Coronavirus (COVID-19) Collection
Emergence and geographic dominance of Omicron subvariants XBB/XBB.1.5 and BF.7 – the public health challengesSince the emergence of the SARS-CoV-2 Omicron variant in November 2021 , it has rapidly replaced former strains as the key driver of the pandemic. As of 27 October 2022, the Omicron variant was considered the only circulating variant of concern (VOC) by the World Health Organization (WHO) . Omicron has spawned subvariants due to its propensity of engendering novel mutations. In January 2022, the original Omicron strain BA.1 was replaced by BA.2; and other subvariants – BA.3, BA.4, BA.5 and XE – have subsequently emerged.
Risk factors for SARS-CoV-2 infection in primary and secondary school students and staff in England in the 2020/2021 school year: a longitudinal studyEarly in the COVID-19 pandemic, concerns that schools might contribute to sustaining or amplifying community transmission of SARS-CoV-2 led to widespread school closures . This impacted education, well-being, and societal health [2,3]. Evidence now indicates that SARS-CoV-2 transmission does occur among and from children but can be reduced by preventive interventions in schools [4–6]. The overall role of schools in community spread is thought to be low-to-moderate, especially with mitigations in place; although, this may vary with virus variants [7–9].
The impact of variant and vaccination on SARS-CoV-2 symptomatology; three prospective household cohortsSince the onset of the COVID-19 pandemic in December 2019, several SARS-CoV-2 variants of concern (VOC) have emerged . With the emergence of the Omicron VOC (BA.1) and its descendants (BA.2 and further), the pandemic has taken a new turn. Omicron variants are characterized by a high number of mutations compared with the ancestral strain and are associated with immune escape and enhanced angiotensin-converting enzyme-2 (ACE-2) binding [2,3]. In addition, the Omicron variants are less capable of infecting the lower respiratory tract due to a shift in cellular tropism away from transmembrane protease, serine 2 (TMPRSS2) expressing cells, promoting faster replication in the upper airways but reduced replication in the lungs [4,5].
Effectiveness of the neutralizing antibody sotrovimab among high-risk patients with mild-to-moderate SARS-CoV-2 in QatarSeveral monoclonal antibodies against SARS-CoV-2 have been developed for the treatment of COVID-19 (Miguez-Rey et al., 2022). One of these is sotrovimab, which significantly reduced the risk of COVID-19 hospitalization and death due to infection with pre-Omicron SARS-CoV-2 variants in a randomized clinical trial (Gupta et al., 2021). The United States Food and Drug Administration (FDA) issued an emergency authorization to permit the use of sotrovimab for the treatment of mild-to-moderate COVID-19 in patients at high risk of progression to severe COVID-19 (US Food and Drug Administration, 2022).
Admissions to a large tertiary care hospital and Omicron BA.1 and BA.2 SARS-CoV-2 polymerase chain reaction positivity: primary, contributing, or incidental COVID-19Monitoring national hospitalization rates for COVID-19 has been essential throughout the pandemic to guide public health decision-making and to evaluate vaccine efficacy. However, with the rapid worldwide spread of the SARS-CoV-2 Omicron variant of concern (associated with a decreased severity) and increasing immunity against SARS-CoV-2, interpreting the true impact of these hospitalization rates has been complicated (Viana et al., 2022; World Health Organization, 2021).
Monitoring the COVID-19 immune landscape in JapanSince the COVID-19 epidemic spread on a global scale in 2020, it considerably altered daily life. With the hope of mitigating the COVID-19 risk, vaccination campaigns began in December 2020 in many countries, often using a prioritization vaccination strategy (Haas et al., 2021; Hall et al., 2021; Jentsch et al., 2021; Mathieu et al., 2021; Sasanami et al., 2022; Thompson et al., 2021). Mass vaccination campaigns occurred primarily when the original (wild-type) strain, the Alpha variant (B.1.1.7), the Beta variant (B.1.351), or other variants were dominant in circulation and against which the available vaccines provided substantial protection (Chemaitelly et al., 2021; Chung et al., 2021; Dagan et al., 2021; Haas et al., 2021; Hall et al., 2021; Pritchard et al., 2021).
Stringency of containment and closures on the growth of SARS-CoV-2 in Canada prior to accelerated vaccine roll-outThroughout 2020, non-pharmaceutical interventions (NPIs) were the primary tools employed by governments and public health agencies to slow the spread of SARS-CoV-2 (Ferguson et al. 2020, Koo et al., 2020). In Canada, as in many other countries, common NPIs included border closures, bans on non-essential travel, and mandatory physical distancing measures (McCoy et al, 2020). However, in contrast to many countries—particularly those in Europe—the authority and responsibility to implement these policies fall on provincial and territorial governments, meaning there is no formally coordinated response between them (Cameron-Blake et al., 2021).
Risk factors, immune response and whole‐genome sequencing of SARS‐CoV‐2 in a cruise ship outbreak in NorwayTo improve understanding of SARS-CoV-2-transmission and prevention measures on cruise ships, we investigated a Norwegian cruise ship outbreak from July to August 2020 using a multidisciplinary approach after a rapid outbreak response launched by local and national health authorities.
Characteristics and Outcomes of COVID-19 in Reproductive-Aged Pregnant and Nonpregnant Women in Osaka, JapanCoronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), was first reported in Wuhan, China (Li et al., 2020, Zhou et al., 2020), and rapidly spread worldwide, imposing a major burden on healthcare systems globally. Pregnant women are considered to be at a higher risk of severe morbidity and mortality from other respiratory infections, such as influenza or SARS (Allotey et al., 2020, Blitz et al., 2020, Vintzileos et al., 2020, Xu et al., 2020), than nonpregnant women.
Hypothyroidism does not lead to worse prognosis in COVID-19: findings from the Brazilian COVID-19 registryA global health crisis was established with the emergence of COVID-19 (Gelfand et al., 2021). It is well known that individuals with some underlying medical conditions, such as cardiovascular diseases, cancer, obesity, diabetes, and hypertension, are more likely to develop severe COVID-19, require hospitalization and intensive care, and have higher mortality rates (Marcolino et al., 2021; Sanyaolu et al., 2020; Centers for Disease Control and Prevention. People with Certain Medical Conditions. September 4th, 2021).
SARS-CoV-2 seroprevalence among 7950 healthcare workers in the Region of Southern DenmarkCoronavirus disease 2019 (COVID-19) surged as an ongoing worldwide pandemic throughout 2020 (Park et al., 2020; Siordia, 2020). The first Danish cases were reported in late February 2020, and the initial spread of infection most likely originated from ski tourists returning from Northern Italy and Austria (Madsen et al., 2021). The first epidemic wave in Denmark peaked in late March and early April, with 9.2 patients admitted to hospital per 100 000 population (Madsen et al., 2021; Statens Serum Institut 2021).
Real-Time SARS-CoV-2 Genotyping by High-Throughput Multiplex PCR Reveals the Epidemiology of the Variants of Concern in QatarComplementing whole genome sequencing strategies with high-throughput multiplex RT-qPCR genotyping allows for more comprehensive and real-time tracking of SARS-CoV-2 variants of concern. During the second and third waves of COVID-19 in Qatar, PCR genotyping, combined with Sanger sequencing of un-typeable samples, was employed to describe the epidemiology of the Alpha, Beta and Delta variants. A total of 9792 nasopharyngeal PCR-positive samples collected between April-June 2021 were successfully genotyped, revealing the importation and transmission dynamics of these three variants in Qatar.
The toll of COVID-19 on African children: A descriptive analysis on COVID-19-related morbidity and mortality among the pediatric population in Sub-Saharan AfricaSince its emergence in December 2019 in the Chinese city of Wuhan, the coronavirus disease 2019 (COVID-19) caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has infected millions of people around the world and caused over 3.9 million officially registered deaths (WHO, 2021). From the onset of this pandemic, the pathogenic aspects in the pediatric population have remained less clear, especially in Sub-Saharan Africa, where specialists' initial projections estimated a high number of cases and deaths (Cabore et al., 2020).
SARS-CoV-2 seroprevalence and associated factors in Manaus, Brazil: baseline results from the DETECTCoV-19 cohort studyInfectious diseases have a profound impact on humans, particularly vulnerable populations (Fauci and Morens, 2012). The emergence of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) and a lack of effective treatment and non-pharmaceutical interventions to curb transmission have led to an exponential increase in the burden of coronavirus disease 2019 (COVID-19) worldwide (Hsiang et al., 2020; Kraemer et al., 2020; Bo et al., 2021).
High seroprevalence for SARS-CoV-2 infection in South America, but still not enough for herd immunity!There has been intense discussion about the importance of reaching herd immunity to achieve global population protection status against SARS-CoV-2/COVID-19. For that reason, vaccination coverage and seroprevalence studies are increasing around the world; some of them have shown an increase in the seroprevalence of different populations. For example, a recent study in Jordan (Sughayer et al., 2021) stated the importance of seroprevalence studies for SARS-CoV-2 infection among healthy blood donors.
Clinical and epidemiological characteristics of children with COVID-19 in Negeri Sembilan, MalaysiaThe coronavirus disease 2019 (COVID-19) pandemic, caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), remains an ongoing challenge to countries worldwide. The disease emerged in Wuhan, China in December 2019 and was declared a pandemic by the World Health Organization (WHO) on 11 March 2020 (World Health Organization, 2000). The COVID-19 outbreak in Malaysia occurred in three waves. The first wave started with three cases imported from China via Singapore on 25 January 2020 (Rahman, 2020).
Hydroxychloroquine as a primary prophylactic agent against SARS-CoV-2 infection: A cohort studyChloroquine and hydroxychloroquine have been shown to be in-vitro inhibitors of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) in infected Vero cells (Liu et al., 2020; Wang et al., 2020; Yao et al., 2020). This contributed to the hypothesis that such drugs could be used as prophylaxis for SARS-CoV-2 infection and for treatment of patients with coronavirus disease 2019 (COVID-19). Hydroxychloroquine is used for long-term treatment of several rheumatic diseases; it has a favourable safety profile (Ruiz-Irastorza et al., 2010; Ponticelli and Moroni, 2017) and a low cost (Ponticelli and Moroni, 2017), which is a key point when facing a pandemic.
COVID-19 within a large UK prison with a high number of vulnerable adults, march to june 2020: An outbreak investigation and screening eventCoronavirus disease (COVID-19) is an infectious disease caused by the most recently discovered severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The virus was unknown before the outbreak began in China in December 2019 and has since spread worldwide (Zhu et al., 2020). The impact of the epidemic has been noted in many community sectors, including institutional settings, such as prisons. Many prison residents are at higher risk of severe COVID-19 and death due to significant co-morbidities, and advanced age in some prisons (Amon, 2020; Kinner et al., 2020).
Epidemiology of COVID-19 in Mexico: Symptomatic profiles and presymptomatic peopleAt the start of the COVID-19 pandemic, the initial reports showed that SARS-CoV-2 infection promotes pneumonia in mainly older adults, which were the group with a major risk of getting hospitalized and getting mechanical ventilation due to severe COVID-19 disease (Berumen et al., 2020; Giannouchos et al., 2020; Zheng et al., 2020). However, other age-groups had similar risks due to different factors. Moreover, with regard to control of the pandemic, asymptomatic people have attracted attention due to their ability to transmit the virus without manifesting infection symptoms, which makes them identifiable only by difficult massive tests on the general population.
Undetected infectives in the Covid-19 pandemicA critical issue in the control of an epidemic is to know the exact number of infective subjects. Current estimates of SARS-CoV-2 infection are significantly hampered by the difficulty to perform large-scale diagnostic tests, despite the current awareness that the spread of the Covid-19 pandemic is mostly caused by undetected carriers.
The collective wisdom in the COVID-19 research: Comparison and synthesis of epidemiological parameter estimates in preprints and peer-reviewed articlesThe outbreak of COVID-19 has posed a significant global threat. In response to the emerging infectious disease, the number of research papers has exploded in both formal publications and preprints (Wellcome Trust, 2020). Many journals used a fast track to publish COVID-19 research and made all COVID-19 work freely accessible to facilitate information sharing. In contrast to previous Zika and Ebola outbreaks, scientists were more enthusiastic about posting articles on preprint archives due to the very high transmissibility of COVID-19 (Fraser et al., 2020; Johansson et al., 2018).
Early transmission of SARS-CoV-2 in South Africa: An epidemiological and phylogenetic reportPubMed, BioRxiv and MedRxiv were searched for reports on epidemiology and phylogenetic analysis using whole genome sequencing (WGS) of SARS-CoV-2. The following keywords were used: SARS-CoV-2, COVID-19, 2019-nCoV or novel coronavirus and transmission genomics, epidemiology, and phylogenetic or reproduction number. The search identified an important lack of molecular epidemiology studies in the southern hemisphere, with a few reports from Latin America and one from Africa. In other early transmission reports on SARS-CoV-2 infections in Africa, authors focused on transmission dynamics, but molecular and phylogenetic methods were missing.
The characteristics and clinical course of patients with COVID-19 who received invasive mechanical ventilation in Osaka, JapanIn Japan, the first laboratory-confirmed case of coronavirus disease 2019 (COVID-19) was detected on January 16, 2020. Subsequently, the first case in Osaka was detected on January 29, 2020. On April 7, 2020, in response to the rapid spread of COVID-19, the Japanese government declared a state of emergency (Ministry of Health, Labour and Welfare of Japan, 2020a). Early studies showed that 2–12% of patients required invasive mechanical ventilation, and the mortality rate of these patients was 26–97% (Zhou et al., 2020; Hu et al., 2020; Richardson et al., 2020; Yang et al., 2020; Grasselli et al., 2020).
The role of case importation in explaining differences in early SARS-CoV-2 transmission dynamics in Canada—A mathematical modeling study of surveillance dataBoth American and Canadian epidemics of coronavirus disease-2019 (COVID-19) are marked by stark geographic heterogeneities (Mishra et al., 2020). Despite reporting its first case on February 28, 2020—close to a month after Ontario on January 25th and British Columbia on January 28th—Quebec quickly became the epicenter of the Canadian COVID-19 epidemic. The disease’s mortality burden in that province, at 653 per million population, was 3.5 times as high as neighboring Ontario (186 per million) and 19 times that of British Columbia (at 35 per million) at the end of the first spring 2020 wave (Groupe de surveillance provinciale de la, 2020).
Epidemiological Characteristics and Factors Associated with Critical Time Intervals of COVID-19 in Eighteen Provinces, China: A Retrospective StudyAs of September 20, 2020, a total of more than 30 million confirmed cases of coronavirus disease 2019 (COVID-19), as well as more than 900,000 deaths had been reported by World Health Organization (WHO) in the worldwide (World Health Organization, 2020a; World Health Organization, 2020b). At the same time, China had reported 85,291 lab confirmed cases with 4,634 deaths (China National Health Commission of the People’s Republic of China, 2020a). Despite the WHO and international community declared and took many efforts to control this pandemic in time, our knowledge about the COVID-19 is still very limited, and the number of daily reported cases is still increasing sharply worldwide (Organization, 2020b).