Serologic Surveillance for SARS-CoV-2 Infection among Wild Rodents, Europe.

We report results from serologic surveillance for exposure to SARS-CoV-2 among 1,237 wild rodents and small mammals across Europe. All samples were negative, with the possible exception of 1. Despite suspected potential for human-to-rodent spillover, no evidence of widespread SARS-CoV-2 circulation in rodent populations has been reported to date.Esitämme tulokset serologisesta tutkimuksesta, jossa seulottiin SARS-CoV-2 tartuntojen varalta 1,237 luonnonvaraista jyrsijää ja piennisäkästä eri puolilta Eurooppaa. Kaikki näytteet olivat negatiivisia, yhtä näytettä lukuun ottamatta. SARS-CoV-2:n läikkymisen ihmisistä jyrsijöihin on arveltu olevan mahdollista, mutta todisteet viruksen laajamittaisesta leviämisestä jyrsijäpopulaatioissa puuttuvat.

Genome Sequence of an Early Imported Case of SARS-CoV-2 Delta Variant (B.1.617.2 AY.122) in Iraq in April 2021.

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Delta variant was first reported in India. Thereafter, the Delta variant became the most prevalent variant globally. Here, we report the complete genome sequence of an early imported case of a SARS-CoV-2 B.1.617.2 AY.122 strain in Iraq. The strain was obtained from a flight passenger from India to Iraq on 20 April 2021.

The phylodynamics of SARS-CoV-2 during 2020 in Finland.

Background: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused millions of infections and fatalities globally since its emergence in late 2019. The virus was first detected in Finland in January 2020, after which it rapidly spread among the populace in spring. However, compared to other European nations, Finland has had a low incidence of SARS-CoV-2. To gain insight into the origins and turnover of SARS-CoV-2 lineages circulating in Finland in 2020, we investigated the phylogeographic and -dynamic history of the virus. Methods: The origins of SARS-CoV-2 introductions were inferred via Travel-aware Bayesian time-measured phylogeographic analyses. Sequences for the analyses included virus genomes belonging to the B.1 lineage and with the D614G mutation from countries of likely origin, which were determined utilizing Google mobility data. We collected all available sequences from spring and fall peaks to study lineage dynamics. Results: We observed rapid turnover among Finnish lineages during this period. Clade 20C became the most prevalent among sequenced cases and was replaced by other strains in fall 2020. Bayesian phylogeographic reconstructions suggested 42 independent introductions into Finland during spring 2020, mainly from Italy, Austria, and Spain. Conclusions: A single introduction from Spain might have seeded one-third of cases in Finland during spring in 2020. The investigations of the original introductions of SARS-CoV-2 to Finland during the early stages of the pandemic and of the subsequent lineage dynamics could be utilized to assess the role of transboundary movements and the effects of early intervention and public health measures.

High prevalence of an alpha variant lineage with a premature stop codon in ORF7a in Iraq, winter 2020-2021.

Since the first reported case of coronavirus disease 2019 (COVID-19) in China, SARS-CoV-2 has been spreading worldwide. Genomic surveillance of SARS-CoV-2 has had a critical role in tracking the emergence, introduction, and spread of new variants, which may affect transmissibility, pathogenicity, and escape from infection or vaccine-induced immunity. As anticipated, the rapid increase in COVID-19 infections in Iraq in February 2021 is due to the introduction of variants of concern during the second wave of the COVID-19 pandemic. To understand the molecular epidemiology of SARS-CoV-2 during the second wave in Iraq (2021), we sequenced 76 complete SARS-CoV-2 genomes using NGS technology and identified genomic mutations and proportions of circulating variants among these. Also, we performed an in silico study to predict the effect of the truncation of NS7a protein (ORF7a) on its function. We detected nine different lineages of SARS-CoV-2. The B.1.1.7 lineage was predominant (80.20%) from February to May 2021, while only one B.1.351 strain was detected. Interestingly, the phylogenetic analysis showed that multiple strains of the B.1.1.7 lineage clustered closely with those from European countries. A notable frequency (43.33%) of stop codon mutation (NS7a Q62stop) was detected among the B.1.1.7 lineage sequences. In silico analysis of NS7a with Q62stop found that this stop codon had no considerable effect on the function of NS7a. This work provides molecular epidemiological insights into the spread variants of SARS-CoV-2 in Iraq, which are most likely imported from Europe.

Incidence Trends for SARS-CoV-2 Alpha and Beta Variants, Finland, Spring 2021.

Severe acute respiratory syndrome coronavirus 2 Alpha and Beta variants became dominant in Finland in spring 2021 but had diminished by summer. We used phylogenetic clustering to identify sources of spreading. We found that outbreaks were mostly seeded by a few introductions, highlighting the importance of surveillance and prevention policies.