Identification of evolutionary trajectories shared across human betacoronaviruses

Comparing the evolution of distantly related viruses can provide insights into common adaptive processes related to shared ecological niches. Phylogenetic approaches, coupled with other molecular evolution tools, can help identify mutations informative on adaptation, whilst the structural contextualization of these to functional sites of proteins may help gain insight into their biological properties. Two zoonotic betacoronaviruses capable of sustained human-to-human transmission have caused pandemics in recent times (SARS-CoV-1 and SARS-CoV-2), whilst a third virus (MERS-CoV) is responsible for sporadic outbreaks linked to animal infections. Moreover, two other betacoronaviruses have circulated endemically in humans for decades (HKU1 and OC43). To search for evidence of adaptive convergence between established and emerging betacoronaviruses capable of sustained human-to-human transmission (HKU1, OC43, SARS-CoV-1 and SARS-CoV-2), we developed a methodological pipeline to classify shared non-synonymous mutations as putatively denoting homoplasy (repeated mutations that do not share direct common ancestry) or stepwise evolution (sequential mutations leading towards a novel genotype). In parallel, we look for evidence of positive selection, and draw upon protein structure data to identify potential biological implications. We find 30 candidate mutations, from which four [codon sites 18121 (nsp14/residue 28), 21623 (spike/21), 21635 (spike/25) and 23948 (spike/796); SARS-CoV-2 genome numbering] further display evolution under positive selection and proximity to functional protein regions. Our findings shed light on potential mechanisms underlying betacoronavirus adaptation to the human host and pinpoint common mutational pathways that may occur during establishment of human endemicity

Identification of Evolutionary Trajectories Shared across Human Betacoronaviruses

Comparing the evolution of distantly related viruses can provide insights into common adaptive processes related to shared ecological niches. Phylogenetic approaches, coupled with other molecular evolution tools, can help identify mutations informative on adaptation, although the structural contextualization of these to functional sites of proteins may help gain insight into their biological properties. Two zoonotic betacoronaviruses capable of sustained human-to-human transmission have caused pandemics in recent times (SARS-CoV-1 and SARS-CoV-2), although a third virus (MERS-CoV) is responsible for sporadic outbreaks linked to animal infections. Moreover, two other betacoronaviruses have circulated endemically in humans for decades (HKU1 and OC43). To search for evidence of adaptive convergence between established and emerging betacoronaviruses capable of sustained human-to-human transmission (HKU1, OC43, SARS-CoV-1, and SARS-CoV-2), we developed a methodological pipeline to classify shared nonsynonymous mutations as putatively denoting homoplasy (repeated mutations that do not share direct common ancestry) or stepwise evolution (sequential mutations leading towards a novel genotype). In parallel, we look for evidence of positive selection and draw upon protein structure data to identify potential biological implications. We find 30 candidate mutations, from which 4 (codon sites 18121 [nsp14/residue 28], 21623 [spike/21], 21635 [spike/25], and 23948 [spike/796]; SARS-CoV-2 genome numbering) further display evolution under positive selection and proximity to functional protein regions. Our findings shed light on potential mechanisms underlying betacoronavirus adaptation to the human host and pinpoint common mutational pathways that may occur during establishment of human endemicity

Hospital admission and emergency care attendance risk for SARS-CoV-2 delta (B.1.617.2) compared with alpha (B.1.1.7) variants of concern: a cohort study

Background: The SARS-CoV-2 delta (B.1.617.2) variant was first detected in England in March, 2021. It has since rapidly become the predominant lineage, owing to high transmissibility. It is suspected that the delta variant is associated with more severe disease than the previously dominant alpha (B.1.1.7) variant. We aimed to characterise the severity of the delta variant compared with the alpha variant by determining the relative risk of hospital attendance outcomes. Methods: This cohort study was done among all patients with COVID-19 in England between March 29 and May 23, 2021, who were identified as being infected with either the alpha or delta SARS-CoV-2 variant through whole-genome sequencing. Individual-level data on these patients were linked to routine health-care datasets on vaccination, emergency care attendance, hospital admission, and mortality (data from Public Health England's Second Generation Surveillance System and COVID-19-associated deaths dataset; the National Immunisation Management System; and NHS Digital Secondary Uses Services and Emergency Care Data Set). The risk for hospital admission and emergency care attendance were compared between patients with sequencing-confirmed delta and alpha variants for the whole cohort and by vaccination status subgroups. Stratified Cox regression was used to adjust for age, sex, ethnicity, deprivation, recent international travel, area of residence, calendar week, and vaccination status. Findings: Individual-level data on 43 338 COVID-19-positive patients (8682 with the delta variant, 34 656 with the alpha variant; median age 31 years [IQR 17–43]) were included in our analysis. 196 (2·3%) patients with the delta variant versus 764 (2·2%) patients with the alpha variant were admitted to hospital within 14 days after the specimen was taken (adjusted hazard ratio [HR] 2·26 [95% CI 1·32–3·89]). 498 (5·7%) patients with the delta variant versus 1448 (4·2%) patients with the alpha variant were admitted to hospital or attended emergency care within 14 days (adjusted HR 1·45 [1·08–1·95]). Most patients were unvaccinated (32 078 [74·0%] across both groups). The HRs for vaccinated patients with the delta variant versus the alpha variant (adjusted HR for hospital admission 1·94 [95% CI 0·47–8·05] and for hospital admission or emergency care attendance 1·58 [0·69–3·61]) were similar to the HRs for unvaccinated patients (2·32 [1·29–4·16] and 1·43 [1·04–1·97]; p=0·82 for both) but the precision for the vaccinated subgroup was low. Interpretation: This large national study found a higher hospital admission or emergency care attendance risk for patients with COVID-19 infected with the delta variant compared with the alpha variant. Results suggest that outbreaks of the delta variant in unvaccinated populations might lead to a greater burden on health-care services than the alpha variant. Funding: Medical Research Council; UK Research and Innovation; Department of Health and Social Care; and National Institute for Health Research

Changes in symptomatology, reinfection, and transmissibility associated with the SARS-CoV-2 variant B.1.1.7: an ecological study

Background The SARS-CoV-2 variant B.1.1.7 was first identified in December, 2020, in England. We aimed to investigate whether increases in the proportion of infections with this variant are associated with differences in symptoms or disease course, reinfection rates, or transmissibility. Methods We did an ecological study to examine the association between the regional proportion of infections with the SARS-CoV-2 B.1.1.7 variant and reported symptoms, disease course, rates of reinfection, and transmissibility. Data on types and duration of symptoms were obtained from longitudinal reports from users of the COVID Symptom Study app who reported a positive test for COVID-19 between Sept 28 and Dec 27, 2020 (during which the prevalence of B.1.1.7 increased most notably in parts of the UK). From this dataset, we also estimated the frequency of possible reinfection, defined as the presence of two reported positive tests separated by more than 90 days with a period of reporting no symptoms for more than 7 days before the second positive test. The proportion of SARS-CoV-2 infections with the B.1.1.7 variant across the UK was estimated with use of genomic data from the COVID-19 Genomics UK Consortium and data from Public Health England on spike-gene target failure (a non-specific indicator of the B.1.1.7 variant) in community cases in England. We used linear regression to examine the association between reported symptoms and proportion of B.1.1.7. We assessed the Spearman correlation between the proportion of B.1.1.7 cases and number of reinfections over time, and between the number of positive tests and reinfections. We estimated incidence for B.1.1.7 and previous variants, and compared the effective reproduction number, Rt, for the two incidence estimates. Findings From Sept 28 to Dec 27, 2020, positive COVID-19 tests were reported by 36 920 COVID Symptom Study app users whose region was known and who reported as healthy on app sign-up. We found no changes in reported symptoms or disease duration associated with B.1.1.7. For the same period, possible reinfections were identified in 249 (0·7% [95% CI 0·6–0·8]) of 36 509 app users who reported a positive swab test before Oct 1, 2020, but there was no evidence that the frequency of reinfections was higher for the B.1.1.7 variant than for pre-existing variants. Reinfection occurrences were more positively correlated with the overall regional rise in cases (Spearman correlation 0·56–0·69 for South East, London, and East of England) than with the regional increase in the proportion of infections with the B.1.1.7 variant (Spearman correlation 0·38–0·56 in the same regions), suggesting B.1.1.7 does not substantially alter the risk of reinfection. We found a multiplicative increase in the Rt of B.1.1.7 by a factor of 1·35 (95% CI 1·02–1·69) relative to pre-existing variants. However, Rt fell below 1 during regional and national lockdowns, even in regions with high proportions of infections with the B.1.1.7 variant. Interpretation The lack of change in symptoms identified in this study indicates that existing testing and surveillance infrastructure do not need to change specifically for the B.1.1.7 variant. In addition, given that there was no apparent increase in the reinfection rate, vaccines are likely to remain effective against the B.1.1.7 variant. Funding Zoe Global, Department of Health (UK), Wellcome Trust, Engineering and Physical Sciences Research Council (UK), National Institute for Health Research (UK), Medical Research Council (UK), Alzheimer's Society

Genomic epidemiology of SARS-CoV-2 in a UK university identifies dynamics of transmission

AbstractUnderstanding SARS-CoV-2 transmission in higher education settings is important to limit spread between students, and into at-risk populations. In this study, we sequenced 482 SARS-CoV-2 isolates from the University of Cambridge from 5 October to 6 December 2020. We perform a detailed phylogenetic comparison with 972 isolates from the surrounding community, complemented with epidemiological and contact tracing data, to determine transmission dynamics. We observe limited viral introductions into the university; the majority of student cases were linked to a single genetic cluster, likely following social gatherings at a venue outside the university. We identify considerable onward transmission associated with student accommodation and courses; this was effectively contained using local infection control measures and following a national lockdown. Transmission clusters were largely segregated within the university or the community. Our study highlights key determinants of SARS-CoV-2 transmission and effective interventions in a higher education setting that will inform public health policy during pandemics.</jats:p

Genomic assessment of quarantine measures to prevent SARS-CoV-2 importation and transmission

Mitigation of SARS-CoV-2 transmission from international travel is a priority. We evaluated the effectiveness of travellers being required to quarantine for 14-days on return to England in Summer 2020. We identified 4,207 travel-related SARS-CoV-2 cases and their contacts, and identified 827 associated SARS-CoV-2 genomes. Overall, quarantine was associated with a lower rate of contacts, and the impact of quarantine was greatest in the 16–20 age-group. 186 SARS-CoV-2 genomes were sufficiently unique to identify travel-related clusters. Fewer genomically-linked cases were observed for index cases who returned from countries with quarantine requirement compared to countries with no quarantine requirement. This difference was explained by fewer importation events per identified genome for these cases, as opposed to fewer onward contacts per case. Overall, our study demonstrates that a 14-day quarantine period reduces, but does not completely eliminate, the onward transmission of imported cases, mainly by dissuading travel to countries with a quarantine requirement

Vampir Fledermaus Virom: Evolutions Auswirkungen in einem immunologischen Kontext

The adaptation of bats to different environments has resulted in the evolution of unique phenotypic and genotypic characteristics such as flight, echolocation and highly specialized diets. Bats have also been increasingly recognized as reservoirs for viruses which can cross species barriers. Among the Neotropical bats, vampire bats (Desmodontinae subfamily) are the only mammals that feed exclusively on the blood from other animals. Because of such an exceptional adaptation to hematophagy these species exhibit a unique set of behavioral, physiological, and morphological characteristics distinct among all other bats. The common vampire bat (Desmodus rotundus) is a known reservoir for rabies-causing lyssaviruses considered to be a major constraint on the cattle industry since bat-transmitted rabies is a primary problem in livestock from Latin America. Nonetheless, the presence of other viruses in this species has hardly been explored. Although bats can be persistently infected with many viruses, they rarely display clinical symptoms and it has been suggested that they might have evolved specific immune strategies to control viral replication. Toll like-receptors (TLRs) are a class of innate immune receptors considered to be the first-line defense mechanism against invading pathogens. The mammalian TLRs 3, 7, 8 and 9 play an important role in triggering acquired immunity as they are activated by nucleic acid ligands. TLRs are of interest from an evolutionary point of view since there is evidence that the ligand binding properties of these receptors may vary among different species thereby having an impact on the evolutionary ecology of infectious diseases. Thus, the analysis of the bat immune variation at a molecular level could reveal patterns of resistance or susceptibility to pathogens within different species and at different taxonomic levels. However, the study of the genetic variability of the immune system in bats has been restricted to a few species and to a few genes. The hypothesis that vampire bats carry viruses common to other mammals was tested based on the premise that their exclusive adaptation to hematophagy could have resulted in viral spill-over events among taxa throughout evolutionary history. Particular focus was made on Retroviruses, given that this viral group is primarily transmitted via body fluid exchange, and thus might have been particularly prone to jump between vampire bats and other taxa. A novel endogenous betaretrovirus (DrERV) was described with an evolutionary pattern that suggests multiple cross- species transmissions among different species throughout their evolutionary history. It was further hypothesized that given the unique adaptations within the Chiroptera, bats as a taxonomic group would have acquired distinctive mutations fixed within the nucleic-acid sensing TLRs with potential consequences on their ligand recognition properties. The nucleic acid sensing TLRs (3, 7, 8 and 9) of the common vampire bat were characterized and the genetic variation of these receptors within different bats species and among other mammals was compared by further testing for ongoing and episodic diversifying selection acting upon specific lineages. Our results provide evidence for potential functional differences between the bat and other mammalian TLRs in terms of recognition of foreign nucleic acids. This project was carried out in close collaboration with several European and Mexican institutions contributing to the development of research on emerging zoonotic diseases and wildlife surveillance.Anpassungen von Fledermäusen an verschiedene Umgebungen haben zu der Entwicklung Die Anpassung von Fledermäusen an ihre Umwelt hat zu der Entwicklung von besonderen phänotypischen und genotypischen Eigenschaften wie Flugfähigkeit, Echoortung und spezifischen Ernährungsweisen geführt. Diese Anpassungen haben auch zur evolutionären Entwicklung potentieller Krankheitserreger beigetragen. So werden Fledermäuse zunehmend als Wirte für Viren erkannt, welche auch interspezifisch übertragen werden können. Unter den Fledermäusen der Neuen Welt sind die Vampirfledermäuse (Unterfamilie Desmodontinae) als die einzigen Säugetiere bekannt, die sich ausschließlich vom Blut anderer Tiere ernähren können. Wegen dieser ungewöhnlichen Anpassung an Hämatophagie, zeigen diese Arten besondere Eigenschaften in ihrem Verhalten, ihrer Physiologie und ihrer Morphologie, die sie von allen anderen Fledermausarten unterscheidet. Der Gemeine Vampir (Desmodus rotundus) ist ein bekannter Wirt für Tollwut-verursachende Lyssaviren und stellt eine große Einschränkung für die Rinderhaltung in Lateinamerika dar. Der Einfluss anderer Virentypen in dieser Art ist bisher kaum erforscht. Obwohl Fledermäuse dauerhaft von vielen Viren infiziert sein können, zeigen sie selten klinische Symptome. Es wird deshalb angenommen dass sie spezifische Immunstrategien entwickelt haben um die Virusreplikation zu kontrollieren. Die Toll like- receptors (TLRs) gehören zu den Immunrezeptoren, die als Bestandteil der primäreren Abwehrantwort gegen eindringende Pathogene angesehen werden. Abhängig von der Tierart unterscheidet man bis zu 13 verschiedene TLRs. Insbesondere die Nukleinsäure-bindenden TLRs 3, 7, 8 und 9 spielen eine wichtige Rolle in der erworbenen Immunreaktion, weil sie diese durch Liganden in Form von Nukleinsäuren aktivieren. Die TLRs sind aus evolutionsbiologischer Sicht besonders interessant, da die Bindungseigenschaften dieser Rezeptoren unter verschiedenen Tierarten variieren können und deshalb einen Einfluss auf die Evolutionsökologie von Infektionskrankheiten haben. Daher könnte die Analyse der Immunvariation bei Fledermäusen auf molekularer Ebene Resistenz- oder Anfälligkeitsmuster gegenüber Pathogenen innerhalb verschiedener Arten und auf unterschiedlichen taxonomischen Ebenen offenlegen. Bisher wurde die genetische Variabilität des Immunsystems von Fledermäusen nur bei wenigen Arten und Genen erforscht. Unserer Hypothese zur Folge könnten Vampirfledermäusen Viren in sich tragen, die auch in anderen Säugetieren vorkommen, da ihre Fähigkeit zur Hämatophagie zu einer Virusübertragung zwischen verschiedenen Taxa in der Evolutionsgeschichte geführt haben könnte. Beispielsweise werden Retroviren hauptsächlich über den Austausch von Körperflüssigkeiten übertragen, weswegen Viren dieser Gruppe leicht zwischen Vampirfledermäusen und Tieren andere Taxa übertragen werden können. Ziel unserer Arbeit war es, neue und bereits bekannte Retroviren in D. rotundus mit Hilfe molekularevolutionärer Methoden zu untersuchen, um interspezifische Übertragungen zu identifizieren. Wir konnten zeigen, dass ein neues endogenes Betaretrovirus (DrERV) in D. rotundus ein Evolutionsmuster aufweist, das auf mehrere interspezifische Übertragungen zwischen verschiedenen Taxa im Laufe der Stammesentwicklung hindeutet. Außerdem sind wir davon ausgegangen dass sich in Fledermäuse, auf Grund ihrer Anpassungen, spezielle Mutationen in den Nukleinsäure-bindenden TLRs fixiert haben, welche wahrscheinlich Auswirkungen auf die Bindungseigenschaften von Liganden haben. Wir haben die Nukleinsäure- bindenden TLRs 3, 7, 8 und 9 des Gemeinen Vampirs grundlegend untersucht und die genetischen Variationen dieser Rezeptoren innerhalb verschiedener Fledermausarten und anderen Säugetieren verglichen. Wir untersuchten ob sich die diversifizierende Selektion fortlaufend oder punktuell auf die Fledermaus- TLRs ausgewirkt hat, um das evolutionäre Muster über lange und kurze Zeiträume beschreiben zu können. Anschließende Analysen der Evolution auf molekularer Ebene ließen spezielle Anpassungsmuster bei den TLRs verschiedener Fledermausarten erkennen. Unsere Ergebnisse konnten außerdem funktionelle Unterschiede in den Bindungseigenschaften von wirtsfremden Nucleinsäuren zwischen den TLRs von Fledermäusen und denen anderer Säugetiere zeigen und lieferten somit entscheidende Hinweise über die Anpassung von Fledermäuse an Viren als potentielle Krankheitserreger. Dieses Projekt wurde in enger Zusammenarbeit mit einigen europäischen und mexikanischen Instituten durchgeführt, die zur Entwicklung von Forschungsbereichen wie Zoonosen und Wildtierüberwachung beitragen

FileS1_Models

3-D models for the D.rotundus nucleic acid sensing TLRs in PBD forma