Εκτίμηση του τρόπου διασποράς του γονότυπου D του ιού της ηπατίτιδας Β (HBV) ανά την υφήλιο

Εισαγωγή: Μεταξύ των γονότυπων της ηπατίτιδας B, ο γονότυπος D αποτελεί τον μοναδικό με παγκόσμια εξάπλωση. Σκοπός: Η εκτίμηση των επιπέδων ομαδοποίησης και του τρόπου διασποράς του γονότυπου D, προκειμένου να εκτιμηθεί ο τρόπος διάδοσης του ιού μεταξύ των διαφορετικών γεωγραφικών περιοχών. Μέθοδοι: Μελετήθηκαν για πρώτη φορά όλες οι διαθέσιμες μη-ανασυνδυασμένες αλληλουχίες πλήρους γονιδιώματος του γονότυπου D (Ν=926). Οι φυλογενετικές τοπολογίες εκτιμήθηκαν με τη μέθοδο μεγίστης πιθανοφάνειας και τα γεγονότα διασποράς με τη μέθοδο μέγιστης φειδωλότητας, ενώ υπολογίστηκε για πρώτη φορά ένας ποσοτικός δείκτης για τον συστηματικό χαρακτηρισμό των γεωγραφικών ενοτήτων σύμφωνα με τα γεγονότα διασποράς του ιού. Αποτελέσματα: Η φυλογενετική ανάλυση ανέδειξε ότι οι αλληλουχίες γονότυπου D ομαδοποιήθηκαν σε διαφορετικά ποσοστά ανάλογα με τη γεωγραφική περιοχή δειγματοληψίας τους, αναδεικνύοντας διαφορετικά μονοφυλετικά πρότυπα σε παγκόσμια κλίμακα. Οι χώρες της Ανατολικής Μεσογείου και της Κεντρικής Ασίας ανέδειξαν τα χαμηλότερα επίπεδα μονοφυλετικότητας. Η στατιστική φυλογεωγραφία και ο ποσοτικός δείκτης εκτίμησαν ότι η Τουρκία, η Ρωσία, η Κεντρική Ασία, η Ανατολική Ευρώπη, η Συρία και η Λατινική Αμερική αποτέλεσαν ενεργές πηγές διασποράς του ιού σε αντίθεση με τη Γροιλανδία, τη Νοτιοανατολική Ασία και την Τυνησία, για τις οποίες δεν βρέθηκε καμία σημαντική δραστηριότητα διασποράς του συγκεκριμένου ιού, δηλαδή αποτέλεσαν απομονωμένες περιοχές. Συμπεράσματα: Η μελέτη ανέδειξε τρεις σημαντικές οδούς διασποράς του ιού, αντικατοπτρίζοντας πιθανότατα τις σημαντικές διαδρομές μετανάστευσης του σύγχρονου ανθρώπου κατά τους Προϊστορικούς χρόνους (Νεολιθική περίοδος) ή και μεταγενέστερα ως συνέπεια σύγχρονων μετακινήσεων πληθυσμών. Επίσης ανέδειξε τον σημαντικό ρόλο που διαδραμάτισε η ευρύτερη περιοχή της Κεντρικής Ασίας στη διασπορά του συγκεκριμένου ιού.Background: Genotype D is the only HBV genotype having a global expansion. This is reflected mainly by the sub-genotypes D1, D2 and D3 which are dominant in North Africa, East Europe and West Asia. In contrast, D4, D5 and D6 circulate mainly in indigenous populations in India, Oceania and Arctic. Aim: The aim of the current study was to estimate the levels of regional clustering and the pattern of dispersal of HBV subtype D in order to shed light on how the virus has been disseminated within different geographic areas over time. Methods: All full-length non-recombinant sequences of genotype D (N=926) available on databases were studied. The available sequences were clustered on different regions according to WHO criteria. Phylogeny reconstruction with bootstrap evaluation was conducted by the maximum likelihood method. The migration events were inferred from viral phylogenies using parsimony. Migration events were formed the basis of a new metric that we used to determine whether a geographical unit (country or region according) is actively spreading (“hub”) or passively receiving (“sink”) viral migrations. Results: The phylogenetic analysis suggests that HBV genotype D sequences form regional clusters at different percentages according to their geographic origin. Specifically sequences from Australasia (90%), Asia-Pacific (83%), Oceania (83%), Southeast Asia (80%), East Asia (69%), Caribbean (64%), Latin America (56%), Sub-Saharan Africa (55%) and North America (50%) formed monophyletic clusters, while sequences from W. Europe (35%), South Asia (26%), East Europe (19%) and North Africa and Middle East (16%) revealed the lowest monophyly levels. The Central Europe and Central Asia did not reveal any monophyletic pattern. Country-wise analyses showed the following monophyly patterns: Greenland: 100%, New Zealand: 97%, Japan: 83%, Tunisia: 66%, China: 65%, India: 27%, Belgium: 22%, Eastern Europe: 19%, Lebanon: 17%, Turkey: 5% and Iran: 4%. Absence of monophyly patterns was observed for Syria and Russia. Based on combined statistical phylogeographic and additional analysis using the newly developed metric, Turkey, Russia, Central Asia, Syria, Eastern Europe and Latin America was found that acted as hubs, while India, Lebanon and New Zealand were sinks of viral migration. Africa and Oceania were classified both as sinks and hubs while for Greenland, Southeast Asia and Tunisia no significant migration was found, suggesting that they provide isolated areas (“islands”) for viral dispersal. Finally for China, Japan and Western Europe, was found no statistical evidence for their epidemic dispersal. Conclusions: The analysis suggests considerable differences in the patterns of HBV genotype D regional clustering around the globe. Notably for Eastern Mediterranean very low levels of regional clustering were found suggesting high levels of viral mobility in contrast to several areas in Africa, Asia and the Americas. These patterns are probably due to expansion of Neolithic farmers from Middle East westwards. On the other hand, exporting migration from Latin America on a global scale was probably more recent, given the recent introduction of genotype D in Latin America as a result of the colonization of Americas by Europeans. Also revealed that Central Asia has played a major role in disseminating genotype D epidemic within Europe and Asia. This study highlights the importance of westward patterns of viral dispersal mirroring the significant routes of human migrations during the Neolithic. One of the potential limitations is the non-uniform availability of sequences across different countries and regions

Εκτίμηση των χαρακτηριστικών της επιδημίας του HIV-1 στην Ελλάδα με μεθόδους μοριακής επιδημιολογίας

Ο ιός της ανθρώπινης ανοσοανεπάρκειας (Human Immunodeficiency Virus – HIV) έχει προκαλέσει μία από τις μεγαλύτερες πανδημίες στα χρονικά της ανθρωπότητας. Στην Ελλάδα, σύμφωνα με στοιχεία του εθνικού συστήματος επιδημιολογικής επιτήρησης της HIV/AIDS λοίμωξης (Εθνικός Οργανισμός Δημόσιας Υγείας – Ε.Ο.Δ.Υ), ο συνολικός αριθμός των ατόμων που έχουν προσβληθεί από τον ιό μέχρι τα τέλη του 2018 ανέρχεται σε 17.389. Επίσης, στην Ελλάδα, με απαρχή το 2011, συνέβη μία από τις μεγαλύτερες επιδημικές εκρήξεις στην Ευρώπη σε χρήστες ενδοφλέβιων ναρκωτικών (ΧΕΝ). Η παρούσα διατριβή είχε σκοπό τη διερεύνηση και την αποτύπωση της επιδημίας του HIV-1 στην Ελλάδα με μοριακές μεθόδους και καινοτόμες εφαρμογές. Συγκεκριμένα, αναλύθηκαν 4.856 μοναδικές HIV-1 νουκλεοτιδικές αλληλουχίες, οι οποίες αποτελούσαν το μεγαλύτερο δυνατό δείγμα διαθέσιμων δεδομένων με δειγματοληψία το χρονικό διάστημα 1999-2015 από το μεγαλύτερο τμήμα της Ελληνικής επικράτειας. Η ανάλυση των αλληλουχιών βασίστηκε σε καινοτόμες εφαρμογές μοριακών μεθόδων, και συγκεκριμένα σε εφαρμογές φυλογενετικής, φυλοδυναμικής και φυλογεωγραφικής ανάλυσης. Η υποτύπηση των υπό μελέτη αλληλουχιών έδειξε ότι επικρατέστεροι HIV-1 τύποι στην Ελλάδα παραμένουν οι υπότυποι B (44,2%) και A1 (25,3%). Παρόλο αυτά, η διαχρονική εκτίμηση του επιπολασμού των HIV-1 υπότυπων το χρονικό διάστημα 1999-2015 έδειξε ότι η επιδημία του HIV-1 στην Ελλάδα διαφοροποιείται σημαντικά με το πέρασμα του χρόνου. Συγκεκριμένα, ο επιπολασμός του υπότυπου Β και όλων των μη Β μη Α1 υπότυπων βρέθηκε να μειώνεται σταδιακά στην πορεία του χρόνου, σε αντίθεση με τον επιπολασμό του υπότυπου Α1 και των ανασυνδυασμένων τύπων του ιού ο οποίος βρέθηκε να παρουσιάζει αυξητική τάση. Η μελέτη των προτύπων διασποράς των επικρατέστερων ΗΙV-1 υπότυπων στην Ελλάδα έδειξε ότι η επιμέρους επιδημία του υπότυπου Α1 (93,8%) παρουσιάζει υψηλότερα επίπεδα τοπικής διασποράς συγκριτικά με του Β (77,1%). H τοπική διασπορά του υπότυπου Α1 βρέθηκε να σχετίζεται σημαντικά με τον τρόπο μετάδοσης (άνδρες που κάνουν σεξ με άνδρες, Men who have Sex with Men – MSM) και την εθνικότητα (Ελληνική), ενώ του Β με την περίοδο δειγματοληψίας (2011-2015). Η μοριακή επιτήρηση της επιδημίας του HIV-1 στους ΧΕΝ της Αθήνας το χρονικό διάστημα 2011-2014 ανέδειξε την ύπαρξη τεσσάρων κύριων τοπικών δικτύων διασποράς του ιού (επιμέρους επιδημίες) σε ΧΕΝ (CRF14_BG, CRF35_AD, Β, A). Στα δίκτυα αυτά βρέθηκαν, επίσης, αλληλουχίες από μη ΧΕΝ, που υποδηλώνουν την ύπαρξη μετάδοσης του ιού από ΧΕΝ και σε άλλες ομάδες κινδύνου. Επιπρόσθετα, βρέθηκε ότι οι επιμέρους επιδημίες του υπότυπου Α1 και του CRF35_AD ξεκίνησαν την ίδια περίπου χρονική περίοδο (Δεκέμβριος 2009 - Μάιος 2010) και παρουσίασαν έντονη αύξηση κατά τα αρχικά στάδια της επιδημίας, σε αντίθεση με εκείνες του υπότυπου Β και του CRF14_BG για τις οποίες εκτιμήθηκε ότι η προέλευση τους ήταν προγενέστερη (B: Μάρτιος 2006, CRF14_BG: Ιούλιος 2008) και ότι οι μεταδόσεις διήρκησαν για μεγαλύτερο χρονικό διάστημα. Εστιάζοντας στους ΧΕΝ με μη Ελληνική εθνικότητα στην Αθήνα βρέθηκε ότι το μεγαλύτερο ποσοστό (94,3%) μολύνθηκε με HIV-1 μετά την άφιξη του στην Ελλάδα. Οι μεταδόσεις σε αυτόν τον ειδικό πληθυσμό πραγματοποιήθηκαν, κυρίως, εντός των τοπικών δικτύων διασποράς των ΧΕΝ (CRF14_BG, CRF35_AD, B, A1). Επίσης, βρέθηκε ότι κατά την επιδημική έκρηξη του HIV-1 στους ΧΕΝ στην Αθήνα οι μεταδόσεις του ιού συνέβησαν με μεγαλύτερη συχνότητα μεταξύ των ΧΕΝ διαφορετικών εθνικοτήτων (με μη Ελληνική εθνικότητα). Η μελέτη των κοινωνικών δικτύων και του τρόπου διασποράς του HIV-1 στους ΧΕΝ που συμμετείχαν στο πρόγραμμα «TRIP» (Transmission Reduction Intervention Project – TRIP) στην Αθήνα έδειξε ότι τo 59,3% των ατόμων είχε μολυνθεί σε κοινά δίκτυα μετάδοσης και είχε κοινωνική δικτύωση πρώτου βαθμού. Το υψηλό αυτό ποσοστό υποδηλώνει ότι κατά την επιδημία του HIV-1 στους ΧΕΝ στην Αθήνα περισσότερες από τις μισές μεταδόσεις πραγματοποιήθηκαν μεταξύ ατόμων με κοινωνική δικτύωση. Επιπρόσθετα, στον ίδιο πληθυσμό δείχθηκε ότι οι μεταδόσεις μεταξύ ατόμων με πρόσφατη HIV-1 λοίμωξη είναι πιο συχνές και, συνεπώς, τα άτομα με πρόσφατη HIV-1 λοίμωξη πιθανόν αποτελούν πηγές μετάδοσης του ιού. Αναφορικά με τον επιπολασμό αντοχής σε οποιαδήποτε κατηγορία φαρμάκων σε μη θεραπευμένα άτομα το διάστημα 2003-2015 εκτιμήθηκε 22,2%, με την αντοχή σε NNRTIs (Non-Nucleoside Reverse Transcriptase Inhibitors) να παρουσιάζει τα υψηλότερα ποσοστά (16,9%) και να αυξάνεται στην πορεία του χρόνου. Επιπρόσθετα, εντοπίστηκαν σημαντικές διαφορές μεταξύ των NRTIs (Nucleoside Reverse Transcriptase Inhibitors) και NNRTIs ως προς τα πρότυπα μετάδοσης των ανθεκτικών στελεχών. Συγκεκριμένα, οι κυρίαρχες μεταλλαγές στα NNRTIs (E138A, K103N) βρέθηκαν να μεταδίδονται σε τοπικά δίκτυα (πέντε επιμέρους επιδημίες) και να σχετίζονται με μεταδόσεις μεταξύ MSM και υπότυπο Α1. Τέλος, για τρεις επιμέρους επιδημίες της E138A εκτιμήθηκε ότι ξεκίνησαν το ίδιο περίπου χρονικό διάστημα (1995-1997) και παρέμεναν ενεργές μεταξύ 2011 και 2015. Σε αντίθεση με τις παραπάνω επιδημίες, για την επιδημία της K103N εκτιμήθηκε ότι ξεκίνησε αρκετά πιο πρόσφατα (2007) και παρέμενε ενεργή το διάστημα 2008-2013. Εν κατακλείδι, σύμφωνα με το Κέντρο Ελέγχου και Πρόληψης Νοσημάτων των Η.Π.Α. (Centers for Disease Control and Prevention – CDC) η διερεύνηση και αποτύπωση των χαρακτηριστικών μιας επιδημίας είναι καίριας σημασίας προκειμένου να επιτευχθεί ο έλεγχος της επιδημίας. Προς αυτήν την κατεύθυνση, τα ευρήματα της παρούσας διατριβής, τα οποία προέκυψαν από την εφαρμογή καινοτόμων μεθόδων μοριακής επιδημιολογίας, οδήγησαν στην παραγωγή τεκμηριωμένης γνώσης που μπορεί να συμβάλει σημαντικά στην προσπάθεια ελέγχου της επιδημίας του HIV-1 στην Ελλάδα.Human Immunodeficiency Virus (HIV) has caused one of the most devastating pandemics in human history. In Greece, according to the national HIV/AIDS surveillance system (National Public Health Organization – NOPH), the total number of HIV-infected individuals was 17,389 in 2018. In addition, Greece has experienced one of the largest HIV-1 outbreaks among people who inject drugs (PWID) in Europe. The aim of the thesis was the investigation of the HIV-1 epidemic in Greece using molecular methods. In the context of the study, most of the available molecular data in Greece were analysed (high coverage). Specifically, the study population consisted of 4,856 unique HIV-1 nucleotide sequences sampled during 1999-06/2015 in Greece. The analysis was based on current state-of-the-art molecular epidemiology methods – phylogenetic, phylodynamic and phylogeographic analyses – which have proven to be powerful tools in public health. Subtyping analysis revealed that although subtype B (44.2%) and A1 (25.3%) are the most prevalent HIV-1 clades in Greece, the HIV-1 epidemic has a significant trend over time. Specifically, the prevalence of subtype B and non-B non-A1 subtypes was found to decrease over time. On the contrary, the prevalence of subtype A1 and CRFs shows an increasing trend. The investigation of the dispersal patters of the most prevalent HIV-1 subtypes in Greece revealed that 93.8% of subtype A1 sequences formed monophyletic clusters (regional dispersal). For subtype B the corresponding proportion was lower and equal to 77.1%. In addition, analysis showed that risk group (Men who have Sex with Men – MSM) and nationality (Greek) were associated with the regional clustering of subtype A1, while period of sampling (2011-2015) was associated with the regional clustering of subtype B. The molecular surveillance of the HIV-1 subepidemic among PWID in Athens (2011-2014) indicated that the majority of sequences from PWID fell within four local transmission networks – LTNs (subepidemics) (CRF14_BG, CRF35_AD, Β, A). In addition to sequences from PWID, a low number of sequences from non-PWID belonged to these networks, corresponding to cross-group transmissions. It was also found that subtype A1 and CRF35_AD subepidemics started around the same time period (December 2009 - May 2010), in contrast to subtype B and CRF14_BG subepidemics which started earlier (B: March 2006, CRF14_BG: July 2008). Furthermore, transmissions within subtype A1 and CRF35_AD LTNs increased sharply during the early stage of the outbreak, while transmissions within subtype B and CRF14_BG LTNs lasted for a longer time period. Focusing on the non-Greek PWID in Athens, analysis revealed that for 94.3% the origin of their HIV-1 infection was assumed to be in Greece (post-migration). Most of the non-Greek PWID had been infected within the PWID-LTNs (CRF14_BG, CRF35_AD, B, A1). Moreover, the recent PWID subepidemic in Athens was found to be a unique case, since for PWID infected within networks, HIV-1 transmissions occurred more frequently among non-Greeks than would be expected by chance. The exploration of associations between transmission links (as estimated by molecular analysis) and social network-based ties among PWID recruited into “TRIP” (Transmission Reduction Intervention Project – TRIP) showed that a high proportion of individuals (59.3%) in phylogenetic clusters had first-degree social ties with at least one member of their cluster. This means that more than half of the individuals with viral linkage were also socially linked, suggesting that during an HIV outbreak among PWID, transmissions occurred preferentially within socially linked individuals. Additionally, it was found that transmissions are more frequent among PWID with high viremia and that recently HIV-infected individuals are more likely to be the source of HIV-1 transmission within transmission pairs. The prevalence of resistance among treatment-naïve individuals during 2003–2015 was estimated 22.2% (HIVdb resistance interpretation algorithm). Resistance to NNRTIs (Non-Nucleoside Reverse Transcriptase Inhibitors) was the most common (16.9%) and was found to increase over time. Analysis revealed that the dispersal patterns of the NRTI (Nucleoside Reverse Transcriptase Inhibitor) and NNRTI resistant strains differed significantly. Specifically, the most frequently observed NNRTI resistant mutations (E138A, K103N) were found to be transmitted within local networks (five subepidemics), suggesting regional dispersal, and, also, to be associated with MSM and subtype A1. Furthermore, it was found that three out of four E138A subepidemics started around the same time period (between 1995 and 1997) and that the number of transmissions within most of the E138A networks increased during 2011-2015. On the other hand, the origin of the K103N subepidemic was more recent (2007) and the number of transmissions within this network increased during 2008-2013. In conclusion, according to the leading national public health institute of the USA (Centers for Disease Control and Prevention – CDC), the investigation and characterization of an epidemic is of crucial importance for the control of the epidemic. Under this perspective, the current findings, which were based on an analysis of almost 5,000 HIV-1 sequences using innovative molecular epidemiology methods, produced evidence-based knowledge that could provide added value on the control of the HIV-1 epidemic in Greece

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

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

Phylogenetic Analysis of SARS-CoV-2 Data Is Difficult

Numerous studies covering some aspects of SARS-CoV-2 data analyses are being published on a daily basis, including a regularly updated phylogeny on nextstrain.org. Here, we review the difficulties of inferring reliable phylogenies by example of a data snapshot comprising a quality-filtered subset of 8,736 out of all 16,453 virus sequences available on May 5, 2020 from gisaid.org. We find that it is difficult to infer a reliable phylogeny on these data due to the large number of sequences in conjunction with the low number of mutations. We further find that rooting the inferred phylogeny with some degree of confidence either via the bat and pangolin outgroups or by applying novel computational methods on the ingroup phylogeny does not appear to be credible. Finally, an automatic classification of the current sequences into subclasses using the mPTP tool for molecular species delimitation is also, as might be expected, not possible, as the sequences are too closely related. We conclude that, although the application of phylogenetic methods to disentangle the evolution and spread of COVID-19 provides some insight, results of phylogenetic analyses, in particular those conducted under the default settings of current phylogenetic inference tools, as well as downstream analyses on the inferred phylogenies, should be considered and interpreted with extreme caution

Bayesian mixture models for phylogenetic source attribution from consensus sequences and time since infection estimates

In stopping the spread of infectious diseases, pathogen genomic data can be used to reconstruct transmission events and characterize population-level sources of infection. Most approaches for identifying transmission pairs do not account for the time that passed since divergence of pathogen variants in individuals, which is problematic in viruses with high within-host evolutionary rates. This is prompting us to consider possible transmission pairs in terms of phylogenetic data and additional estimates of time since infection derived from clinical biomarkers. We develop Bayesian mixture models with an evolutionary clock as signal component and additional mixed effects or covariate random functions describing the mixing weights to classify potential pairs into likely and unlikely transmission pairs. We demonstrate that although sources cannot be identified at the individual level with certainty, even with the additional data on time elapsed, inferences into the population-level sources of transmission are possible, and more accurate than using only phylogenetic data without time since infection estimates. We apply the approach to estimate age-specific sources of HIV infection in Amsterdam MSM transmission networks between 2010-2021. This study demonstrates that infection time estimates provide informative data to characterize transmission sources, and shows how phylogenetic source attribution can then be done with multi-dimensional mixture models

Spatiotemporal Characteristics of the Largest HIV-1 CRF02_AG Outbreak in Spain: Evidence for Onward Transmissions.

Background and Aim: The circulating recombinant form 02_AG (CRF02_AG) is the predominant clade among the human immunodeficiency virus type-1 (HIV-1) non-Bs with a prevalence of 5.97% (95% Confidence Interval-CI: 5.41-6.57%) across Spain. Our aim was to estimate the levels of regional clustering for CRF02_AG and the spatiotemporal characteristics of the largest CRF02_AG subepidemic in Spain. Methods: We studied 396 CRF02_AG sequences obtained from HIV-1 diagnosed patients during 2000-2014 from 10 autonomous communities of Spain. Phylogenetic analysis was performed on the 391 CRF02_AG sequences along with all globally sampled CRF02_AG sequences (N = 3,302) as references. Phylodynamic and phylogeographic analysis was performed to the largest CRF02_AG monophyletic cluster by a Bayesian method in BEAST v1.8.0 and by reconstructing ancestral states using the criterion of parsimony in Mesquite v3.4, respectively. Results: The HIV-1 CRF02_AG prevalence differed across Spanish autonomous communities we sampled from (

Real-world effectiveness of molnupiravir and nirmatrelvir/ritonavir as treatments for COVID-19 in patients at high risk

Background Using a retrospective cohort study design, we aimed to evaluate the effectiveness of molnupiravir and nirmatrelvir/ritonavir in patients with SARS-CoV-2 who were highly vulnerable. Methods The impact of each drug was determined via comparisons with age-matched control groups of patients positive for SARS-CoV-2 who did not receive oral antiviral therapy. Results Administration of molnupiravir significantly reduced the risk of hospitalization (odds ratio [OR], 0.40; P < .001) and death (OR, 0.31; P < .001) among these patients based on data adjusted for age, previous SARS-CoV-2 infection, vaccination status, and time elapsed since the most recent vaccination. The reductions in risk were most profound among elderly patients (≥75 years old) and among those with high levels of drug adherence. Administration of nirmatrelvir/ritonavir also resulted in significant reductions in the risk of hospitalization (OR, 0.31; P < .001) and death (OR, 0.28; P < .001). Similar to molnupiravir, the impact of nirmatrelvir/ritonavir was more substantial among elderly patients and in those with high levels of drug adherence. Conclusions Collectively, these real-world findings suggest that although the risks of hospitalization and death due to COVID-19 have been reduced, antivirals can provide additional benefits to members of highly vulnerable patient populations

SARS-CoV-2 Molecular Transmission Clusters and Containment Measures in Ten European Regions during the First Pandemic Wave

International audienceBackground: The spatiotemporal profiling of molecular transmission clusters (MTCs) using viral genomic data can effectively identify transmission networks in order to inform public health actions targeting SARS-CoV-2 spread. Methods: We used whole genome SARS-CoV-2 sequences derived from ten European regions belonging to eight countries to perform phylogenetic and phylodynamic analysis. We developed dedicated bioinformatics pipelines to identify regional MTCs and to assess demographic factors potentially associated with their formation. Results: The total number and the scale of MTCs varied from small household clusters identified in all regions, to a super-spreading event found in Uusimaa-FI. Specific age groups were more likely to belong to MTCs in different regions. The clustered sequences referring to the age groups 50–100 years old (y.o.) were increased in all regions two weeks after the establishment of the lockdown, while those referring to the age group 0–19 y.o. decreased only in those regions where schools’ closure was combined with a lockdown. Conclusions: The spatiotemporal profiling of the SARS-CoV-2 MTCs can be a useful tool to monitor the effectiveness of the interventions and to reveal cryptic transmissions that have not been identified through contact tracing

Spatiotemporal Characteristics of the Largest HIV-1 CRF02_AG Outbreak in Spain: Evidence for Onward Transmissions

Background and Aim: The circulating recombinant form 02_AG (CRF02_AG) is the predominant clade among the human immunodeficiency virus type-1 (HIV-1) non-Bs with a prevalence of 5.97% (95% Confidence Interval-CI: 5.41–6.57%) across Spain. Our aim was to estimate the levels of regional clustering for CRF02_AG and the spatiotemporal characteristics of the largest CRF02_AG subepidemic in Spain.Methods: We studied 396 CRF02_AG sequences obtained from HIV-1 diagnosed patients during 2000–2014 from 10 autonomous communities of Spain. Phylogenetic analysis was performed on the 391 CRF02_AG sequences along with all globally sampled CRF02_AG sequences (N = 3,302) as references. Phylodynamic and phylogeographic analysis was performed to the largest CRF02_AG monophyletic cluster by a Bayesian method in BEAST v1.8.0 and by reconstructing ancestral states using the criterion of parsimony in Mesquite v3.4, respectively.Results: The HIV-1 CRF02_AG prevalence differed across Spanish autonomous communities we sampled from (p &lt; 0.001). Phylogenetic analysis revealed that 52.7% of the CRF02_AG sequences formed 56 monophyletic clusters, with a range of 2–79 sequences. The CRF02_AG regional dispersal differed across Spain (p = 0.003), as suggested by monophyletic clustering. For the largest monophyletic cluster (subepidemic) (N = 79), 49.4% of the clustered sequences originated from Madrid, while most sequences (51.9%) had been obtained from men having sex with men (MSM). Molecular clock analysis suggested that the origin (tMRCA) of the CRF02_AG subepidemic was in 2002 (median estimate; 95% Highest Posterior Density-HPD interval: 1999–2004). Additionally, we found significant clustering within the CRF02_AG subepidemic according to the ethnic origin.Conclusion: CRF02_AG has been introduced as a result of multiple introductions in Spain, following regional dispersal in several cases. We showed that CRF02_AG transmissions were mostly due to regional dispersal in Spain. The hot-spot for the largest CRF02_AG regional subepidemic in Spain was in Madrid associated with MSM transmission risk group. The existence of subepidemics suggest that several spillovers occurred from Madrid to other areas. CRF02_AG sequences from Hispanics were clustered in a separate subclade suggesting no linkage between the local and Hispanic subepidemics