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1.
Frontiers in Behavioral Neuroscience ; 2022.
Article in English | ProQuest Central | ID: covidwho-1963496

ABSTRACT

Since the dawn of cognitive neuroscience, emotions have been recognized to impact on several executive processes, such as action inhibition. However, the complex interplay between emotional stimuli and action control is not yet fully understood. One way to measure inhibitory control is the stop-signal task (SST), which estimates the ability to cancel outright an action to the presentation of a stop signal by means of the stop signal reaction times (SSRT). Impaired as well as facilitated action control has been found when faced with intrinsic emotional stimuli as stop signals in SSTs. Here, we aimed at investigating more deeply the power of negative stimuli to influence our action control, testing the hypothesis that a previously neutral stimulus (i.e., the image of the SARS-CoV-2), which has been conditioned through vicarious fear learning, has the same impact on reactive action inhibition performance as an intrinsically negative stimulus (i.e., a fearful face or body). Action control capabilities were tested in 90 participants by means of a Stop Signal Task (SST), in which the stop signals were represented by different negative stimuli. Results showed that the SARS-CoV-2 image enhanced the ability to suppress an ongoing action similarly to observing fearful facial expressions or fearful body postures. Interestingly, we found that this effect was predicted by impulsivity traits: for example, the less self-control the participants had, the less they showed emotional facilitation for inhibitory performance. These results demonstrated that vicarious fear learning has a critical impact on cognitive abilities, making a neutral image as threatening as phylogenetically innate negative stimuli and able to impact on our behavioural control.

2.
Syst Biol ; 2022 Jul 22.
Article in English | MEDLINE | ID: covidwho-1961150

ABSTRACT

Modern phylogenetic methods allow inference of ancestral molecular sequences given an alignment and phylogeny relating present day sequences. This provides insight into the evolutionary history of molecules, helping to understand gene function and to study biological processes such as adaptation and convergent evolution across a variety of applications. Here we propose a dynamic programming algorithm for fast joint likelihood-based reconstruction of ancestral sequences under the Poisson Indel Process (PIP). Unlike previous approaches, our method, named ARPIP, enables the reconstruction with insertions and deletions based on an explicit indel model. Consequently, inferred indel events have an explicit biological interpretation. Likelihood computation is achieved in linear time with respect to the number of sequences. Our method consists of two steps, namely finding the most probable indel points and reconstructing ancestral sequences. First, we find the most likely indel points and prune the phylogeny to reflect the insertion and deletion events per site. Second, we infer the ancestral states on the pruned subtree in a manner similar to FastML. We applied ARPIP on simulated datasets and on real data from the Betacoronavirus genus. ARPIP reconstructs both the indel events and substitutions with a high degree of accuracy. Our method fares well when compared to established state-of-the-art methods such as FastML and PAML. Moreover, the method can be extended to explore both optimal and suboptimal reconstructions, include rate heterogeneity through time and more. We believe it will expand the range of novel applications of ancestral sequence reconstruction.

3.
Biomedica ; 42(Suppl. 2), 2022.
Article in Spanish | CAB Abstracts | ID: covidwho-1957852

ABSTRACT

Introduction: The severe acute respiratory syndrome of the new coronavirus (SARS-CoV-2) is the causal agent of the health emergency due to the COVID-19 pandemic. Although humans are the main susceptible host, experimental studies and reported cases of natural infection have evidenced scenarios of SARS-CoV-2 reverse zoonosis in animals.

4.
Journal of Medical Virology ; 94(5):1757-2307, 2022.
Article in English | GIM | ID: covidwho-1957722

ABSTRACT

This special issue contains 74 articles (2 commentaries, 17 letters to the editor, 8 reviews, 40 research articles, 7 short communications) that discusses topics related to COVID-19 and its variants. Topics include new drugs against COVID-19, detection of variants, antibody response, evolution and phylogeny, monoclonal antibodies, symptoms, among others.

5.
Chinese Journal of Microbiology and Immunology (China) ; 41(11):821-828, 2021.
Article in Chinese | EMBASE | ID: covidwho-1957485

ABSTRACT

Human coronavirus OC43 (HCoV-OC43) and severe acute respiratory syndrome coronavirus 2(SARS-CoV-2) belong to the β-coronavirus genus. Since the discovery in 1967, HCoV-OC43 has been continuously circulating in human population and has become one of the common seasonal respiratory viruses. SARS-CoV-2, which has a higher morbidity and fatality rate, appeared at the end of 2019, followed by the emergence of a variety of variants, and the transmission and infection capacity of SARS-CoV-2 has been enhanced. HCoV-OC43 may be similar to SARS-CoV-2 in terms of genomic structure and function, species evolution, epidemic characteristics and clinical manifestations. In this review, the epidemiology, genomics, phylogenetic evolution and other aspects of HCoV-OC43 and SARS-CoV-2 were analyzed. Such an analysis would be helpful to understand the association and differences between the two viruses, and provide reference for understanding the potential threats of HCoV-OC43.

6.
Front Microbiol ; 13: 895741, 2022.
Article in English | MEDLINE | ID: covidwho-1952425

ABSTRACT

Deltacoronavirus (DCoV) is a genus of coronavirus (CoV) commonly found in avian and swine, but some DCoVs are capable of infecting humans, which causes the concern about interspecies transmission of DCoVs. Thus, monitoring the existence of DCoVs in animals near communities is of great importance for epidemic prevention. Black-headed gulls (Chroicocephalus ridibundus) are common migratory birds inhabiting in most urban and rural wetlands of Yunnan Province, China, which is a typical habitat for black-headed gulls to overwinter. Whether Yunnan black-headed gulls carry CoV has never been determined. In this study, we identified three strains of DCoVs in fecal samples of Yunnan black-headed gulls by reverse-transcriptional PCR and sequenced their whole genomes. Genomic analysis revealed that these three strains shared genomic identity of more than 99%, thus named DCoV HNU4-1, HNU4-2, and HNU4-3; their NSP12 showed high similarity of amino acid sequence to the homologs of falcon coronavirus UAE-HKU27 (HKU27), houbara coronavirus UAE-HKU28 (HKU28), and pigeon coronavirus UAE-HKU29 (HKU29). Since both HKU28 and HKU29 were found in Dubai, there might be cross-border transmission of these avian DCoVs through specific routes. Further coevolutionary analysis supported this speculation that HNU4 (or its ancestors) in black-headed gulls originated from HKU28 (or its homologous strain) in houbara, which was interspecies transmission between two different avian orders. In addition, interspecies transmission of DCoV, from houbara to falcon, pigeon and white-eye, from sparrow to common-magpie, and quail and mammal including porcine and Asian leopard cat, from munia to magpie-robin, was predicted. This is the first report of black-headed gull DCoV in Asia which was highly homolog to other avian DCoVs, and the very "active" host-switching events in DCoV were predicted, which provides important reference for the study of spread and transmission of DCoVs.

7.
Saudi J Biol Sci ; 29(9): 103372, 2022 Sep.
Article in English | MEDLINE | ID: covidwho-1937146

ABSTRACT

The world has been combating different variants of SARS-COV-19 since its first outbreak in Wuhan city. SARS-COV-19 is caused by the coronavirus. The corona virus mutates and becomes more transmissible than earlier variants as the day passes. Till 24 November 2021, SARS-COV-19 has four variants Alpha, Beta, Gamma, and Delta, respectively. Among them, the delta variant caused severe havoc across the world. South Africa registered a new variant with the World Health Organization (WHO) on 24 November 2021, which is much more transmissible than previous variants. The WHO classified it as a variant of concern (VOC) on 26 November 2021 and called it the Greek letter Omicron (B.1.1.529), the fifteenth letter in the alphabet. Here a serious attempt was made to comprehend the omicron variant's origin, nomenclature, characteristics, mutations, the difference between delta and omicron variant, epidemiology, transmission, clinical features, impact on immunity, immune evasion, vaccines efficacy, etc.

8.
Thai Journal of Veterinary Medicine ; 52(2):303-309, 2022.
Article in English | EMBASE | ID: covidwho-1928906

ABSTRACT

FCoV viruses exhibit great genetic diversity, leading to the presence of FIPV-causing variants. Current molecular evolution analysis and genetic variation studies of FCoV in China are predominately focused on gene encoding the spike protein or other structural proteins, while few studies have evaluated genetic variations in nonstructural FCoV genes, which can play an important role in disease pathogenesis. In this study, the gene encoding the open reading frame (ORF) 7b nonstructural FCoV protein of the Chinese Fujian strain FJLY20201 was amplified from the ascitic fluid of a Chinese domestic cat infected with FIPV and compared with ORF 7b from previously published FCoV strains. Multiple sequence alignment revealed that FJLY20201 exhibited high identity with other Chinese FCoV strains. Phylogenetic analyses indicated that the Chinese strains did not differentiate between type I and type II serotypes of FCoV based on S proteins. In addition, they formed clades and differed genetically from strains originating outside China. This study provides the molecular epidemiology data about the ORF 7b genes of FCoV strains in China. Our results show that the identity of ORF 7b genes was closer between the Chinese isolates, and suggest that variation in ORF 7b is more dependent on geographical origin.

9.
J Infect Public Health ; 15(8): 878-891, 2022 Aug.
Article in English | MEDLINE | ID: covidwho-1926679

ABSTRACT

BACKGROUND: With the rapid development of the genomic sequence data for the Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and its variants Delta (B.1.617.2) and Omicron (B.1.1.529), it is vital to successfully identify mutations within the genome. OBJECTIVE: The main objective of the study is to investigate the full-length genome mutation analysis of 157 SARS-CoV-2 and its variant Delta and Omicron isolates. This study also provides possible effects at the structural level to understand the role of mutations and new insights into the evolution of COVID-19 and evaluates the differential level analysis in viral genome sequence among different nations. We have also tried to offer a mutation snapshot for these differences that could help in vaccine formulation. This study utilizes a unique and efficient method of targeting the stable genes for the drug discovery approach. METHODS: Complete genome sequence information of SARS-CoV-2, Delta, and Omicron from online resources were used to predict structure domain identification, data mining, and screening; employing different bioinformatics tools. BioEdit software was used to perform their genomic alignments across countries and a phylogenetic tree as per the confidence of 500 bootstrapping values was constructed. Heterozygosity ratios were determined in-silico. A minimum spanning network (MSN) of selected populations was determined by Bruvo's distance role-based framework. RESULTS: Out of all 157 different strains of SARS-CoV-2 and its variants, and their complete genome sequences from different countries, Corona nucleoca and DUF5515 were observed to be the most conserved domains. All genomes obtained changes in comparison to the Wuhan-Hu-1 strain, mainly in the TRS region (CUAAAC or ACGAAC). We discovered 596 mutations in all genes, with the highest number (321) found in ORF1ab (QHD43415.1), or TRS site mutations found only in ORF7a (1) and ORF10 (2). The Omicron variant has 30 mutations in the Spike protein and has a higher alpha-helix shape (23.46%) than the Delta version (22.03%). T478 was also discovered to be a prevalent polymorphism in Delta and Omicron variations, as well as genomic gaps ranging from 45 to 65aa. All 157 sequences contained variations and conformed to Nei's Genetic distance. We discovered heterozygosity (Hs) 0.01, mean anticipated Hs 0.32, the genetic diversity index (GDI) 0.01943989, and GD within population 0.01266951. The Hedrick value was 0.52324978, the GD coefficient was 0.52324978, the average Hs was 0.01371452, and the GD coefficient was 0.52324978. Among other countries, Brazil has the highest standard error (SE) rate (1.398), whereas Japan has the highest ratio of Nei's gene diversity (0.01). CONCLUSIONS: The study's findings will assist in comprehending the shape and kind of complete genome, their streaming genomic sequences, and mutations in various additions of SARS-CoV-2, as well as its different variant strains like Omicron. These results will provide a scientific basis to design the vaccines and understand the genomic study of these viruses.


Subject(s)
COVID-19 , SARS-CoV-2 , Genomics , Humans , Mutation , Phylogeny , SARS-CoV-2/genetics
10.
African Journal of Infectious Diseases ; 16(2):1-12, 2022.
Article in English | EMBASE | ID: covidwho-1918238

ABSTRACT

Background: Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has infected over 100 million individuals worldwide with diverse impacts on nations. The rising cases of new strains and resultant infection waves create an urgent need to assess the readiness of countries especially in Africa to mitigate the impact on community transmission. This paper delivers a brief synopsis of the novel SARS-CoV-2, emerging cases of new variants reported worldwide, and implications for genetic surveillance of disease transmission in low-and middle-income countries (LMICs) especially Africa. Materials and Methods: Literature search used keywords like SARS-CoV-2;COVID-19 epidemiology;pandemic waves;corona outbreak, clinical syndromes, treatments, prevention and control. Cross-sectional and observational studies published on COVID-19 from 2019 till date of study provided main information sources. Databases such as Web of Science, Embase, PubMed and Google Scholar were utilised. Main findings: Over 220 countries have documented COVID-19 cases with varied severity till date. Before the spikes in resurgence, a highly virulent mutated (>90% fatality rate) novel strain of COVID-19 had been documented. There is very little data to ascertain the impact of the COVID-19 infection waves in LMICs. Discussion: LMICs especially African countries still grapple with significant challenges like inefficient surveillance mechanisms, inadequate vaccination coverage, inadequate enforcement of environmental health strategies, poor health systems etc. Hence, Africa’s fate remains dicey in the face of the dynamic evolution of the SARS-CoV-2 and other identified challenges. Conclusion: The adoption of a multidisciplinary approach to mitigate the impact of emergence of mutant SARS-CoV-2 variants and resurgence of infection spike is recommended.

11.
Microorganisms ; 10(7)2022 Jul 05.
Article in English | MEDLINE | ID: covidwho-1917629

ABSTRACT

Here, we report the emergence of the variant lineage B.1.1.523 that contains a set of mutations including 156_158del, E484K and S494P in the spike protein. E484K and S494P are known to significantly reduce SARS-CoV-2 neutralization by convalescent and vaccinated sera and are considered as mutations of concern. Lineage B.1.1.523 presumably originated in the Russian Federation and spread across European countries with the peak of transmission in April-May 2021. The B.1.1.523 lineage has now been reported from 31 countries. In this article, we analyze the possible origin of this mutation subset and its immune response using in silico methods.

12.
Microbiol Spectr ; : e0141122, 2022 Jun 30.
Article in English | MEDLINE | ID: covidwho-1909615

ABSTRACT

Bats harbor the largest number of coronavirus (CoV) species among mammals, serving as major reservoirs of alphaCoVs and betaCoVs, which can jump between bat species or to different mammalian hosts, including humans. Bat-CoV diversity is correlated with host taxonomic diversity, with the highest number of CoV species found in areas with the highest levels of bat species richness. Although the Americas harbor a unique and distinctive CoV diversity, no cross-species transmission (CST) or phylogeographic analysis has yet been performed. This study analyzes a large sequence data set from across the Americas through a Bayesian framework to understand how codivergence and cross-species transmission have shaped long-term bat-CoV evolution and ultimately identify bat hosts and regions where the risk of CST is the highest. Substantial levels of CST were found only among alphaCoVs. In contrast, cospeciation prevailed along the evolution of betaCoVs. Brazil is the center of diversification for both alpha and betaCoVs, with the highest levels of bat species richness. The bat family Phyllostomidae has played a key role in the evolution of American bat-CoVs, supported by the highest values of host transition rates. Although the conclusions drawn from this study are supported by biological/ecological evidence, it is likely that novel lineages will be discovered, which could also reveal undetected CSTs given that sequences are available from 11 of the 35 countries encompassing the Americas. The findings of this study can be useful for conducting targeted discovery of bat-CoVs in the region, especially in countries of the Americas with no reported sequences. IMPORTANCE Coronaviruses (CoVs) have a strong zoonotic potential due to their high rates of evolvability and their capacity for overcoming host-specific barriers. Bats harbor the largest number of CoV species among mammals, with the highest CoV diversity found in areas with the highest levels of bat species richness. Understanding their origin and patterns of cross-species transmission is crucial for pandemic preparedness. This study aims to understand how bat-CoVs diversify in the Americas, circulate among and transmit between bat families and genera, and ultimately identify bat hosts and regions where the risk of CoV spillover is the highest.

13.
Pakistan Journal of Zoology ; 54(4):1899-1904, 2022.
Article in English | CAB Abstracts | ID: covidwho-1904009

ABSTRACT

Coronavirus consists of single-stranded, enveloped and RNA virus, largest genome among all RNA viruses and has 4 proteins i.e. envelope, spike, nucleocapsid and membrane. Coronaviruses are classified into 4 genera: Alphacoronavirus, Betacoronavirus, Gammacoronavirus and Deltacoronavirus. Betacoronavirus most probably originated from bats and the virus may have jumped to avian species and evolved as Deltacoronavirus group. The avian coronaviruses jumped among other avian species, giving rise to Gammacoronavirus from Deltacoronavirus, while Betacoronavirus may have given rise to Alphacoronavirus. It is known that SARS-CoV-2 belongs to Betacoronavirus. This most similar virus is verified in bat and Malayan Pangolin. Analysis showed that SARS-CoV-2 most probably originated by recombination of both bat and pangolin viruses. Viral protein seroconversion and viral specific nucleotide positive documented in all COVID-19 patients tested provides confirmation of a link between the presence of this virus and the disease.

14.
Virology ; 572: 55-63, 2022 Jul.
Article in English | MEDLINE | ID: covidwho-1895488

ABSTRACT

Porcine bocavirus (PBoV) was first identified in Sweden in 2009. Due to its association with healthy as well as diseased pigs, its role in clinical disease has not been reported yet. In the present study, bocavirus was identified from the intestinal content of a 30-day-old piglet and its whole genome was constructed and phylogenetic analysis was carried on. The pathogenesis of bocavirus was investigated following orogastric inoculation of the colostrum-deprived newborn piglet with bacteria free intestinal content. The bocavirus-inoculated piglets developed diarrhea, shed virus in the rectal swabs from 18 h post inoculation and developed macroscopic and microscopic lesions in small intestine with virus confirmed by conventional PCR. This study experimentally confirmed pathogenicity and characterized bocavirus as the etiological agent of diarrhea in the colostrum-deprived newborn piglets. On phylogenetic analysis, it was observed that this virus has long evolutionary history with subsequent mutation as well as better host adaptation. This study highlights the importance of identifying bocavirus as the etiological agent of viral diarrhea that could threaten livestock, public health as well as economic loss.


Subject(s)
Bocavirus , Parvoviridae Infections , Swine Diseases , Animals , Bocavirus/genetics , China , Diarrhea/veterinary , Evolution, Molecular , Parvoviridae Infections/veterinary , Phylogeny , Swine
15.
Emerg Infect Dis ; 28(8): 1551-1558, 2022 Aug.
Article in English | MEDLINE | ID: covidwho-1892586

ABSTRACT

A COVID-19 outbreak occurred among Cameron Peak Fire responders in Colorado, USA, during August 2020-January 2021. The Cameron Peak Fire was the largest recorded wildfire in Colorado history, lasting August-December 2020. At least 6,123 responders were involved, including 1,260 firefighters in 63 crews who mobilized to the fire camps. A total of 79 COVID-19 cases were identified among responders, and 273 close contacts were quarantined. State and local public health investigated the outbreak and coordinated with wildfire management teams to prevent disease spread. We performed whole-genome sequencing and applied social network analysis to visualize clusters and transmission dynamics. Phylogenetic analysis identified 8 lineages among sequenced specimens, implying multiple introductions. Social network analysis identified spread between and within crews. Strategies such as implementing symptom screening and testing of arriving responders, educating responders about overlapping symptoms of smoke inhalation and COVID-19, improving physical distancing of crews, and encouraging vaccinations are recommended.


Subject(s)
COVID-19 , Firefighters , Wildfires , COVID-19/epidemiology , Colorado/epidemiology , Disease Outbreaks , Humans , Phylogeny
16.
Human Gene ; 33, 2022.
Article in English | EMBASE | ID: covidwho-1885811

ABSTRACT

SARS-CoV-2 inherits a high rate of mutations making it better suited to the host since its fundamental role in evolution is to provide diversity into the genome. This research aims to identify variations in Turkish isolates and predict their impacts on proteins. To identify novel variations and predict their impacts on protein dynamics, in silico methodology was used. The 411 sequences from Turkey were analysed. Secondary structure prediction by Garnier-Osguthorpe-Robson (GOR) was used. To find the effects of identified Spike mutations on protein dynamics, the SARS-CoV-2 structures (PDB:6VYB, 6M0J) were uploaded and predicted by Cutoff Scanning Matrix (mCSM), DynaMut and MutaBind2. To understand the effects of these mutations on Spike protein molecular dynamics (MD) simulation was employed. Turkish sequences were aligned with sequences worldwide by MUSCLE, and phylogenetic analysis was performed via MegaX. The 13 novel mutations were identified, and six of them belong to spike glycoprotein. Ten of these variations revealed alteration in the secondary structure of the protein. Differences of free energy between the reference sequence and six mutants were found below zero for each of six isolates, demonstrating these variations have stabilizing effects on protein structure. Differences in vibrational entropy calculation revealed that three variants have rigidification, while the other three have a flexibility effect. MD simulation revealed that point mutations in spike glycoprotein and RBD:ACE-2 complex cause changes in protein dynamics compared to the wild-type, suggesting possible alterations in binding affinity. The phylogenetic analysis showed Turkish sequences distributed throughout the tree, revealing multiple entrances to Turkey.

17.
Acta Veterinaria Eurasia ; 48(2):117-122, 2022.
Article in English | EMBASE | ID: covidwho-1885087

ABSTRACT

After the identification of Middle East respiratory syndrome coronavirus from camels in Saudi Arabia by 2012, it has been believed that camel is a primary reservoir of Middle East respiratory syndrome coronavirus, and viral transmission from camel to human could occur. The current study is the initial announcement on Middle East respiratory syndrome coronavirus detection from camels in Iran. Middle East respiratory syndrome genome was analyzed by real-time reverse transcription polymerase chain reaction in samples taken from camels that illegally entered Iran. The presence of Middle East respiratory syndrome coronavirus was investigated in nasal and rectal swab samples by real-time reverse transcription polymerase chain reaction using primers specific for upE and ORF 1a genes. Positive samples were then subjected to ORF 1a and N gene-distinct polymerase chain reaction and sequencing. The acquired sequences were applied for phylogenetic analysis in comparison with sequences of related regional human cases and non-regional camel isolates. Nasal swabs from 3 out of 18 camels showed positive results in both real-time reverse transcription polymerase chain reactions. The nucleotide sequencing revealed that N and ORF 1a fragments of the studied viruses had a high level of similarity to the Middle East respiratory syndrome coronaviruses isolated from camels in African countries, Arabian Peninsula, Pakistan, and to those isolated from a person in Iran. The current study is the primary report on the characterization of Middle East respiratory syndrome coronavirus from Iranian camels.

18.
Pathogens ; 11(6)2022 Jun 03.
Article in English | MEDLINE | ID: covidwho-1884298

ABSTRACT

While disease control in racing pigeons and the potential role of pigeons as vectors transmitting viruses to poultry are of importance, there is still a paucity of data concerning the occurrence of coronaviruses in pigeons. In this study, 215 domestic pigeons were tested for the presence of coronaviral genetic material using the nested PCR method, which revealed 57 positive samples (26.51%). The difference in coronavirus prevalence between young and adult pigeons (34.34% and 19.83%, respectively) has been found statistically significant. In contrast, no statistically significant difference has been demonstrated between the prevalence in symptomatic and asymptomatic birds, leaving the influence of coronavirus presence on pigeon health uncertain. Phylogenetic analysis of the RdRp gene fragment allowed us to assign all the obtained strains to the Gammacoronavirus genus and Igacovirus subgenus. The phylogenetic tree plotted using the ML method revealed that those sequences formed a group most similar to pigeon coronavirus strains from China, Finland, and Poland, and to a single strain from a common starling from Poland, which suggests wide geographical distribution of the virus and its possible transmission between various species.

19.
Topics in Antiviral Medicine ; 30(1 SUPPL):301-302, 2022.
Article in English | EMBASE | ID: covidwho-1880119

ABSTRACT

Background: In 2020, France reported 2.7 million cases of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), making it the second most affected European country by the COVID-19 pandemic after the United Kingdom. However, dynamics of SARS-CoV-2 transmissions within France or between France and other countries remains partially characterized. We propose an analysis of these dynamics on multiple scales, from the continents to the French administrative regions. Methods: We produced 736 SARS-CoV-2 sequences from Ile-de-France (Paris area, France) and analyzed them concomitantly with GISAID deposited sequences to elucidate the origins and spread of the virus from January 2020 to December 2020. A total of 4,571 worldwide sequences, including 1,652 French sequences, constituted the final dataset. All sequences were selected to be representative of each country temporal distribution of SARS-CoV-2 to the week resolution. We used a maximum likelihood phylogenetic framework to estimate the most probable temporal and geographic spread of SARS-CoV-2 within France and worldwide. Depending on the geographical focus (France, Europe or worldwide), we pruned the tree accordingly in 1,000 independent replicates. Results: Phylogenetic analysis revealed that, during the 1st French epidemic wave (from March to May), the majority of viruses introduced to France came from North America (USA) and Europe (Spain, Italy, ?). France regularly transmitted to neighboring European countries: Belgium, Germany, Italy and United Kingdom. Contrary to the 1st wave, inter-country transmission events were limited to neighboring countries and intercontinental transmission were almost absent during the French 2nd wave (from September to November). At the French regions-scale, we observed that Ile-de-France (IDF) was the main source of infections for all other French regions during the 1st epidemic wave, with a minor participation of Provence-Alpes-Côte d'Azur (PACA). For the 2nd epidemic wave, PACA was the main source of infections for all other French regions, with a lower participation of IDF and other regions. Conclusion: Overall, our findings allow a more comprehensive representation of SARS-CoV-2 transmission chains related to and within France and the global temporal distribution of those events, in link with control measures applied during the whole 2020 period. IDF and PACA were the main hubs of transmissions in France for the 1st and the 2nd epidemic waves, respectively.

20.
Topics in Antiviral Medicine ; 30(1 SUPPL):314-315, 2022.
Article in English | EMBASE | ID: covidwho-1880037

ABSTRACT

Background: Ending the HIV Epidemic by 2030 initiative includes phylogenetics as a molecular framework to track patterns of HIV spread. In this study, phylogenetics was combined with available epidemiological data to elucidate track evolving trends in HIV-1 spread among Men having Sex with Men (MSM) and Heterosexual (HET) populations in Quebec. Methods: Phylogenetic linkage analysis was performed using MEGA-10 and HIV-TRACE/Microbe-TRACE methodologies. New infections genotyped between 2014-2020 were stratified into groups: i) Subtype B MSM (subtype B male singletons/male-male clusters, n=1812);ii) Subtype B Heterosexual (female singletons/female-male clusters, n=432), including migrants from the Caribbean and Americas;and iii) Non-B subtype (n=737) epidemics. Test requisition data and clinical data from Clinique Actuel (n=141 and 50, 2016-2018) monitored epidemiological features in a subset of newly diagnosed persons. Results: Among MSM, annual new infections declined by 20% and 40% over the 2015-2017 and 2018-2020 periods, respectively. Overall, 45% of new infections in MSM were associated with 20 active large clusters, adding 8-96 infections/clusters from 2014-2020. Clinical data showed 37% newly diagnosed MSM were born outside Canada, 28% of whom were linked to large cluster outbreaks. Among heterosexuals with subtype B infections, there was a 31% increase from 2015-2017 followed by a 36% decline from 2018-2020 post-COVID. Of note, large cluster HET outbreaks occurred in Quebec City, Richelieu, and Northern Quebec Overall, non-B subtype infections remained steady (median 100 annually) over the 2014 to 2020 period. Several non-B subtype clusters reflect the domestic introduction and spread of subtype CRF02- AG variants. Cluster membership and cluster size was associated with recent stage infection, viral sequence recency (based on % mixed base calls) and younger age of members within individual clusters. Conclusion: Annual numbers of new HIV-1 infections have steadily declined among MSM post-2008, concomitant to improved HIV prevention paradigms. Epidemic control among MSM and HET groups has been thwarted by large cluster outbreaks. Recent arrivals to Quebec accounted for a growing number of subtype B and non-B subtype infections. HIV prevention efforts must continue in the post-COVID era, tailored to avert transmission cascades in younger persons and recent migrant populations.

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