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12 pages, 4303 KiB

Open AccessArticle

SARS-CoV-2 Omicron BA.1 Variant Infection of Human Colon Epithelial Cells

by Avan Antia, David M. Alvarado, Qiru Zeng, Luis A. Casorla-Perez, Deanna L. Davis, Naomi M. Sonnek, Matthew A. Ciorba and Siyuan Ding

Viruses 2024, 16(4), 634; https://doi.org/10.3390/v16040634 - 19 Apr 2024

Cited by 1 | Viewed by 2269

Abstract

The Omicron variant of SARS-CoV-2, characterized by multiple subvariants including BA.1, XBB.1.5, EG.5, and JN.1, became the predominant strain in early 2022. Studies indicate that Omicron replicates less efficiently in lung tissue compared to the ancestral strain. However, the infectivity of Omicron in [...] Read more.

The Omicron variant of SARS-CoV-2, characterized by multiple subvariants including BA.1, XBB.1.5, EG.5, and JN.1, became the predominant strain in early 2022. Studies indicate that Omicron replicates less efficiently in lung tissue compared to the ancestral strain. However, the infectivity of Omicron in the gastrointestinal tract is not fully defined, despite the fact that 70% of COVID-19 patients experience digestive disease symptoms. Here, using primary human colonoids, we found that, regardless of individual variability, Omicron infects colon cells similarly or less effectively than the ancestral strain or the Delta variant. The variant induced limited type III interferon expression and showed no significant impact on epithelial integrity. Further experiments revealed inefficient cell-to-cell spread and spike protein cleavage in the Omicron spike protein, possibly contributing to its lower infectious particle levels. The findings highlight the variant-specific replication differences in human colonoids, providing insights into the enteric tropism of Omicron and its relevance to long COVID symptoms. Full article

(This article belongs to the Special Issue Molecular Epidemiology of SARS-CoV-2: 2nd Edition)

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13 pages, 517 KiB

Open AccessArticle

Assessing the Clinical Impact of the SARS-CoV-2 Gamma Variant on Intensive Care Unit Admissions: Insights from a Reference Hospital in Northeastern Brazil

by Carolina Kymie Vasques Nonaka, Adlas Michel de Jesus Ribeiro, Gisele Vieira Rocha, Helena Souza da Hora, Antônio Augusto Fonseca Junior, Fernanda de Macêdo Lima, Iasmin Nogueira Bastos, Samara Alves Sa Teles, Thamires Gomes Lopes Weber, Vanessa Ferreira Costa, Zaquer Suzana Costa-Ferro, Clarissa Araújo Gurgel Rocha, Silvia Inês Sardi, Gúbio Soares, Ana Verena Almeida Mendes and Bruno Solano de Freitas Souza

Viruses 2024, 16(3), 467; https://doi.org/10.3390/v16030467 - 20 Mar 2024

Viewed by 1173

Abstract

The global challenge posed by the prolonged COVID-19 pandemic underscores the critical need for ongoing genomic surveillance to identify emerging variants and formulate effective public health strategies. This retrospective observational study, conducted in a reference hospital in Northeast Brazil and comprising 2116 cases, [...] Read more.

The global challenge posed by the prolonged COVID-19 pandemic underscores the critical need for ongoing genomic surveillance to identify emerging variants and formulate effective public health strategies. This retrospective observational study, conducted in a reference hospital in Northeast Brazil and comprising 2116 cases, employed PCR genotyping together with epidemiological data to elucidate the impact of the Gamma variant during its emergence, revealing distinct patterns in hospitalization rates, severity of illness, and outcomes. The study emphasizes the challenges posed by the variant, particularly an increased tendency for ICU admissions and respiratory support, especially among adults aged 18 to 59 without comorbidities. Laboratory analyses further demonstrate elevated inflammatory, coagulation, and hepatic markers in the Gamma variant cohort, suggesting a more severe systemic response. Despite limitations, including a retrospective approach and single-institution data, the study underscores the importance of ongoing genomic surveillance. Overall, this research contributes valuable insights into the impact of the Gamma variant on COVID-19 dynamics, advocating for continued research and surveillance to inform effective public health strategies regarding evolving viral variants. Full article

(This article belongs to the Special Issue Molecular Epidemiology of SARS-CoV-2: 2nd Edition)

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13 pages, 1600 KiB

Open AccessArticle

Clinical Manifestations of Infections with the Omicron Sub-Lineages BA.1, BA.2, and BA.5: A Retrospective Follow-Up Analysis of Public Health Data from Mecklenburg-Western Pomerania, Germany

by Katja Verena Goller, Janine Ziemann, Christian Kohler, Karsten Becker, Nils-Olaf Hübner and on behalf of the CoMV-Gen Study Group

Viruses 2024, 16(3), 454; https://doi.org/10.3390/v16030454 - 15 Mar 2024

Cited by 1 | Viewed by 1068

Abstract

The Omicron variants BA.1, BA.2, and BA.5 caused several waves of SARS-CoV-2 in Germany in 2022. In this comparative study, public health data on SARS-CoV-2 infections from Mecklenburg-Western Pomerania, Germany, between January and October 2022 were examined retrospectively using Pearson’s chi-squared tests and [...] Read more.

The Omicron variants BA.1, BA.2, and BA.5 caused several waves of SARS-CoV-2 in Germany in 2022. In this comparative study, public health data on SARS-CoV-2 infections from Mecklenburg-Western Pomerania, Germany, between January and October 2022 were examined retrospectively using Pearson’s chi-squared tests and Fisher’s exact tests for testing for statistical significance. Compared to BA.5 infections, BA.1 and BA.2 infections affected younger individuals aged up to 19 years significantly more often, whereas BA.5 infections occurred significantly more frequently in patients between 40 and 59 years of age when compared to BA.1 and BA.2. Infections with all three variants predominantly caused flu-like symptoms; nevertheless, there were significant differences between the reported symptoms of BA.1, BA.2, and BA.5 infections. Especially, the symptoms of ‘fever’, ‘severe feeling of sickness’, ‘loss of taste’, and ‘loss of smell’ were significantly more often present in patients with BA.5 infections compared to BA.1 and BA.2 cases. Additionally, BA.2 and BA.5 cases reported significantly more often the symptoms of ‘runny nose’ and ‘cough’ than BA.1-infected cases. Our findings indicate remarkable differences in the clinical presentations among the sub-lineages, especially in BA.5 infections. Furthermore, the study demonstrates a powerful tool to link epidemiological data with genetic data in order to investigate their potential impact on public health. Full article

(This article belongs to the Special Issue Molecular Epidemiology of SARS-CoV-2: 2nd Edition)

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22 pages, 4102 KiB

Open AccessArticle

The Nucleocapsid Protein of SARS-CoV-2, Combined with ODN-39M, Is a Potential Component for an Intranasal Bivalent Vaccine with Broader Functionality

by Yadira Lobaina, Rong Chen, Edith Suzarte, Panchao Ai, Vivian Huerta, Alexis Musacchio, Ricardo Silva, Changyuan Tan, Alejandro Martín, Laura Lazo, Gerardo Guillén-Nieto, Ke Yang, Yasser Perera and Lisset Hermida

Viruses 2024, 16(3), 418; https://doi.org/10.3390/v16030418 - 8 Mar 2024

Cited by 3 | Viewed by 1689

Abstract

Despite the rapid development of vaccines against COVID-19, they have important limitations, such as safety issues, the scope of their efficacy, and the induction of mucosal immunity. The present study proposes a potential component for a new generation of vaccines. The recombinant nucleocapsid [...] Read more.

Despite the rapid development of vaccines against COVID-19, they have important limitations, such as safety issues, the scope of their efficacy, and the induction of mucosal immunity. The present study proposes a potential component for a new generation of vaccines. The recombinant nucleocapsid (N) protein from the SARS-CoV-2 Delta variant was combined with the ODN-39M, a synthetic 39 mer unmethylated cytosine-phosphate-guanine oligodeoxynucleotide (CpG ODN), used as an adjuvant. The evaluation of its immunogenicity in Balb/C mice revealed that only administration by intranasal route induced a systemic cross-reactive, cell-mediated immunity (CMI). In turn, this combination was able to induce anti-N IgA in the lungs, which, along with the specific IgG in sera and CMI in the spleen, was cross-reactive against the nucleocapsid protein of SARS-CoV-1. Furthermore, the nasal administration of the N + ODN-39M preparation, combined with RBD Delta protein, enhanced the local and systemic immune response against RBD, with a neutralizing capacity. Results make the N + ODN-39M preparation a suitable component for a future intranasal vaccine with broader functionality against Sarbecoviruses. Full article

(This article belongs to the Special Issue Molecular Epidemiology of SARS-CoV-2: 2nd Edition)

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7 pages, 2928 KiB

Open AccessCommunication

Timely Monitoring of SARS-CoV-2 RNA Fragments in Wastewater Shows the Emergence of JN.1 (BA.2.86.1.1, Clade 23I) in Berlin, Germany

by Alexander Bartel, José Horacio Grau, Julia Bitzegeio, Dirk Werber, Nico Linzner, Vera Schumacher, Sonja Garske, Karsten Liere, Thomas Hackenbeck, Sofia Isabell Rupp, Daniel Sagebiel, Uta Böckelmann and Martin Meixner

Viruses 2024, 16(1), 102; https://doi.org/10.3390/v16010102 - 10 Jan 2024

Cited by 11 | Viewed by 5452

Abstract

The importance of COVID-19 surveillance from wastewater continues to grow since case-based surveillance in the general population has been scaled back world-wide. In Berlin, Germany, quantitative and genomic wastewater monitoring for SARS-CoV-2 is performed in three wastewater treatment plants (WWTP) covering 84% of [...] Read more.

The importance of COVID-19 surveillance from wastewater continues to grow since case-based surveillance in the general population has been scaled back world-wide. In Berlin, Germany, quantitative and genomic wastewater monitoring for SARS-CoV-2 is performed in three wastewater treatment plants (WWTP) covering 84% of the population since December 2021. The SARS-CoV-2 Omicron sublineage JN.1 (B.2.86.1.1), was first identified from wastewater on 22 October 2023 and rapidly became the dominant sublineage. This change was accompanied by a parallel and still ongoing increase in the notification-based 7-day-hospitalization incidence of COVID-19 and COVID-19 ICU utilization, indicating increasing COVID-19 activity in the (hospital-prone) population and a higher strain on the healthcare system. In retrospect, unique mutations of JN.1 could be identified in wastewater as early as September 2023 but were of unknown relevance at the time. The timely detection of new sublineages in wastewater therefore depends on the availability of new sequences from GISAID and updates to Pango lineage definitions and Nextclade. We show that genomic wastewater surveillance provides timely public health evidence on a regional level, complementing the existing indicators. Full article

(This article belongs to the Special Issue Molecular Epidemiology of SARS-CoV-2: 2nd Edition)

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21 pages, 2637 KiB

Open AccessArticle

Molecular Epidemiology of SARS-CoV-2 and Clinical Manifestations among Organ Transplant Recipients with COVID-19

by Abeer N. Alshukairi, Ahmed A. Al-Qahtani, Dalia A. Obeid, Ashraf Dada, Reem S. Almaghrabi, Maha A. Al-Abdulkareem, Basma M. Alahideb, Madain S. Alsanea, Feda A. Alsuwairi and Fatimah S. Alhamlan

Viruses 2024, 16(1), 25; https://doi.org/10.3390/v16010025 - 22 Dec 2023

Cited by 1 | Viewed by 1660

Abstract

RNA viruses, including SARS-CoV-2, rely on genetic mutation as a major evolutionary mechanism, leading to the emergence of variants. Organ transplant recipients (OTRs) may be particularly vulnerable to such mutations, making it crucial to monitor the spread and evolution of SARS-CoV-2 in this [...] Read more.

RNA viruses, including SARS-CoV-2, rely on genetic mutation as a major evolutionary mechanism, leading to the emergence of variants. Organ transplant recipients (OTRs) may be particularly vulnerable to such mutations, making it crucial to monitor the spread and evolution of SARS-CoV-2 in this population. This cohort study investigated the molecular epidemiology of SARS-CoV-2 by comparing the SARS-CoV-2 whole genome, demographic characteristics, clinical conditions, and outcomes of COVID-19 illness among OTRs (n = 19) and non-OTRs with (n = 38) or without (n = 30) comorbid conditions. Most patients without comorbidities were female, whereas most OTRs were male. Age varied significantly among the three groups: patients with comorbidities were the oldest, and patients without comorbidities were the youngest. Whole-genome sequencing revealed that OTRs with mild disease had higher numbers of unusual mutations than patients in the other two groups. Additionally, OTRs who died had similar spike monoclonal antibody resistance mutations and 3CLpro mutations, which may confer resistance to nirmatrelvir, ensitrelvir, and GC37 therapy. The presence of those unusual mutations may impact the severity of COVID-19 illness in OTRs by affecting the virus’s ability to evade the immune system or respond to treatment. The higher mutation rate in OTRs may also increase the risk of the emergence of new virus variants. These findings highlight the importance of monitoring the genetic makeup of SARS-CoV-2 in all immunocompromised populations and patients with comorbidity. Full article

(This article belongs to the Special Issue Molecular Epidemiology of SARS-CoV-2: 2nd Edition)

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12 pages, 8915 KiB

Open AccessArticle

Enhancement of SARS-CoV-2 Infection via Crosslinking of Adjacent Spike Proteins by N-Terminal Domain-Targeting Antibodies

by Tina Lusiany, Tohru Terada, Jun-ichi Kishikawa, Mika Hirose, David Virya Chen, Fuminori Sugihara, Hendra Saputra Ismanto, Floris J. van Eerden, Songling Li, Takayuki Kato, Hisashi Arase, Matsuura Yoshiharu, Masato Okada and Daron M. Standley

Viruses 2023, 15(12), 2421; https://doi.org/10.3390/v15122421 - 13 Dec 2023

Cited by 1 | Viewed by 1878

Abstract

The entry of SARS-CoV-2 into host cells is mediated by the interaction between the spike receptor-binding domain (RBD) and host angiotensin-converting enzyme 2 (ACE2). Certain human antibodies, which target the spike N-terminal domain (NTD) at a distant epitope from the host cell binding [...] Read more.

The entry of SARS-CoV-2 into host cells is mediated by the interaction between the spike receptor-binding domain (RBD) and host angiotensin-converting enzyme 2 (ACE2). Certain human antibodies, which target the spike N-terminal domain (NTD) at a distant epitope from the host cell binding surface, have been found to augment ACE2 binding and enhance SARS-CoV-2 infection. Notably, these antibodies exert their effect independently of the antibody fragment crystallizable (Fc) region, distinguishing their mode of action from previously described antibody-dependent infection-enhancing (ADE) mechanisms. Building upon previous hypotheses and experimental evidence, we propose that these NTD-targeting infection-enhancing antibodies (NIEAs) achieve their effect through the crosslinking of neighboring spike proteins. In this study, we present refined structural models of NIEA fragment antigen-binding region (Fab)–NTD complexes, supported by molecular dynamics simulations and hydrogen–deuterium exchange mass spectrometry (HDX-MS). Furthermore, we provide direct evidence confirming the crosslinking of spike NTDs by NIEAs. Collectively, our findings advance our understanding of the molecular mechanisms underlying NIEAs and their impact on SARS-CoV-2 infection. Full article

(This article belongs to the Special Issue Molecular Epidemiology of SARS-CoV-2: 2nd Edition)

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11 pages, 2146 KiB

Open AccessArticle

Genomic Surveillance of SARS-CoV-2 in México: Three Years since Wuhan, China’s First Reported Case

by Juan Daniel Lira-Morales, Osvaldo López-Cuevas, José Andrés Medrano-Félix, Jean Pierre González-Gómez, Irvin González-López, Nohelia Castro-Del Campo, Bruno Gomez-Gil and Cristóbal Chaidez

Viruses 2023, 15(11), 2223; https://doi.org/10.3390/v15112223 - 8 Nov 2023

Cited by 1 | Viewed by 1980

Abstract

Objective: The aim of this work was to analyze the metadata of the SARS-CoV-2 sequences obtained from samples collected in Mexico from 2020 to 2022. Materials and Methods: Metadata of SARS-CoV-2 sequences from samples collected in Mexico up to 31 December 2022 was [...] Read more.

Objective: The aim of this work was to analyze the metadata of the SARS-CoV-2 sequences obtained from samples collected in Mexico from 2020 to 2022. Materials and Methods: Metadata of SARS-CoV-2 sequences from samples collected in Mexico up to 31 December 2022 was retrieved from GISAID and manually cured for interpretation. Results: As of December 2022, Mexican health authorities and the scientific community have sequenced up to 81,983 SARS-CoV-2 viral genomes deposited in GISAID, representing 1.1% of confirmed cases. The number of sequences obtained per state corresponded to the gross domestic product (GDP) of each state for the first (Mexico City) and the last (Tlaxcala). Approximately 25% of the sequences were obtained from CoViGen-Mex, an interdisciplinary initiative of health and scientific institutions to collect and sequence samples nationwide. The metadata showed a clear dominance of sequences retrieved by women. A similar variant distribution over time was found in Mexico and overseas, with the Omicron variant predominating. Finally, the age group with the highest representation in the sequences was adults aged 21 to 50 years, accounting for more than 50% of the total. Conclusions: Mexico presents diverse sociodemographic and economic characteristics. The COVID-19 pandemic has been and continues to be a challenge for collaboration across the country and around the world. Full article

(This article belongs to the Special Issue Molecular Epidemiology of SARS-CoV-2: 2nd Edition)

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11 pages, 2128 KiB

Open AccessArticle

Epidemiological and Genomic Analysis of Asymptomatic SARS-CoV-2 Infections during the Delta and Omicron Epidemic Waves in São Paulo City, Brazil

by Svetoslav N. Slavov, Alex R. J. Lima, Gabriela Ribeiro, Loyze P. O. de Lima, Claudia R. dos S. Barros, Elaine C. Marqueze, Antonio J. Martins, Maiara Martininghi, Melissa Palmieri, Luiz A. V. Caldeira, Fabiana E. V. da Silva, Giselle Cacherik, Aline L. Nicolodelli, Simone Kashima, Marta Giovanetti, Luiz Carlos Junior Alcantara, Sandra C. Sampaio and Maria C. Elias

Viruses 2023, 15(11), 2210; https://doi.org/10.3390/v15112210 - 3 Nov 2023

Viewed by 980

Abstract

We examined the asymptomatic rates of SARS-CoV-2 infection during the Delta and Omicron waves in the city of São Paulo. Nasopharyngeal swabs were collected at strategic points of the city (open-air markets, bus terminals, airports) for SARS-CoV-2 RNA testing. Applying the questionnaire, the [...] Read more.

We examined the asymptomatic rates of SARS-CoV-2 infection during the Delta and Omicron waves in the city of São Paulo. Nasopharyngeal swabs were collected at strategic points of the city (open-air markets, bus terminals, airports) for SARS-CoV-2 RNA testing. Applying the questionnaire, the symptomatic individuals were excluded, and only asymptomatic cases were analyzed. During the Delta wave, a total of 4315 samples were collected, whereas 2372 samples were collected during the first Omicron wave. The incidence of the asymptomatic SARS-CoV-2 infection was 0.6% during the Delta wave and 0.8% during the Omicron wave. No statistical differences were found in the threshold amplification cycle. However, there was a statistical difference observed in the sublineage distribution between asymptomatic and symptomatic individuals. Our study determined the incidence of asymptomatic infection by monitoring individuals who remained symptom-free, thereby providing a reliable evaluation of asymptomatic SARS-CoV-2 carriage. Our findings reveal a relatively low proportion of asymptomatic cases, which could be attributed to our rigorous monitoring protocol for the presence of clinical symptoms. Investigating asymptomatic infection rates is crucial to develop and implement effective disease control strategies. Full article

(This article belongs to the Special Issue Molecular Epidemiology of SARS-CoV-2: 2nd Edition)

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14 pages, 1778 KiB

Open AccessArticle

Genomic and Epidemiologic Surveillance of SARS-CoV-2 in the Pandemic Period: Sequencing Network of the Lazio Region, Italy

by Martina Rueca, Giulia Berno, Alessandro Agresta, Martina Spaziante, Cesare Ernesto Maria Gruber, Lavinia Fabeni, Emanuela Giombini, Ornella Butera, Alessandra Barca, Paola Scognamiglio, Enrico Girardi, Fabrizio Maggi, Maria Beatrice Valli, Francesco Vairo and SARS-CoV-2 Lazio Genomic Surveillance Study Group

Viruses 2023, 15(11), 2192; https://doi.org/10.3390/v15112192 - 31 Oct 2023

Viewed by 1263

Abstract

Since the beginning of the COVID-19 pandemic, large-scale genomic sequencing has immediately pointed out that SARS-CoV-2 has rapidly mutated during the course of the pandemic, resulting in the emergence of variants with a public health impact. In this context, strictly monitoring the circulating [...] Read more.

Since the beginning of the COVID-19 pandemic, large-scale genomic sequencing has immediately pointed out that SARS-CoV-2 has rapidly mutated during the course of the pandemic, resulting in the emergence of variants with a public health impact. In this context, strictly monitoring the circulating strains via NGS has proven to be crucial for the early identification of new emerging variants and the study of the genomic evolution and transmission of SARS-CoV-2. Following national and international guidelines, the Lazio region has created a sequencing laboratory network (WGSnet-Lazio) that works in synergy with the reference center for epidemiological surveillance (SERESMI) to monitor the circulation of SARS-CoV-2. Sequencing was carried out with the aims of characterizing outbreak transmission dynamics, performing the genomic analysis of viruses infecting specific categories of patients (i.e., immune-depressed, travelers, and people with severe symptoms) and randomly monitoring variant circulation. Here we report data emerging from sequencing activities carried out by WGSnet-Lazio (from February 2020 to October 2022) linked with epidemiological data to correlate the circulation of variants with the clinical and demographic characteristics of patients. The model of the sequencing network developed in the Lazio region proved to be a useful tool for SARS-CoV-2 surveillance and to support public health measures for epidemic containment. Full article

(This article belongs to the Special Issue Molecular Epidemiology of SARS-CoV-2: 2nd Edition)

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37 pages, 5183 KiB

Open AccessArticle

Unraveling the Dynamics of Omicron (BA.1, BA.2, and BA.5) Waves and Emergence of the Deltacron Variant: Genomic Epidemiology of the SARS-CoV-2 Epidemic in Cyprus (Oct 2021–Oct 2022)

by Andreas C. Chrysostomou, Bram Vrancken, Christos Haralambous, Maria Alexandrou, Ioanna Gregoriou, Marios Ioannides, Costakis Ioannou, Olga Kalakouta, Christos Karagiannis, Markella Marcou, Christina Masia, Michail Mendris, Panagiotis Papastergiou, Philippos C. Patsalis, Despo Pieridou, Christos Shammas, Dora C. Stylianou, Barbara Zinieri, Philippe Lemey, The COMESSAR Network and Leondios G. Kostrikis Show full author list Hide full author list

Viruses 2023, 15(9), 1933; https://doi.org/10.3390/v15091933 - 15 Sep 2023

Cited by 4 | Viewed by 3270

Abstract

Commencing in December 2019 with the emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), three years of the coronavirus disease 2019 (COVID-19) pandemic have transpired. The virus has consistently demonstrated a tendency for evolutionary adaptation, resulting in mutations that impact both immune [...] Read more.

Commencing in December 2019 with the emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), three years of the coronavirus disease 2019 (COVID-19) pandemic have transpired. The virus has consistently demonstrated a tendency for evolutionary adaptation, resulting in mutations that impact both immune evasion and transmissibility. This ongoing process has led to successive waves of infections. This study offers a comprehensive assessment spanning genetic, phylogenetic, phylodynamic, and phylogeographic dimensions, focused on the trajectory of the SARS-CoV-2 epidemic in Cyprus. Based on a dataset comprising 4700 viral genomic sequences obtained from affected individuals between October 2021 and October 2022, our analysis is presented. Over this timeframe, a total of 167 distinct lineages and sublineages emerged, including variants such as Delta and Omicron (1, 2, and 5). Notably, during the fifth wave of infections, Omicron subvariants 1 and 2 gained prominence, followed by the ascendancy of Omicron 5 in the subsequent sixth wave. Additionally, during the fifth wave (December 2021–January 2022), a unique set of Delta sequences with genetic mutations associated with Omicron variant 1, dubbed “Deltacron”, was identified. The emergence of this phenomenon initially evoked skepticism, characterized by concerns primarily centered around contamination or coinfection as plausible etiological contributors. These hypotheses were predominantly disseminated through unsubstantiated assertions within the realms of social and mass media, lacking concurrent scientific evidence to validate their claims. Nevertheless, the exhaustive molecular analyses presented in this study have demonstrated that such occurrences would likely lead to a frameshift mutation—a genetic aberration conspicuously absent in our provided sequences. This substantiates the accuracy of our initial assertion while refuting contamination or coinfection as potential etiologies. Comparable observations on a global scale dispelled doubt, eventually leading to the recognition of Delta-Omicron variants by the scientific community and their subsequent monitoring by the World Health Organization (WHO). As our investigation delved deeper into the intricate dynamics of the SARS-CoV-2 epidemic in Cyprus, a discernible pattern emerged, highlighting the major role of international connections in shaping the virus’s local trajectory. Notably, the United States and the United Kingdom were the central conduits governing the entry and exit of the virus to and from Cyprus. Moreover, notable migratory routes included nations such as Greece, South Korea, France, Germany, Brazil, Spain, Australia, Denmark, Sweden, and Italy. These empirical findings underscore that the spread of SARS-CoV-2 within Cyprus was markedly influenced by the influx of new, highly transmissible variants, triggering successive waves of infection. This investigation elucidates the emergence of new waves of infection subsequent to the advent of highly contagious and transmissible viral variants, notably characterized by an abundance of mutations localized within the spike protein. Notably, this discovery decisively contradicts the hitherto hypothesis of seasonal fluctuations in the virus’s epidemiological dynamics. This study emphasizes the importance of meticulously examining molecular genetics alongside virus migration patterns within a specific region. Past experiences also emphasize the substantial evolutionary potential of viruses such as SARS-CoV-2, underscoring the need for sustained vigilance. However, as the pandemic’s dynamics continue to evolve, a balanced approach between caution and resilience becomes paramount. This ethos encourages an approach founded on informed prudence and self-preservation, guided by public health authorities, rather than enduring apprehension. Such an approach empowers societies to adapt and progress, fostering a poised confidence rooted in well-founded adaptation. Full article

(This article belongs to the Special Issue Molecular Epidemiology of SARS-CoV-2: 2nd Edition)

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11 pages, 3092 KiB

Open AccessArticle

Genomic Epidemiology and Lineage Dynamics of SARS-CoV-2 in Bulgaria: Insights from a Three-Year Pandemic Analysis

by Marta Giovanetti, Eleonora Cella, Ivan Ivanov, Lyubomira Grigorova, Ivan Stoikov, Deyan Donchev, Reneta Dimitrova, Svetoslav Nanev Slavov, Carla Mavian, Vagner Fonseca, Fabio Scarpa, Alessandra Borsetti, Neli Korsun, Ivelina Trifonova, Veselin Dobrinov, Todor Kantardjiev, Iva Christova, Massimo Ciccozzi and Ivailo Alexiev

Viruses 2023, 15(9), 1924; https://doi.org/10.3390/v15091924 - 15 Sep 2023

Cited by 1 | Viewed by 1595

Abstract

The COVID-19 pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has brought about significant challenges worldwide. In this study, we present a comprehensive analysis of the genomic epidemiology and lineage dynamics of SARS-CoV-2 in Bulgaria over a three-year period. Through extensive [...] Read more.

The COVID-19 pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has brought about significant challenges worldwide. In this study, we present a comprehensive analysis of the genomic epidemiology and lineage dynamics of SARS-CoV-2 in Bulgaria over a three-year period. Through extensive genomic sequencing and data analysis, we investigated the evolution of the virus, the emergence of variants of concern (VOCs), and their impact on the country’s pandemic trajectory. We also assessed the relationship between viral diversity and COVID-19 morbidity and mortality in Bulgaria. Our findings shed light on the temporal and spatial distribution of SARS-CoV-2 lineages and provide crucial insights into the dynamics of the pandemic in the country. The interplay between international travel and viral transmission plays a significant role in the emergence and dissemination of different SARS-CoV-2 variants. The observed proportions of exportation to various continents provide insights into the potential pathways through which these lineages spread globally. Understanding the genomic epidemiology of SARS-CoV-2 in Bulgaria is essential for formulating targeted public health strategies, enhancing vaccination efforts, and effectively managing future outbreaks. Full article

(This article belongs to the Special Issue Molecular Epidemiology of SARS-CoV-2: 2nd Edition)

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17 pages, 2928 KiB

Open AccessArticle

Frequency of Atypical Mutations in the Spike Glycoprotein in SARS-CoV-2 Circulating from July 2020 to July 2022 in Central Italy: A Refined Analysis by Next Generation Sequencing

by Maria Concetta Bellocchi, Rossana Scutari, Luca Carioti, Marco Iannetta, Greta Marchegiani, Lorenzo Piermatteo, Luigi Coppola, Simona Tedde, Leonardo Duca, Vincenzo Malagnino, Lorenzo Ansaldo, Neva Braccialarghe, Stefano D′Anna, Maria Mercedes Santoro, Andrea Di Lorenzo, Romina Salpini, Elisabetta Teti, Valentina Svicher, Massimo Andreoni, Loredana Sarmati, Francesca Ceccherini-Silberstein and on behalf of the PTV-UTV-ID-COVID Group Show full author list Hide full author list

Viruses 2023, 15(8), 1711; https://doi.org/10.3390/v15081711 - 9 Aug 2023

Cited by 3 | Viewed by 1689

Abstract

In this study, we provided a retrospective overview in order to better define SARS-CoV-2 variants circulating in Italy during the first two years of the pandemic, by characterizing the spike mutational profiles and their association with viral load (expressed as ct values), N-glycosylation [...] Read more.

In this study, we provided a retrospective overview in order to better define SARS-CoV-2 variants circulating in Italy during the first two years of the pandemic, by characterizing the spike mutational profiles and their association with viral load (expressed as ct values), N-glycosylation pattern, hospitalization and vaccination. Next-generation sequencing (NGS) data were obtained from 607 individuals (among them, 298 vaccinated and/or 199 hospitalized). Different rates of hospitalization were observed over time and among variants of concern (VOCs), both in the overall population and in vaccinated individuals (Alpha: 40.7% and 31.3%, Beta: 0%, Gamma: 36.5% and 44.4%, Delta: 37.8% and 40.2% and Omicron: 11.2% and 7.1%, respectively, both p-values < 0.001). Approximately 32% of VOC-infected individuals showed at least one atypical major spike mutation (intra-prevalence > 90%), with a distribution differing among the strains (22.9% in Alpha, 14.3% in Beta, 41.8% in Gamma, 46.5% in Delta and 15.4% in Omicron, p-value < 0.001). Overall, significantly less atypical variability was observed in vaccinated individuals than unvaccinated individuals; nevertheless, vaccinated people who needed hospitalization showed an increase in atypical variability compared to vaccinated people that did not need hospitalization. Only 5/607 samples showed a different putative N-glycosylation pattern, four within the Delta VOC and one within the Omicron BA.2.52 sublineage. Interestingly, atypical minor mutations (intra-prevalence < 20%) were associated with higher Ct values and a longer duration of infection. Our study reports updated information on the temporal circulation of SARS-CoV-2 variants circulating in Central Italy and their association with hospitalization and vaccination. The results underline how SARS-CoV-2 has changed over time and how the vaccination strategy has contributed to reducing severity and hospitalization for this infection in Italy. Full article

(This article belongs to the Special Issue Molecular Epidemiology of SARS-CoV-2: 2nd Edition)

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Jump to: Research

10 pages, 2186 KiB

Open AccessBrief Report

Evolution of a Distinct SARS-CoV-2 Lineage Identified during an Investigation of a Hospital Outbreak

by Hosoon Choi, Munok Hwang, Lisa Cornelius, Dhammika H. Navarathna, Piyali Chatterjee and Chetan Jinadatha

Viruses 2024, 16(3), 337; https://doi.org/10.3390/v16030337 - 22 Feb 2024

Cited by 1 | Viewed by 1151

Abstract

The SARS-CoV-2 virus steadily evolves, and numerous antigenically distinct variants have emerged over the past three years. Tracking the evolution of the virus would help us understand the process that generates the diverse variants and predict the future evolutionary trajectory of SARS-CoV-2. Here, [...] Read more.

The SARS-CoV-2 virus steadily evolves, and numerous antigenically distinct variants have emerged over the past three years. Tracking the evolution of the virus would help us understand the process that generates the diverse variants and predict the future evolutionary trajectory of SARS-CoV-2. Here, we report the evolutionary trajectory of a unique Omicron lineage identified during an outbreak investigation that occurred in a residence unit in the healthcare system. The new lineage had four distinct non-synonymous and two distinct synonymous mutations apart from its parental lineage. Since this lineage of virus was exclusively found during the outbreak, we were able to track the detailed evolutionary history of the entire lineage along the transmission path. Furthermore, we estimated the evolutionary rate of the SARS-CoV-2 Omicron variant from the analysis of the evolution of the lineage. This new Omicron sub-lineage acquired 3 mutations in a 12-day period, and the evolutionary rate was estimated as 3.05 × 10⁻³ subs/site/year. This study provides more insight into an ever-evolving virus. Full article

(This article belongs to the Special Issue Molecular Epidemiology of SARS-CoV-2: 2nd Edition)

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Genomic Surveillance Reveals the Rapid Expansion of the XBB Lineage among Circulating SARS-CoV-2 Omicron Lineages in Southeastern Wisconsin, USA

by Arunachalam Ramaiah, Manjeet Khubbar, Katherine Akinyemi, Amy Bauer, Francisco Carranza, Joshua Weiner, Sanjib Bhattacharyya, David Payne and Nandhakumar Balakrishnan

Viruses 2023, 15(9), 1940; https://doi.org/10.3390/v15091940 - 16 Sep 2023

Cited by 5 | Viewed by 2016

Abstract

SARS-CoV-2 caused a life-threatening COVID-19 pandemic outbreak worldwide. The Southeastern Region of Wisconsin, USA (SERW) includes large urban Milwaukee and six suburban counties, namely Kenosha, Ozaukee, Racine, Walworth, Washington and Waukesha. Due to the lack of detailed SARS-CoV-2 genomic surveillance in the suburban [...] Read more.

SARS-CoV-2 caused a life-threatening COVID-19 pandemic outbreak worldwide. The Southeastern Region of Wisconsin, USA (SERW) includes large urban Milwaukee and six suburban counties, namely Kenosha, Ozaukee, Racine, Walworth, Washington and Waukesha. Due to the lack of detailed SARS-CoV-2 genomic surveillance in the suburban populations of the SERW, whole-genome sequencing was employed to investigate circulating SARS-CoV-2 lineages and characterize dominant XBB lineages among this SERW population from November 2021 to April 2023. For an unbiased data analysis, we combined our 6709 SARS-CoV-2 sequences with 1520 sequences from the same geographical region submitted by other laboratories. Our study shows that SARS-CoV-2 genomes were distributed into 357 lineages/sublineages belonging to 13 clades, of which 88.8% were from Omicron. We document dominant sublineages XBB.1.5 and surging XBB.1.16 and XBB.1.9.1 with a few additional functional mutations in Spike, which are known to contribute to higher viral reproduction, enhanced transmission and immune evasion. Mutational profile assessment of XBB.1.5 Spike identifies 38 defining mutations with high prevalence occurring in 49.8–99.6% of the sequences studied, of which 32 mutations were in three functional domains. Phylogenetic and genetic relatedness between XBB.1.5 sequences reveal potential virus transmission occurring within households and within and between Southeastern Wisconsin counties. A comprehensive phylogeny of XBB.1.5 with global sub-dataset sequences confirms the wide spread of genetically similar SARS-CoV-2 strains within the same geographical area. Altogether, this study identified proportions of circulating Omicron variants and genetic characterization of XBB.1.5 in the SERW population, which helped state and national public health agencies to make compelling mitigation efforts to reduce COVID-19 transmission in the communities and monitor emerging lineages for their impact on diagnostics, treatments and vaccines. Full article

(This article belongs to the Special Issue Molecular Epidemiology of SARS-CoV-2: 2nd Edition)

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