significant advantages in monitoring SARS-CoV-2 viral spread, technical challenges remain, including poor sequencing coverage and quality due to viral RNA degradation. As a result, the viral RNAs in wastewater have low concentrations and are often fragmented, making sequencing difficult. WWGS analysis requires advanced computational tools that are yet to be developed and benchmarked. The existing bioinformatics tools used to analyze wastewater sequencing data are often based on previously developed methods for quantifying the expression of transcripts or viral diversity. Those methods were not developed for wastewater sequencing data specifically, and are not optimized to address unique challenges associated with wastewater. While specialized tools for analysis of wastewater sequencing data have also been developed recently, it remains to be seen how they will perform given the ongoing evolution of SARS-CoV-2 and the decline in testing and patient-based genomic surveillance. Here, we discuss opportunities and challenges associated with WWGS, including sample preparation, sequencing technology, and bioinformatics methods., Comment: V Munteanu and M Saldana contributed equally to this work. M H\"olzer, A Smith and S Mangul jointly supervised this work. For correspondence: serghei.mangul@gmail.com

Published
2023

10. CHANGES IN MACULAR GANGLION CELL AND RETINAL NERVE FIBER LAYER THICKNESS DURING RECOVERY FROM INFECTION WITH THE B. 1. 1. 7 VARIANT OF SARS-COV-2 IN PREVIOUSLY HOSPITALIZED PATIENTS WITH COVID-19 BILATERAL PNEUMONIA.

Author

KAL, M., BRZDEK, M., KARSKA-BASTA, I., RZYMSKI, P., PINNA, A., MACKIEWICZ, J., ODROBINA, D., WINIARCZYK, M., and ZAREBSKA-MICHALUK, D.

Subjects
COVID-19, SARS-CoV-2, OPTIC disc, RETINAL ganglion cells, OPTICAL coherence tomography
Abstract

Coronavirus disease 2019 (COVID-19) has been associated with various systemic complications, including potential impacts on ocular health. Recent studies have suggested that COVID-19 may lead to changes in retinal structure, particularly in the neuroretinal and retinal nerve fiber layers (RNFL). This study aimed to examine changes in neuroretinal and RNFL of the optic dics based on optical coherence tomography (OCT) in patients hospitalized due to COVID-19 bilateral pneumonia at 2 time points after discharge. A prospective study involved 49 patients with COVID-19 bilateral pneumonia hospitalized between March and May 2021. Baseline ocular evaluations were conducted 2 months post-discharge, with follow-up examinations 6 months later. Retinal parameters, including RNFL and ganglion cell layers (GCL), were assessed. Control group of healthy individuals also underwent similar ophthalmic examinations for comparative analysis. We found that the average thickness of the retinal nerve fiber layer (RNFL) of the optic disc was lower in the COVID-19 group than in controls (p£0.01). The ganglion cell layer (GCL) was thicker in the inner inferior ring (p=0.008) but thinner in the outer superior, outer nasal, and outer inferior rings (p=0.044, p<0.01, and p<0.01, respectively). OCT parameters were assessed according to sex. At 6 months, the RNFL of the inner inferior and outer temporal rings was thinner in women than in men (p=0.022 and p=0.020, respectively). The GCL of the inner temporal and outer temporal rings was also thinner in women than in men (p=0.004 and p=0.005, respectively). In conclusion: at 6-month follow-up, RNFL and GCL thickness was significantly lower in some areas of the retina compared with baseline. COVID-19 seems to cause changes in the macular retina, highlighting the need for ophthalmologic screening of patients with a history of SARS-CoV-2 infection. [ABSTRACT FROM AUTHOR]

Published
2024
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21. Revolutionizing hepatitis C treatment: next-gen direct-acting antivirals

Author

Dobrowolska, Krystyna, Brzdęk, Michał, Rzymski, Piotr, Flisiak, Robert, Pawłowska, Małgorzata, Janczura, Jakub, Brzdęk, Kinga, and Zarębska-Michaluk, Dorota

Abstract

ABSTRACTIntroductionWith the introduction of highly effective and safe therapies with next-generation direct-acting antivirals (DAAs), that act without interferon, hepatitis C virus (HCV) infection remains the only treatable chronic infectious disease.Areas coveredThe review aims to provide an overview of the therapy revolution with a description of specific DAAs, their mechanisms of action, a summary of the safety and efficacy of specific regimens, and a discussion of populations requiring special therapeutic approaches.Expert OpinionDAAs are highly effective, safe, and easy to use. However, challenges such as access to health services and loss of patients from the cascade of care, especially in groups disproportionately affected by HCV infection, such as substance abusers, make it difficult to achieve the WHO’s goal of HCV elimination. The proposed strategy to combat these difficulties involves a one-step approach to diagnosing and treating the infection, the availability of long-lasting forms of medication, and the development of an effective vaccine. The aforementioned opportunities are all the more important as the world is facing an opioid epidemic that is translating into an increase in HCV prevalence. This phenomenon is of greatest concern in women of childbearing age and in those already pregnant due to treatment limitations.

Published
2024
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22. The Database of Cross-Linguistic Colexifications, reproducible analysis of cross-linguistic polysemies

Author

Rzymski, Christoph, Tresoldi, Tiago, Greenhill, Simon J., Wu, Mei-Shin, Schweikhard, Nathanael E., Koptjevskaja-Tamm, Maria, Gast, Volker, Bodt, Timotheus A., Hantgan, Abbie, Kaiping, Gereon A., Chang, Sophie, Lai, Yunfan, Morozova, Natalia, Arjava, Heini, Hübler, Nataliia, Koile, Ezequiel, Pepper, Steve, Proos, Mariann, Van Epps, Briana, Blanco, Ingrid, Hundt, Carolin, Monakhov, Sergei, Pianykh, Kristina, Ramesh, Sallona, Gray, Russell D., Forkel, Robert, and List, Johann-Mattis

Published
2020
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39. Could chronic HBV infection explain Beethoven's hearing loss? Implications for patients currently living with hepatitis B.

Author

Rzymski, Piotr, Zarębska-Michaluk, Dorota, and Flisiak, Robert

Abstract

The cause of Ludwig van Beethoven's health deterioration, i.e., hearing loss and cirrhosis, have been subject to various studies. The genomic analysis of his hair indicates infection with the hepatitis B virus (HBV) at least 6 months prior to death. However, considering his first documented case of jaundice in the summer of 1821, second jaundice months prior to his death, and increased risk of hearing loss in HBV-infected patients, we offer an alternative hypothesis of chronic HBV infection as a cause of deafness and cirrhosis. According to it, HBV was acquired early, progressed from immune-tolerant to an immune-reactive phase, and triggered Beethoven's hearing issues when aged 28. Later, HBV infection entered the non-replication phase with at least two episodes of reactivation in the fifth decade of life accompanied by jaundice. More studies examining hearing loss in patients with chronic HBV infection are encouraged to better understand their potential otologic needs. [Display omitted] • We hypothesize that Beethoven's hearing loss was due to a chronic HBV infection. • Hearing loss is not classically attributed to hepatitis B. • HBV infection increases the odds of sudden sensorineural hearing loss. • Hearing loss in HBV patients should be communicated to hepatologists. • More studies addressing otologic issues in hepatitis B are needed. [ABSTRACT FROM AUTHOR]

Published
2023
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