The origin and early spread of SARS-CoV-2 in Europe.

Abstract: Non-pharmaceutical interventions (NPIs) have been implemented worldwide to curb COVID-19 spread. Belarus is a rare case of a country with a relatively modern healthcare system, where highly limited NPIs have been enacted. Thus, investigation of Belarusian COVID-19 dynamics is essential for the local and global assessment of the impact of NPI strategies. We integrate genomic epidemiology and surveillance methods to investigate the spread of SARS-CoV-2 in Belarus in 2020. We utilize phylodynamics, phylogeography, and probabilistic bias inference to study the virus import and export routes, the dynamics of the effective reproduction number, and the incidence of SARS-CoV-2 infection. Here we show that the estimated cumulative number of infections by June 2020 exceeds the confirmed case number by a factor of ~4 (95% confidence interval (2; 9)). Intra-country SARS-CoV-2 genomic diversity originates from at least 18 introductions from different regions, with a high proportion of regional transmissions. Phylodynamic analysis indicates a moderate reduction of the effective reproductive number after the introduction of limited NPIs, but its magnitude is lower than for developed countries with large-scale NPIs. On the other hand, the effective reproduction number estimate is comparable with that for the neighboring Ukraine, where NPIs were broader. The example of Belarus demonstrates how countries with relatively low outward population mobility continue to be integral parts of the global epidemiological environment. Comparison of the effective reproduction number dynamics for Belarus and other countries reveals the effect of different NPI strategies but also emphasizes the role of regional Eastern European sociodemographic factors in the virus spread. Belarus is one of few European countries that has enacted limited measures to contain SARS-CoV-2, the virus that causes COVID-19. We study the genetic sequences of the SARS-CoV-2 virus circulating in Belarus and other countries in 2020 to investigate how it might have been imported into the country and spread there. We show that the virus was repeatedly imported from and exported to different regions, including a large portion of regional transmissions that occurred despite stricter measures implemented by Belarus’ neighbors. There was a moderate reduction of the virus reproductive number—a measure of virus transmission speed—after April 2020, but its magnitude was lower than for developed countries with more stringent epidemiological interventions. These findings shed light on the COVID-19 spread in Eastern Europe and highlight the impact of public health policies and of regional factors on this spread. Nemira et al. study the genomic epidemiology and phylodynamics of SARS-CoV-2 in Belarus. They identify potential introduction routes of the virus from other countries, determine that during the first wave of the pandemic the number of infections was likely several times higher than reported case numbers, and estimate the impact of early non-pharmaceutical interventions on SARS-CoV-2 transmission.

Abstract: Background In December 2020, the United Kingdom (UK) reported a SARS-CoV-2 Variant of Concern (VoC) which is now coined B.1.1.7. Based on the UK data and later additional data from other countries, a transmission advantage of around 40-80% was estimated for this variant [1, 2, 3]. Aim The goal of this study is to estimate the transmission fitness advantage and the effective reproductive number of B.1.1.7 through time for data from Switzerland. Methods We collected genomic surveillance data from 11.8% of all SARS-CoV-2 confirmed cases across Switzerland between 14.12.2020 and 11.03.2021. It allows us to determine the relative proportion of the B.1.1.7 variant on a daily basis and to quantify the transmission advantage of the B.1.1.7 variant on a national and a regional scale. Results We propose a transmission advantage of 43-52% of B.1.1.7 compared to the other circulating variants. Further, we estimate a reproductive number for B.1.1.7 above 1 for Jan. 1, 2021 until now while the reproductive number for the other variants was below 1. In particular, for the time period up to Jan. 17 we obtain a reproductive number of 1.24 [1.07-1.41] and from Jan. 18 until March 1 we obtain 1.18 [1.06-1.30] based on the whole genome sequencing data. For March 10-16, we obtain 1.14 [1.00-1.26] based on all confirmed cases among which B.1.1.7 is dominant at this stage. Switzerland tightened measures on 18.01.2021 and released measures on 01.03.2021. Conclusion In summary, the dynamics of increase in the frequency of B.1.1.7 is as expected based on the observations in the UK. B.1.1.7 increased in absolute numbers exponentially with the point estimate for the doubling time being around 2-3.5 weeks. Our plots are available online and are currently regularly updated with new data to closely monitor the spread of B.1.1.7.

Abstract: The origin of the SARS-CoV-2 virus is not yet defined, but a viral zoonosis from bats - with or without an alternative animal as an intermediate host - is still the most likely hypothesis. The intensive virological and epidemiological research combined with massive sequencing efforts of whole viral genomes allowed an unprecedented analysis of an unfolding pandemic at the level of viral evolution with the documentation of extinction events, prevalence increases and rise to dominance for different viral lineages that provide not only fundamental insights into mechanisms of viral evolution, but influence also public health measures to contain the virus.

Abstract: SARS-CoV-2 infection fatality ratios (IFR) remain controversially discussed with implications for political measures. The German county of Tirschenreuth suffered a severe SARS-CoV-2 outbreak in spring 2020, with particularly high case fatality ratio (CFR). To estimate seroprevalence, underreported infections, and IFR for the Tirschenreuth population aged ≥14 years in June/July 2020, we conducted a population-based study including home visits for the elderly, and analyzed 4203 participants for SARS-CoV-2 antibodies via three antibody tests. Latent class analysis yielded 8.6% standardized county-wide seroprevalence, a factor of underreported infections of 5.0, and 2.5% overall IFR. Seroprevalence was two-fold higher among medical workers and one third among current smokers with similar proportions of registered infections. While seroprevalence did not show an age-trend, the factor of underreported infections was 12.2 in the young versus 1.7 for ≥85-year-old. Age-specific IFRs were <0.5% below 60 years of age, 1.0% for age 60–69, and 13.2% for age 70+. Senior care homes accounted for 45% of COVID-19-related deaths, reflected by an IFR of 7.5% among individuals aged 70+ and an overall IFR of 1.4% when excluding senior care home residents from our computation. Our data underscore senior care home infections as key determinant of IFR additionally to age, insufficient targeted testing in the young, and the need for further investigations on behavioral or molecular causes of the fewer infections among current smokers.

Abstract: The objective of this meta-analysis was to evaluate the factors associated with the mortality of elderly Italians diagnosed with coronavirus who resided in institutions or who were hospitalized because of the disease. Methods: A systematic review following the recommendations of The Joanna Briggs Institute (JBI) was carried out, utilizing the PEO strategy, i.e., Population, Exposure and Outcome. In this case, the population was the elderly aged over 65 years old, the exposure referred to the SARS-CoV-2 pandemic and the outcome was mortality. The National Center for Biotechnology Information (NCBI/PubMed), Latin American and Caribbean Literature in Health Sciences (LILACS), Excerpta Medica Database (EMBASE) and Cumulative Index to Nursing and Allied Health Literature (CINAHL) databases were used until 31 July 2020. Results: Five Italian studies were included in this meta-analysis, with the number of elderly people included varying between 18 and 1591 patients. The main morbidities presented by the elderly in the studies were dementia, diabetes, chronic kidney disease and hypertension. Conclusions: The factors associated with the mortality of elderly Italian people diagnosed with SARS-CoV-2 who lived in institutions or who were hospitalized because of the disease were evaluated. It was found that dementia, diabetes, chronic kidney disease and hypertension were the main diagnosed diseases for mortality in elderly people with COVID-19.

Abstract: Emerging infectious diseases, such as severe acute respiratory syndrome (SARS) and Zika virus disease, present a major threat to public health1–3. Despite intense research efforts, how, when and where new diseases appear are still a source of considerable uncertainty. A severe respiratory disease was recently reported in Wuhan, Hubei province, China. As of 25 January 2020, at least 1,975 cases had been reported since the first patient was hospitalized on 12 December 2019. Epidemiological investigations have suggested that the outbreak was associated with a seafood market in Wuhan. Here we study a single patient who was a worker at the market and who was admitted to the Central Hospital of Wuhan on 26 December 2019 while experiencing a severe respiratory syndrome that included fever, dizziness and a cough. Metagenomic RNA sequencing4 of a sample of bronchoalveolar lavage fluid from the patient identified a new RNA virus strain from the family Coronaviridae, which is designated here ‘WH-Human 1’ coronavirus (and has also been referred to as ‘2019-nCoV’). Phylogenetic analysis of the complete viral genome (29,903 nucleotides) revealed that the virus was most closely related (89.1% nucleotide similarity) to a group of SARS-like coronaviruses (genus Betacoronavirus, subgenus Sarbecovirus) that had previously been found in bats in China5. This outbreak highlights the ongoing ability of viral spill-over from animals to cause severe disease in humans. Phylogenetic and metagenomic analyses of the complete viral genome of a new coronavirus from the family Coronaviridae reveal that the virus is closely related to a group of SARS-like coronaviruses found in bats in China.

Abstract: Bayesian inference of phylogeny using Markov chain Monte Carlo (MCMC) plays a central role in understanding evolutionary history from molecular sequence data. Visualizing and analyzing the MCMC-generated samples from the posterior distribution is a key step in any non-trivial Bayesian inference. We present the software package Tracer (version 1.7) for visualizing and analyzing the MCMC trace files generated through Bayesian phylogenetic inference. Tracer provides kernel density estimation, multivariate visualization, demographic trajectory reconstruction, conditional posterior distribution summary, and more. Tracer is open-source and available at http://beast.community/tracer.

Abstract: 2019-nCoV Transmission from Asymptomatic Patient In this report, investigators in Germany detected the spread of the novel coronavirus (2019-nCoV) from a person who had recently traveled from China...

Abstract: Teaser: Our review found the average R0 for 2019-nCoV to be 3.28, which exceeds WHO estimates of 1.4 to 2.5.

Abstract: Motivated by the rapid spread of coronavirus disease 2019 (COVID-19) in mainland China, we use a global metapopulation disease transmission model to project the impact of travel limitations on the national and international spread of the epidemic. The model is calibrated on the basis of internationally reported cases and shows that, at the start of the travel ban from Wuhan on 23 January 2020, most Chinese cities had already received many infected travelers. The travel quarantine of Wuhan delayed the overall epidemic progression by only 3 to 5 days in mainland China but had a more marked effect on the international scale, where case importations were reduced by nearly 80% until mid-February. Modeling results also indicate that sustained 90% travel restrictions to and from mainland China only modestly affect the epidemic trajectory unless combined with a 50% or higher reduction of transmission in the community.