Topic Editors

Department of Hygiene, Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, 115 27 Athens, Greece
Faculty of Medicine, Institute of Microbiology and Immunology, University of Belgrade, 11000 Belgrade, Serbia

Transmission Clusters and Containment Measures in Global Different Regions during COVID-19 Pandemic

Abstract submission deadline
closed (30 June 2023)
Manuscript submission deadline
closed (31 August 2023)
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Topic Information

Dear Colleagues,

SARS-CoV-2 caused a devastating pandemic with serious consequences for global health and economy. As of mid-June 2022, there have been over 500 million confirmed cases of COVID-19 worldwide, including over 6 million fatalities.

Although SARS-CoV-2 has a lower nucleotide substitution rate compared to other RNA viruses, a number of variants changed the face of the pandemic. Some of the emerging variants, namely alpha (B.1.1.7), beta (B.1.351), gamma (P.1), delta (B.1.617.2), and omicron (B.1.1.529), have been designated variants of concern (VOC) due to their altered biological properties, posing an increased risk to global public health. This prompted heightened surveillance and monitoring to inform the ongoing response to the COVID-19 pandemic. Notably, omicron is the only VOC still in circulation. This includes BA.1, BA.2, BA.3, BA.4, BA.5 and descendent lineages, as well as circulating recombinant forms such as XE.

Genomic surveillance and molecular epidemiology of SARS-CoV-2 can provide added value, monitoring newly emerging variants, and can also improve our understanding of the characteristics of SARS-CoV-2 global transmission. This knowledge could guide public health measures and help to control the pandemic. Thus, we seek contributions that address the impact of COVID-19 molecular surveillance and molecular epidemiology studies on epidemiology and public health. Investigations into virology and genetic characteristics of infection are also welcome, as are relevant epidemiological findings.

Dr. Dimitrios Paraskevis
Dr. Maja Stanojevic
Topic Editors

Keywords

  • SARS-⁠CoV-⁠2
  • COVID-⁠19
  • genomic surveillance
  • phylogenetics
  • phylodynamics
  • transmission clusters
  • public health measures
  • epidemiology
  • viral dispersal
  • phylogeography
  • prevalence
  • vaccines
  • immunity
  • pandemic
  • virology

Participating Journals

Journal Name Impact Factor CiteScore Launched Year First Decision (median) APC
Genes
genes
3.5 5.1 2010 16.5 Days CHF 2600
International Journal of Environmental Research and Public Health
ijerph
- 5.4 2004 29.6 Days CHF 2500
Life
life
3.2 2.7 2011 17.5 Days CHF 2600
Vaccines
vaccines
7.8 7.0 2013 19.2 Days CHF 2700
Viruses
viruses
4.7 7.1 2009 13.8 Days CHF 2600

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Published Papers (8 papers)

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13 pages, 1772 KiB  
Article
The Omicron Lineages BA.1 and BA.2 (Betacoronavirus SARS-CoV-2) Have Repeatedly Entered Brazil through a Single Dispersal Hub
by Alessandra P. Lamarca, Ueric José Borges de Souza, Filipe Romero Rebello Moreira, Luiz G. P. de Almeida, Mariane Talon de Menezes, Adrieli Barboza de Souza, Alessandro Clayton de Souza Ferreira, Alexandra L. Gerber, Aline B. de Lima, Ana Paula de C. Guimarães, Andréa Cony Cavalcanti, Aryel B. Paz e Silva, Bruna Israel Lima, Cirley Lobato, Cristiane Gomes Da Silva, Cristiane P. T. B. Mendonça, Daniel Costa Queiroz, Danielle Alves Gomes Zauli, Diego Menezes, Fábio Sossai Possebon, Franciano Dias Pereira Cardoso, Frederico Scott Varella Malta, Isabela Braga-Paz, Joice do Prado Silva, Jorge Gomes Goulart Ferreira, Jucimária Dantas Galvão, Leandro Magalhães de Souza, Leonardo Ferreira, Lia Gonçalves Possuelo, Liliane Tavares de Faria Cavalcante, Luige B. Alvim, Luiz Fellype Alves de Souza, Luiza C. G. de Araújo E Santos, Rillery Calixto Dias, Rutilene Barbosa Souza, Thaís Regina y Castro, Andréia Rosane de Moura Valim, Fabrício Souza Campos, João Pessoa Araujo, Jr., Priscila de Arruda Trindade, Renato S. Aguiar, Robson Michael Delai and Ana Tereza R de Vasconcelosadd Show full author list remove Hide full author list
Viruses 2023, 15(4), 888; https://doi.org/10.3390/v15040888 - 30 Mar 2023
Cited by 5 | Viewed by 2356
Abstract
Brazil currently ranks second in absolute deaths by COVID-19, even though most of its population has completed the vaccination protocol. With the introduction of Omicron in late 2021, the number of COVID-19 cases soared once again in the country. We investigated in this [...] Read more.
Brazil currently ranks second in absolute deaths by COVID-19, even though most of its population has completed the vaccination protocol. With the introduction of Omicron in late 2021, the number of COVID-19 cases soared once again in the country. We investigated in this work how lineages BA.1 and BA.2 entered and spread in the country by sequencing 2173 new SARS-CoV-2 genomes collected between October 2021 and April 2022 and analyzing them in addition to more than 18,000 publicly available sequences with phylodynamic methods. We registered that Omicron was present in Brazil as early as 16 November 2021 and by January 2022 was already more than 99% of samples. More importantly, we detected that Omicron has been mostly imported through the state of São Paulo, which in turn dispersed the lineages to other states and regions of Brazil. This knowledge can be used to implement more efficient non-pharmaceutical interventions against the introduction of new SARS-CoV variants focused on surveillance of airports and ground transportation. Full article
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10 pages, 830 KiB  
Article
An Oral Galectin Inhibitor in COVID-19—A Phase II Randomized Controlled Trial
by Alben Sigamani, Kevin H. Mayo, Michelle C. Miller, Hana Chen-Walden, Surendar Reddy and David Platt
Vaccines 2023, 11(4), 731; https://doi.org/10.3390/vaccines11040731 - 25 Mar 2023
Cited by 4 | Viewed by 12577
Abstract
Background: SARS-CoV-2 vaccines play an important role in reducing disease severity, hospitalization, and death, although they failed to prevent the transmission of SARS-CoV-2 variants. Therefore, an effective inhibitor of galectin-3 (Gal-3) could be used to treat and prevent the transmission of COVID-19. ProLectin-M [...] Read more.
Background: SARS-CoV-2 vaccines play an important role in reducing disease severity, hospitalization, and death, although they failed to prevent the transmission of SARS-CoV-2 variants. Therefore, an effective inhibitor of galectin-3 (Gal-3) could be used to treat and prevent the transmission of COVID-19. ProLectin-M (PL-M), a Gal-3 antagonist, was shown to interact with Gal-3 and thereby prevent cellular entry of SARS-CoV-2 in previous studies. Aim: The present study aimed to further evaluate the therapeutic effect of PL-M tablets in 34 subjects with COVID-19. Methods: The efficacy of PL-M was evaluated in a randomized, double-blind, placebo-controlled clinical study in patients with mild to moderately severe COVID-19. Primary endpoints included changes in the absolute RT-PCR Ct values of the nucleocapsid and open reading frame (ORF) genes from baseline to days 3 and 7. The incidence of adverse events, changes in blood biochemistry, inflammatory biomarkers, and levels of antibodies against COVID-19 were also evaluated as part of the safety evaluation. Results: PL-M treatment significantly (p = 0.001) increased RT-PCR cycle counts for N and ORF genes on days 3 (Ct values 32.09 ± 2.39 and 30.69 ± 3.38, respectively) and 7 (Ct values 34.91 ± 0.39 and 34.85 ± 0.61, respectively) compared to a placebo treatment. On day 3, 14 subjects in the PL-M group had cycle counts for the N gene above the cut-off value of 29 (target cycle count 29), whereas on day 7, all subjects had cycle counts above the cut-off value. Ct values in placebo subjects were consistently less than 29, and no placebo subjects were RT-PCR-negative until day 7. Most of the symptoms disappeared completely after receiving PL-M treatment for 7 days in more patients compared to the placebo group. Conclusion: PL-M is safe and effective for clinical use in reducing viral loads and promoting rapid viral clearance in COVID-19 patients by inhibiting SARS-CoV-2 entry into cells through the inhibition of Gal-3. Full article
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11 pages, 2252 KiB  
Article
Impact of the COVID-19 Pandemic and Governmental Policies on Rehabilitation Services and Physical Medicine in Jordan: A Retrospective Study
by Nihad A. Almasri, Carl J. Dunst, Hikmat Hadoush, Jaber Aldaod, Yousef Khader, Ali Alrjoub and Ahmad Almasri
Int. J. Environ. Res. Public Health 2023, 20(3), 1972; https://doi.org/10.3390/ijerph20031972 - 20 Jan 2023
Cited by 1 | Viewed by 1190
Abstract
Background: Although the COVID-19 pandemic led to a series of governmental policies and regulations around the world, the effect of these policies on access to and provision of rehabilitation services has not been examined, especially in low and middle- income countries. Aims [...] Read more.
Background: Although the COVID-19 pandemic led to a series of governmental policies and regulations around the world, the effect of these policies on access to and provision of rehabilitation services has not been examined, especially in low and middle- income countries. Aims: The aim of this study was to investigate the impact of governmental policies and procedures on the number of patients who accessed rehabilitation services in the public sector in Jordan during the pandemic and to examine the combined effect of sociodemographic factors (age and gender) and the governmental procedures on this number of patients. Methods: A retrospective cohort study was conducted based on records of 32,503 patients who visited the rehabilitation center between January 2020 and February 2021. Interrupted time-series analysis was conducted with three periods and by age and gender. Results: The number of patients who visited the rehabilitation clinics decreased significantly between January 2020 and May 2020 due to government-imposed policies, then increased significantly until peaking in September 2020 (p = 0.0002). Thereafter, the number of patients decreased between October 2020 and February 2021 as a result of the second wave of the COVID-19 pandemic (p = 0.02). The numbers of male and female patients did not differ (p > 0.05). There were more patients aged 20 years and older attending rehabilitation clinics than younger patients during the first strict lock down and the following reduction of restriction procedures periods (p < 0.05). Conclusions: The COVID-19 public measures in Jordan reduced access to rehabilitation services. New approaches to building resilience and access to rehabilitation during public health emergencies are needed. A further examination of strategies and new approaches to building resilience and increasing access to rehabilitation during public health emergencies is warranted. Full article
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18 pages, 2983 KiB  
Article
Perception of the Impact of COVID-19 on a Sample of Spaniards with Hearing Disabilities
by Mª Ángeles Martínez Sánchez, Antonio Muñoz-García and Cristina Ros Gil
Int. J. Environ. Res. Public Health 2023, 20(2), 1460; https://doi.org/10.3390/ijerph20021460 - 13 Jan 2023
Cited by 1 | Viewed by 1238
Abstract
This paper describes an empirical study carried out with 40 Spanish deaf people, users of sign language, between 19 and 45 years of age, which gathers their perceptions of aspects related to the incidence of the COVID-19 pandemic and its repercussions. During the [...] Read more.
This paper describes an empirical study carried out with 40 Spanish deaf people, users of sign language, between 19 and 45 years of age, which gathers their perceptions of aspects related to the incidence of the COVID-19 pandemic and its repercussions. During the pandemic, people with hearing disabilities, among other groups, were forgotten. They suffered from accessibility problems to the information issued by the authorities, violating their right to be informed and exposing their health to COVID-19. In this work, we identify the problems they suffered and what effects COVID-19 had on their lives. This will help to take the appropriate measures to restore their rights and design policies and strategies to deal with any new future health emergency. For this, an ad hoc questionnaire was designed, adapted to easy reading and sign language. This was publicized via email and WhatsApp through the Association of Deaf People of Granada and Province (Spain) and was responded to online and by video call with the collaboration of sign language interpreters using the LimeSurvey platform. The results discover (1) the difficulties of communication barriers in the relationship with health professionals and institutions, as well as in the spheres of work and education, (2) similarities with the rest of the population in the negative effects of confinement, and (3) presence of positive effects, such as the development of positive activities and emotions. The study highlights the need to increase economic and institutional support aimed at improving coping resources, access to information, and the reduction of social and institutional barriers that would allow people with hearing disabilities to successfully face future health problems of a global nature such as that experienced with COVID-19. Full article
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11 pages, 975 KiB  
Article
Mapping the Early Dispersal Patterns of SARS-CoV-2 Omicron BA.4 and BA.5 Subvariants in the Absence of Travel Restrictions and Testing at the Borders in Europe
by Evangelia Georgia Kostaki, Elias Mossialos, Ioulia Tseti, Petros P. Sfikakis and Dimitrios Paraskevis
Viruses 2023, 15(1), 133; https://doi.org/10.3390/v15010133 - 31 Dec 2022
Cited by 1 | Viewed by 1721
Abstract
The circulation of SARS-CoV-2 omicron BA.4 and BA.5 subvariants with enhanced transmissibility and capacity for immune evasion resulted in a recent pandemic wave that began in April–May of 2022. We performed a statistical phylogeographic study that aimed to define the cross-border transmission patterns [...] Read more.
The circulation of SARS-CoV-2 omicron BA.4 and BA.5 subvariants with enhanced transmissibility and capacity for immune evasion resulted in a recent pandemic wave that began in April–May of 2022. We performed a statistical phylogeographic study that aimed to define the cross-border transmission patterns of BA.4 and BA.5 at the earliest stages of virus dispersal. Our sample included all BA.4 and BA.5 sequences that were publicly available in the GISAID database through mid-May 2022. Viral dispersal patterns were inferred using maximum likelihood phylogenetic trees with bootstrap support. We identified South Africa as the major source of both BA.4 and BA.5 that migrated to other continents. By contrast, we detected no significant export of these subvariants from Europe. Belgium was identified as a major hub for BA.4 transmission within Europe, while Portugal and Israel were identified as major sources of BA.5. Western and Northern European countries exhibited the highest rates of cross-border transmission, as did several popular tourist destinations in Southern and Central/Western Europe. Our study provides a detailed map of the early dispersal patterns of two highly transmissible SARS-CoV-2 omicron subvariants at a time when there was an overall relaxation of public health measures in Europe. Full article
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13 pages, 1152 KiB  
Article
Effects of Wearing FFP2 Masks on SARS-CoV-2 Infection Rates in Classrooms
by Gerald Jarnig, Reinhold Kerbl and Mireille N. M. van Poppel
Int. J. Environ. Res. Public Health 2022, 19(20), 13511; https://doi.org/10.3390/ijerph192013511 - 19 Oct 2022
Cited by 1 | Viewed by 7259
Abstract
In this retrospective cohort study involving 614 secondary school students, the likelihood of becoming infected with SARS-CoV-2 in schools with different focus (sports focus vs. general branch; the only difference in the sports focus school was that PE was allowed at all times [...] Read more.
In this retrospective cohort study involving 614 secondary school students, the likelihood of becoming infected with SARS-CoV-2 in schools with different focus (sports focus vs. general branch; the only difference in the sports focus school was that PE was allowed at all times without restrictions) and different prevailing restrictions were compared. A significantly higher likelihood of infection with SARS-CoV-2 was found in sports classes during the period with a strict FFP-2 mask requirement compared to general branch classes (for Delta from November 2021 to December 2021, and for Omicron from January 2022 to February 2022). The higher likelihood of infection was observed both during the Delta and the Omicron wave. After the relaxation of the mitigation measures, however, students in general branch classes showed a clear “catch-up” of infections, leading to a higher incidence of infections during this phase. By the end of the observation period (30 April 2022), only a small difference in cumulative SARS-CoV-2 infection rates (p = 0.037, φ = 0.09) was detected between classes with a sports focus and those without a sports focus. The results suggest that SARS-CoV-2 transmission can be reduced in school classes by mandatory FFP-2 mask use. In many cases, however, infection appears to be postponed rather than avoided. Full article
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7 pages, 251 KiB  
Review
Role and Limits of COVID-19 Vaccines in the Delicate Transition from Pandemic Mitigation to Endemic Control
by Marie Mura, Fabrice Simon, Vincent Pommier de Santi, Frédéric Tangy and Jean-Nicolas Tournier
Vaccines 2022, 10(9), 1555; https://doi.org/10.3390/vaccines10091555 - 18 Sep 2022
Cited by 3 | Viewed by 1435
Abstract
The recent surge of COVID-19 related to the Omicron variant emergence has thrown a harsh light upon epidemic control in the near future. This should lead the scientific and medical community to question the long-term vaccine strategy for SARS-CoV-2 control. We provide here [...] Read more.
The recent surge of COVID-19 related to the Omicron variant emergence has thrown a harsh light upon epidemic control in the near future. This should lead the scientific and medical community to question the long-term vaccine strategy for SARS-CoV-2 control. We provide here a critical point of view regarding the virological evolution, epidemiological aspects, and immunological drivers for COVID-19 control, including a vaccination strategy. Overall, we need more innovations in vaccine development to reduce the COVID-19 burden long term. The most adequate answer might be better cooperation between universities, biotech and pharmaceutical companies Full article
10 pages, 1093 KiB  
Article
The Effect of Strict Lockdown on Omicron SARS-CoV-2 Variant Transmission in Shanghai
by Haibo Yang, Hao Nie, Dewei Zhou, Yujia Wang and Wei Zuo
Vaccines 2022, 10(9), 1392; https://doi.org/10.3390/vaccines10091392 - 25 Aug 2022
Cited by 7 | Viewed by 2185
Abstract
Omicron, the current SARS-CoV-2 variant of concern, is much more contagious than other previous variants. Whether strict lockdown could effectively curb the transmission of Omicron is largely unknown. In this retrospective study, we compared the strictness of government lockdown policies in Shanghai and [...] Read more.
Omicron, the current SARS-CoV-2 variant of concern, is much more contagious than other previous variants. Whether strict lockdown could effectively curb the transmission of Omicron is largely unknown. In this retrospective study, we compared the strictness of government lockdown policies in Shanghai and other countries. Based on the daily Omicron case number from 1 March 2022 to 30 April 2022, the effective reproductive numbers in this Shanghai Omicron wave were calculated to confirm the impact of strict lockdown on Omicron transmission. Pearson correlation was conducted to illustrate the determining factor of strict lockdown outcomes in the 16 different districts of Shanghai. After a very strict citywide lockdown since April 1st, the average daily effective reproductive number reduced significantly, indicating that strict lockdown could slow down the spreading of Omicron. Omicron control is more challenging in districts with higher population mobility and lockdown is more likely to decrease the number of asymptomatic carriers than the symptomatic cases. All these findings indicate that the strict lockdown could curb the transmission of Omicron effectively, especially for the asymptomatic spread, and suggest that differentiated COVID-19 prevention and control measures should be adopted according to the population density and demographic composition of each community. Full article
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