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1.
J Virol ; 97(12): e0136923, 2023 Dec 21.
Artículo en Inglés | MEDLINE | ID: mdl-38038429

RESUMEN

IMPORTANCE: Viral host adaptation plays an important role in inter-species transmission of coronaviruses and influenza viruses. Multiple human-adaptive mutations have been identified in influenza viruses but not so far in MERS-CoV that circulates widely in dromedary camels in the Arabian Peninsula leading to zoonotic transmission. Here, we analyzed clade B MERS-CoV sequences and identified an amino acid substitution L232F in nsp6 that repeatedly occurs in human MERS-CoV. Using a loss-of-function reverse genetics approach, we found the nsp6 L232F conferred increased viral replication competence in vitro, in cultures of the upper human respiratory tract ex vivo, and in lungs of mice infected in vivo. Our results showed that nsp6 L232F may be an adaptive mutation associated with zoonotic transmission of MERS-CoV. This study highlighted the capacity of MERS-CoV to adapt to transmission to humans and also the need for continued surveillance of MERS-CoV in camels.


Asunto(s)
Infecciones por Coronavirus , Coronavirus del Síndrome Respiratorio de Oriente Medio , Proteínas no Estructurales Virales , Animales , Humanos , Ratones , Sustitución de Aminoácidos , Camelus , Infecciones por Coronavirus/virología , Coronavirus del Síndrome Respiratorio de Oriente Medio/genética , Mutación , Proteínas no Estructurales Virales/genética
2.
PLoS Pathog ; 18(5): e1010150, 2022 05.
Artículo en Inglés | MEDLINE | ID: mdl-35536868

RESUMEN

Most of our understanding of the ecology and evolution of avian influenza A virus (AIV) in wild birds is derived from studies conducted in the northern hemisphere on waterfowl, with a substantial bias towards dabbling ducks. However, relevant environmental conditions and patterns of avian migration and reproduction are substantially different in the southern hemisphere. Through the sequencing and analysis of 333 unique AIV genomes collected from wild birds collected over 15 years we show that Australia is a global sink for AIV diversity and not integrally linked with the Eurasian gene pool. Rather, AIV are infrequently introduced to Australia, followed by decades of isolated circulation and eventual extinction. The number of co-circulating viral lineages varies per subtype. AIV haemagglutinin (HA) subtypes that are rarely identified at duck-centric study sites (H8-12) had more detected introductions and contemporary co-circulating lineages in Australia. Combined with a lack of duck migration beyond the Australian-Papuan region, these findings suggest introductions by long-distance migratory shorebirds. In addition, on the available data we found no evidence of directional or consistent patterns in virus movement across the Australian continent. This feature corresponds to patterns of bird movement, whereby waterfowl have nomadic and erratic rainfall-dependant distributions rather than consistent intra-continental migratory routes. Finally, we detected high levels of virus gene segment reassortment, with a high diversity of AIV genome constellations across years and locations. These data, in addition to those from other studies in Africa and South America, clearly show that patterns of AIV dynamics in the Southern Hemisphere are distinct from those in the temperate north.


Asunto(s)
Virus de la Influenza A , Gripe Aviar , Animales , Animales Salvajes , Australia/epidemiología , Aves , Patos , Variación Genética , Virus de la Influenza A/genética , Gripe Aviar/epidemiología , Filogenia
3.
Int J Mol Sci ; 25(5)2024 Feb 23.
Artículo en Inglés | MEDLINE | ID: mdl-38473829

RESUMEN

CoronaVac immunogenicity decreases with time, and we aimed to investigate whether gut microbiota associate with longer-term immunogenicity of CoronaVac. This was a prospective cohort study recruiting two-dose CoronaVac recipients from three centres in Hong Kong. We collected blood samples at baseline and day 180 after the first dose and used chemiluminescence immunoassay to test for neutralizing antibodies (NAbs) against the receptor-binding domain (RBD) of wild-type SARS-CoV-2 virus. We performed shotgun metagenomic sequencing performed on baseline stool samples. The primary outcome was the NAb seroconversion rate (seropositivity defined as NAb ≥ 15AU/mL) at day 180. Linear discriminant analysis [LDA] effect size analysis was used to identify putative bacterial species and metabolic pathways. A univariate logistic regression model was used to derive the odds ratio (OR) of seropositivity with bacterial species. Of 119 CoronaVac recipients (median age: 53.4 years [IQR: 47.8-61.3]; male: 39 [32.8%]), only 8 (6.7%) remained seropositive at 6 months after vaccination. Bacteroides uniformis (log10LDA score = 4.39) and Bacteroides eggerthii (log10LDA score = 3.89) were significantly enriched in seropositive than seronegative participants. Seropositivity was associated with B. eggerthii (OR: 5.73; 95% CI: 1.32-29.55; p = 0.022) and B. uniformis with borderline significance (OR: 3.27; 95% CI: 0.73-14.72; p = 0.110). Additionally, B. uniformis was positively correlated with most enriched metabolic pathways in seropositive vaccinees, including the superpathway of adenosine nucleotide de novo biosynthesis I (log10LDA score = 2.88) and II (log10LDA score = 2.91), as well as pathways related to vitamin B biosynthesis, all of which are known to promote immune functions. In conclusion, certain gut bacterial species (B. eggerthii and B. uniformis) and metabolic pathways were associated with longer-term CoronaVac immunogenicity.


Asunto(s)
Vacunas contra la COVID-19 , Microbioma Gastrointestinal , Vacunas de Productos Inactivados , Humanos , Masculino , Persona de Mediana Edad , Estudios Prospectivos , Adenosina , Anticuerpos Neutralizantes , Anticuerpos Antivirales
4.
N Engl J Med ; 382(13): 1199-1207, 2020 03 26.
Artículo en Inglés | MEDLINE | ID: mdl-31995857

RESUMEN

BACKGROUND: The initial cases of novel coronavirus (2019-nCoV)-infected pneumonia (NCIP) occurred in Wuhan, Hubei Province, China, in December 2019 and January 2020. We analyzed data on the first 425 confirmed cases in Wuhan to determine the epidemiologic characteristics of NCIP. METHODS: We collected information on demographic characteristics, exposure history, and illness timelines of laboratory-confirmed cases of NCIP that had been reported by January 22, 2020. We described characteristics of the cases and estimated the key epidemiologic time-delay distributions. In the early period of exponential growth, we estimated the epidemic doubling time and the basic reproductive number. RESULTS: Among the first 425 patients with confirmed NCIP, the median age was 59 years and 56% were male. The majority of cases (55%) with onset before January 1, 2020, were linked to the Huanan Seafood Wholesale Market, as compared with 8.6% of the subsequent cases. The mean incubation period was 5.2 days (95% confidence interval [CI], 4.1 to 7.0), with the 95th percentile of the distribution at 12.5 days. In its early stages, the epidemic doubled in size every 7.4 days. With a mean serial interval of 7.5 days (95% CI, 5.3 to 19), the basic reproductive number was estimated to be 2.2 (95% CI, 1.4 to 3.9). CONCLUSIONS: On the basis of this information, there is evidence that human-to-human transmission has occurred among close contacts since the middle of December 2019. Considerable efforts to reduce transmission will be required to control outbreaks if similar dynamics apply elsewhere. Measures to prevent or reduce transmission should be implemented in populations at risk. (Funded by the Ministry of Science and Technology of China and others.).


Asunto(s)
Betacoronavirus , Infecciones por Coronavirus/epidemiología , Infecciones por Coronavirus/transmisión , Transmisión de Enfermedad Infecciosa/estadística & datos numéricos , Epidemias , Periodo de Incubación de Enfermedades Infecciosas , Neumonía Viral/epidemiología , Neumonía Viral/transmisión , Adolescente , Adulto , Anciano , Betacoronavirus/genética , COVID-19 , China/epidemiología , Control de Enfermedades Transmisibles/métodos , Infecciones por Coronavirus/virología , Transmisión de Enfermedad Infecciosa/prevención & control , Epidemias/prevención & control , Femenino , Humanos , Incidencia , Masculino , Persona de Mediana Edad , Pandemias , Neumonía Viral/virología , Reacción en Cadena de la Polimerasa , SARS-CoV-2 , Adulto Joven
5.
Environ Sci Technol ; 57(26): 9713-9721, 2023 07 04.
Artículo en Inglés | MEDLINE | ID: mdl-37310875

RESUMEN

Surveillance of antibiotic resistance genes (ARGs) has been increasingly conducted in environmental sectors to complement the surveys in human and animal sectors under the "One-Health" framework. However, there are substantial challenges in comparing and synthesizing the results of multiple studies that employ different test methods and approaches in bioinformatic analysis. In this article, we consider the commonly used quantification units (ARG copy per cell, ARG copy per genome, ARG density, ARG copy per 16S rRNA gene, RPKM, coverage, PPM, etc.) for profiling ARGs and suggest a universal unit (ARG copy per cell) for reporting such biological measurements of samples and improving the comparability of different surveillance efforts.


Asunto(s)
Antibacterianos , Genes Bacterianos , Animales , Humanos , Antibacterianos/farmacología , ARN Ribosómico 16S/genética , Farmacorresistencia Microbiana/genética , Metagenómica/métodos
6.
Emerg Infect Dis ; 28(6): 1276-1278, 2022 06.
Artículo en Inglés | MEDLINE | ID: mdl-35394420

RESUMEN

We studied SARS-CoV-2 genomes from travelers arriving in Hong Kong during November 2021-February 2022. In addition to Omicron and Delta variants, we detected a BA.1/BA.2 recombinant with a breakpoint near the 5' end of the spike gene in 2 epidemiologically linked case-patients. Continued surveillance for SARS-CoV-2 recombinants is needed.


Asunto(s)
COVID-19 , Orthopoxvirus , COVID-19/epidemiología , Hong Kong/epidemiología , Humanos , SARS-CoV-2/genética
7.
Annu Rev Genomics Hum Genet ; 17: 193-218, 2016 08 31.
Artículo en Inglés | MEDLINE | ID: mdl-27216777

RESUMEN

The emergence and reemergence of rapidly evolving RNA viruses-particularly those responsible for respiratory diseases, such as influenza viruses and coronaviruses-pose a significant threat to global health, including the potential of major pandemics. Importantly, recent advances in high-throughput genome sequencing enable researchers to reveal the genomic diversity of these viral pathogens at much lower cost and with much greater precision than they could before. In particular, the genome sequence data generated allow inferences to be made on the molecular basis of viral emergence, evolution, and spread in human populations in real time. In this review, we introduce recent computational methods that analyze viral genomic data, particularly in combination with metadata such as sampling time, geographic location, and virulence. We then outline the insights these analyses have provided into the fundamental patterns and processes of evolution and emergence in human respiratory RNA viruses, as well as the major challenges in such genomic analyses.


Asunto(s)
Genoma Humano/genética , Virus ARN/genética , ARN/genética , Sistema Respiratorio/virología , Biología Computacional , Evolución Molecular , Variación Genética , Humanos , Filogenia , Virus ARN/patogenicidad
8.
Ecol Lett ; 21(2): 253-263, 2018 02.
Artículo en Inglés | MEDLINE | ID: mdl-29207441

RESUMEN

Accumulating evidence indicates that biodiversity has an important impact on parasite evolution and emergence. The vast majority of studies in this area have only considered the diversity of species within an environment as an overall measure of biodiversity, overlooking the role of genetic diversity within a particular host species. Although theoretical models propose that host genetic diversity in part shapes that of the infecting parasite population, and hence modulates the risk of parasite emergence, this effect has seldom been tested empirically. Using Rabies virus (RABV) as a model parasite, we provide evidence that greater host genetic diversity increases both parasite genetic diversity and the likelihood of a host being a donor in RABV cross-species transmission events. We conclude that host genetic diversity may be an important determinant of parasite evolution and emergence.


Asunto(s)
Biodiversidad , Variación Genética , Virus de la Rabia , Animales , Especificidad del Huésped , Parásitos , Virus de la Rabia/genética
9.
Curr Top Microbiol Immunol ; 370: 57-68, 2013.
Artículo en Inglés | MEDLINE | ID: mdl-21948002

RESUMEN

The pig is one of the main hosts of influenza A viruses and plays important roles in shaping the current influenza ecology. The occurrence of the 2009 H1N1 pandemic influenza virus demonstrated that pigs could independently facilitate the genesis of a pandemic influenza strain. Genetic analyses revealed that this virus was derived by reassortment between at least two parent swine influenza viruses (SIV), from the northern American triple reassortant H1N2 (TR) and European avian-like H1N1 (EA) lineages. The movement of live pigs between different continents and subsequent virus establishment are preconditions for such a reassortment event to occur. Asia, especially China, has the largest human and pig populations in the world, and seems to be the only region frequently importing pigs from other continents. Virological surveillance revealed that not only classical swine H1N1 (CS), and human-origin H3N2 viruses circulated, but all of the EA, TR and their reassortant variants were introduced into and co-circulated in pigs in this region. Understanding the long-term evolution and history of SIV in Asia would provide insights into the emergence of influenza viruses with epidemic potential in swine and humans.


Asunto(s)
Epidemias/historia , Infecciones por Orthomyxoviridae/veterinaria , Orthomyxoviridae/aislamiento & purificación , Enfermedades de los Porcinos/historia , Enfermedades de los Porcinos/virología , Animales , Asia/epidemiología , Historia del Siglo XX , Historia del Siglo XXI , Humanos , Subtipo H1N1 del Virus de la Influenza A/genética , Subtipo H1N1 del Virus de la Influenza A/aislamiento & purificación , Subtipo H1N2 del Virus de la Influenza A/genética , Subtipo H1N2 del Virus de la Influenza A/aislamiento & purificación , Subtipo H3N2 del Virus de la Influenza A/genética , Gripe Humana/epidemiología , Gripe Humana/historia , Gripe Humana/virología , Orthomyxoviridae/genética , Infecciones por Orthomyxoviridae/epidemiología , Infecciones por Orthomyxoviridae/historia , Infecciones por Orthomyxoviridae/virología , Porcinos , Enfermedades de los Porcinos/epidemiología
10.
J Virol ; 86(4): 2375-8, 2012 Feb.
Artículo en Inglés | MEDLINE | ID: mdl-22171260

RESUMEN

The 2009 pandemic influenza virus (pdm/09) has been frequently introduced to pigs and has reassorted with other swine viruses. Recently, H3N2 reassortants with pdm/09-like internal genes were isolated in Guangxi and Hong Kong, China. Genetic and epidemiological analyses suggest that these viruses have circulated in swine for some time. This is the first evidence that swine reassortant viruses with pdm/09-like genes may have become established in the field, altering the landscape of human and swine influenza.


Asunto(s)
Subtipo H1N1 del Virus de la Influenza A/genética , Subtipo H3N2 del Virus de la Influenza A/genética , Infecciones por Orthomyxoviridae/veterinaria , Virus Reordenados/aislamiento & purificación , Enfermedades de los Porcinos/virología , Animales , China/epidemiología , Subtipo H1N1 del Virus de la Influenza A/clasificación , Subtipo H1N1 del Virus de la Influenza A/aislamiento & purificación , Subtipo H3N2 del Virus de la Influenza A/clasificación , Subtipo H3N2 del Virus de la Influenza A/aislamiento & purificación , Datos de Secuencia Molecular , Infecciones por Orthomyxoviridae/epidemiología , Infecciones por Orthomyxoviridae/virología , Pandemias , Filogenia , Virus Reordenados/clasificación , Virus Reordenados/genética , Porcinos , Enfermedades de los Porcinos/epidemiología , Proteínas Virales/genética
11.
J Gastroenterol Hepatol ; 28(10): 1624-31, 2013 Oct.
Artículo en Inglés | MEDLINE | ID: mdl-23800182

RESUMEN

BACKGROUND AND AIM: In irritable bowel syndrome (IBS), the gut microbiota may be altered. Probiotic bacteria appear to be therapeutically effective. We characterized the mucosa-associated microbiota, and determined the clinical and microbiological effects of orally administered probiotic bacteria, in patients with IBS. METHODS: Mucosal microbiota from rectal biopsies of IBS patients and controls were assessed on the V1 and V2 variable regions of the 16S ribosomal RNA gene amplified using 454 pyrosequencing. Clinical symptoms and changes in mucosal microbiota were assessed in IBS patients before and after 4 weeks of treatment with probiotic mix VSL#3. RESULTS: Ten IBS subjects (eight female; mean age 46 years) were included. At week 4 of probiotic therapy, six patients showed symptom improvement on global symptom assessment compared with baseline (P = 0.031). Before therapy, intestinal microbiota of IBS subjects differed significantly from that of healthy controls, with less diversity and evenness than controls (n = 9; P < 0.05), increased abundance of Bacteroidetes (P = 0.014) and Synegitestes (P = 0.017), and reduced abundance of Actinobacteria (P = 0.004). The classes Flavobacteria (P = 0.028) and Epsilonproteobacteria (P = 0.017) were less enriched in IBS. Abundance differences were largely consistent from the phylum to genus level. Probiotic treatment in IBS patients was associated with a significant reduction of the genus Bacteroides (all taxonomy levels; P < 0.05) to levels similar to that of controls. CONCLUSION: In this pilot study, global and deep molecular analysis demonstrates an altered mucosal microbiota composition in IBS. Probiotic leads to detectable changes in the microbiota. These effects of probiotic bacteria may contribute to their therapeutic benefit.


Asunto(s)
Bacterias/aislamiento & purificación , Mucosa Intestinal/microbiología , Síndrome del Colon Irritable/microbiología , Probióticos/administración & dosificación , Administración Oral , Adulto , Bacterias/genética , Femenino , Genes Bacterianos/genética , Humanos , Síndrome del Colon Irritable/terapia , Masculino , Persona de Mediana Edad , Filogenia , Reacción en Cadena de la Polimerasa , ARN Ribosómico 16S
12.
Virus Evol ; 9(1): veac125, 2023.
Artículo en Inglés | MEDLINE | ID: mdl-36694817

RESUMEN

Virus emergence may occur through interspecies transmission and recombination of viruses coinfecting a host, with potential to pair novel and adaptive gene combinations. Camels are known to harbor diverse ribonucleic acid viruses with zoonotic and epizootic potential. Among them, astroviruses are of particular interest due to their cross-species transmission potential and endemicity in diverse host species, including humans. We conducted a molecular epidemiological survey of astroviruses in dromedaries from Saudi Arabia and Bactrian camels from Inner Mongolia, China. Herein, we deployed a hybrid sequencing approach coupling deep sequencing with rapid amplification of complementary deoxyribonucleic acid ends to characterize two novel Bactrian and eight dromedary camel astroviruses, including both partial and complete genomes. Our reported sequences expand the known diversity of dromedary camel astroviruses, highlighting potential recombination events among the astroviruses of camelids and other host species. In Bactrian camels, we detected partially conserved gene regions bearing resemblance to human astrovirus types 1, 4, and 8 although we were unable to recover complete reading frames from these samples. Continued surveillance of astroviruses in camelids, particularly Bactrian species and associated livestock, is highly recommended to identify patterns of cross-species transmission and to determine any epizootic threats and zoonotic risks posed to humans. Phylogenomic approaches are needed to investigate complex patterns of recombination among the astroviruses and to infer their evolutionary history across diverse host species.

13.
Antibiotics (Basel) ; 12(3)2023 Feb 23.
Artículo en Inglés | MEDLINE | ID: mdl-36978313

RESUMEN

BACKGROUND: Sri Lanka is a low-income country, as defined by the World Bank. The country suffered further economic downturn during the COVID-19 pandemic. This situation adversely affected the prioritization of policies and programs around healthcare and public health. In particular, inflation, fuel prices, and shortage of food supplies increased struggles to implement antimicrobial resistance (AMR) programs. However, in the long run, it is crucial to gather data and evidence to plan AMR policies and track interventions. (1) Aim: To establish and reiterate the importance of prioritizing AMR programs in the One Health framework, the Fleming Fellows collected and studied antimicrobial use/consumption (AMU/AMC) and resistance (AMR) in humans, food-producing animals, and the environment. (2) Methods: A systematic and cross-sectional study was conducted between 2019 and 2021. By way of coordinating an AMU/AMC and AMR prevalence study across six agencies from human health and food-producing animal sectors, the authors established a field epidemiology study, laboratory testing, and data processing at their institutions. AMU/AMC patterns were surveyed using questionnaires and interviews, while AMR samples were collected for antibiotic susceptibility tests and genomic tests. Samples were tested for phenotypic and genotypic resistance. (3) Results: In human samples, resistance was highest to beta-lactam antibiotics. In non-human samples, resistance was highest to erythromycin, a highest-priority, critically important antibiotic defined by the World Health Organization. From government records, tylosin was sold the most in the food-producing animal sector. (4) Conclusions: Sri Lanka AMU and AMR trends in human and non-human sectors can be ascertained by a One Health framework. Further coordinated, consistent, and sustainable planning is feasible, and can help implement an AMU/AMR surveillance system in Sri Lanka.

14.
Nat Commun ; 14(1): 1793, 2023 03 31.
Artículo en Inglés | MEDLINE | ID: mdl-37002233

RESUMEN

Viral and host factors can shape SARS-CoV-2 evolution. However, little is known about lineage-specific and vaccination-specific mutations that occur within individuals. Here, we analysed deep sequencing data from 2,820 SARS-CoV-2 respiratory samples with different viral lineages to describe the patterns of within-host diversity under different conditions, including vaccine-breakthrough infections. In unvaccinated individuals, variant of Concern (VOC) Alpha, Delta, and Omicron respiratory samples were found to have higher within-host diversity and were under neutral to purifying selection at the full genome level compared to non-VOC SARS-CoV-2. Breakthrough infections in 2-dose or 3-dose Comirnaty and CoronaVac vaccinated individuals did not increase levels of non-synonymous mutations and did not change the direction of selection pressure. Vaccine-induced antibody or T cell responses did not appear to have significant impact on within-host SARS-CoV-2 sequence diversification. Our findings suggest that vaccination does not increase exploration of SARS-CoV-2 protein sequence space and may not facilitate emergence of viral variants.


Asunto(s)
COVID-19 , Humanos , COVID-19/epidemiología , COVID-19/prevención & control , SARS-CoV-2/genética , Anticuerpos Antivirales , Infección Irruptiva , Vacunas contra la COVID-19 , Mutación
15.
J Virol ; 85(20): 10432-9, 2011 Oct.
Artículo en Inglés | MEDLINE | ID: mdl-21849442

RESUMEN

Pigs are considered to be intermediate hosts and "mixing vessels," facilitating the genesis of pandemic influenza viruses, as demonstrated by the emergence of the 2009 H1N1 pandemic (pdm/09) virus. The prevalence and repeated introduction of the pdm/09 virus into pigs raises the possibility of generating novel swine influenza viruses with the potential to infect humans. To address this, an active influenza surveillance program was conducted with slaughtered pigs in abattoirs in southern China. Over 50% of the pigs tested were found to be seropositive for one or more H1 influenza viruses, most commonly pdm/09-like viruses. Out of 36 virus isolates detected, one group of novel reassortants had Eurasian avian-like swine H1N1 surface genes and pdm/09 internal genes. Animal experiments showed that this virus transmitted effectively from pig to pig and from pig to ferret, and it could also replicate in ex vivo human lung tissue. Immunization against the 2009 pandemic virus gave only partial protection to ferrets. The continuing prevalence of the pdm/09 virus in pigs could lead to the genesis of novel swine reassortant viruses with the potential to infect humans.


Asunto(s)
Virus de la Influenza A/genética , Infecciones por Orthomyxoviridae/virología , Virus Reordenados/genética , Porcinos/virología , Animales , China , Hurones , Humanos , Técnicas In Vitro , Virus de la Influenza A/clasificación , Virus de la Influenza A/aislamiento & purificación , Virus de la Influenza A/patogenicidad , Pulmón/virología , Masculino , Datos de Secuencia Molecular , Infecciones por Orthomyxoviridae/transmisión , ARN Viral/genética , Virus Reordenados/clasificación , Virus Reordenados/aislamiento & purificación , Virus Reordenados/patogenicidad , Análisis de Secuencia de ADN
16.
Res Sq ; 2022 Aug 11.
Artículo en Inglés | MEDLINE | ID: mdl-35982671

RESUMEN

Viral and host factors can shape SARS-CoV-2 within-host viral diversity and virus evolution. However, little is known about lineage-specific and vaccination-specific mutations that occur within individuals. Here we analysed deep sequencing data from 2,146 SARS-CoV-2 samples with different viral lineages to describe the patterns of within-host diversity in different conditions, including vaccine-breakthrough infections. Variant of Concern (VOC) Alpha, Delta, and Omicron samples were found to have higher within-host nucleotide diversity while being under weaker purifying selection at full genome level compared to non-VOC SARS-CoV-2 viruses. Breakthrough Delta and Omicron infections in Comirnaty and CoronaVac vaccinated individuals appeared to have higher within-host purifying selection at the full-genome and/or Spike gene levels. Vaccine-induced antibody or T cell responses did not appear to have significant impact on within-host SARS-CoV-2 evolution. Our findings suggest that vaccination does not increase SARS-CoV-2 protein sequence space and may not facilitate emergence of more viral variants.

17.
Pathogens ; 12(1)2022 Dec 26.
Artículo en Inglés | MEDLINE | ID: mdl-36678384

RESUMEN

Clade 2.3.4.4 H5Nx influenza viruses have further diversified into several subclades. Sub-clade 2.3.4.4b H5N1 viruses have been widely circulating in wild birds and detected in Europe, Africa, Asia, and North America since October 2020. In this study, we report the first detection of highly pathogenic avian influenza H5N1 clade 2.3.4.4b viruses in wild birds and domestic ducks from live bird markets in Egypt. Phylogenetic analysis revealed that the Egyptian H5N1 virus retained the genomic composition of Eurasian strains. Mutations in the viral proteins associated with zoonotic potential and pathogenicity were detected in Egyptian isolates. Egypt is considered a hot spot for the evolution of the influenza virus, so active surveillance of avian influenza viruses in Egypt is warranted.

18.
Nat Commun ; 13(1): 736, 2022 02 08.
Artículo en Inglés | MEDLINE | ID: mdl-35136039

RESUMEN

Hong Kong employed a strategy of intermittent public health and social measures alongside increasingly stringent travel regulations to eliminate domestic SARS-CoV-2 transmission. By analyzing 1899 genome sequences (>18% of confirmed cases) from 23-January-2020 to 26-January-2021, we reveal the effects of fluctuating control measures on the evolution and epidemiology of SARS-CoV-2 lineages in Hong Kong. Despite numerous importations, only three introductions were responsible for 90% of locally-acquired cases. Community outbreaks were caused by novel introductions rather than a resurgence of circulating strains. Thus, local outbreak prevention requires strong border control and community surveillance, especially during periods of less stringent social restriction. Non-adherence to prolonged preventative measures may explain sustained local transmission observed during wave four in late 2020 and early 2021. We also found that, due to a tight transmission bottleneck, transmission of low-frequency single nucleotide variants between hosts is rare.


Asunto(s)
COVID-19/epidemiología , SARS-CoV-2/genética , COVID-19/transmisión , COVID-19/virología , Genómica , Hong Kong/epidemiología , Humanos , Salud Pública , SARS-CoV-2/aislamiento & purificación , SARS-CoV-2/fisiología , Viaje
19.
Int J Infect Dis ; 104: 132-138, 2021 Mar.
Artículo en Inglés | MEDLINE | ID: mdl-33359440

RESUMEN

BACKGROUND: The ongoing coronavirus disease 2019 (COVID-19) pandemic has caused a tremendous health burden and impact on the world economy. The UK Government implemented the biggest lockdown of society during peacetime in British history at the end of March 2020, aiming to contain the rapid spread of the virus. The UK lockdown was maintained for 7 weeks, but the effectiveness of the control measures in suppressing disease transmission remains incompletely understood. METHODS: A Bayesian SEIR (susceptible-exposed-infected-removed) epidemiological model was used to rebuild the local transmission dynamics of the spread of COVID-19 in nine regions of England. RESULTS: The basic reproduction number (R0) in England was found to be relatively high compared with China. The estimate of the temporally varying effective reproduction number (Rt) suggests that the control measures, especially the forced lockdown, were effective to reduce transmissibility and curb the COVID-19 epidemic. Although the overall incidence rate in the UK has declined, forecasting highlights the possibility of a second epidemic wave in several regions. CONCLUSION: This study enhances understanding of the current outbreak and the effectiveness of control measures in the UK.


Asunto(s)
COVID-19/transmisión , Predicción , Pandemias , SARS-CoV-2/aislamiento & purificación , Número Básico de Reproducción , Teorema de Bayes , COVID-19/epidemiología , COVID-19/prevención & control , COVID-19/virología , Inglaterra/epidemiología , Femenino , Humanos , Incidencia , Masculino , Modelos Teóricos , SARS-CoV-2/genética
20.
Nat Med ; 27(3): 388-395, 2021 03.
Artículo en Inglés | MEDLINE | ID: mdl-33723452

RESUMEN

Epidemic nowcasting broadly refers to assessing the current state by understanding key pathogenic, epidemiologic, clinical and socio-behavioral characteristics of an ongoing outbreak. Its primary objective is to provide situational awareness and inform decisions on control responses. In the event of large-scale sustained emergencies, such as the COVID-19 pandemic, scientists need to constantly update their aims and analytics with respect to the rapidly evolving emergence of new questions, data and findings in order to synthesize real-time evidence for policy decisions. In this Perspective, we share our views on the functional aims, rationale, data requirements and challenges of nowcasting at different stages of an epidemic, drawing on the ongoing COVID-19 experience. We highlight how recent advances in the computational and laboratory sciences could be harnessed to complement traditional approaches to enhance the scope, timeliness, reliability and utility of epidemic nowcasting.


Asunto(s)
COVID-19/epidemiología , Enfermedades Transmisibles Emergentes/epidemiología , Epidemias , Predicción/métodos , Enfermedades Transmisibles Emergentes/diagnóstico , Brotes de Enfermedades/historia , Epidemias/historia , Historia del Siglo XXI , Humanos , Pandemias , Reproducibilidad de los Resultados
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