Showing papers on "Outbreak published in 2023"

Outbreak.info genomic reports: scalable and dynamic surveillance of SARS-CoV-2 variants and mutations

Abstract: The emergence of SARS-CoV-2 variants has prompted the need for near real-time genomic surveillance to inform public health interventions. In response to this need, the global scientific community, through unprecedented effort, has sequenced over 7 million genomes as of December 2021. The extraordinarily high sampling rate provides a unique opportunity to track the evolution of the virus in near real-time. Here, we present outbreak.info, a platform that can be used to track over 40 million combinations of PANGO lineages and individual mutations, across over 7,000 locations, to provide insights for researchers, public health officials, and the general public. We describe the data pipelines that enable the scalable ingestion and standardization of heterogeneous data on SARS-CoV-2 variants, the server infrastructure that enables the dissemination of the processed data, and the client-side applications that provide intuitive visualizations of the underlying data.

Highly pathogenic avian influenza A(H5N1) virus infection in farmed minks, Spain, October 2022

Abstract: In October 2022, an outbreak in Europe of highly pathogenic avian influenza (HPAI) A(H5N1) in intensively farmed minks occurred in northwest Spain. A single mink farm hosting more than 50,000 minks was involved. The identified viruses belong to clade 2.3.4.4b, which is responsible of the ongoing epizootic in Europe. An uncommon mutation (T271A) in the PB2 gene with potential public health implications was found. Our investigations indicate onward mink transmission of the virus may have occurred in the affected farm.

Viral loads in clinical samples of men with monkeypox virus infection: a French case series

Abstract: BackgroundMonkeypox virus (MPXV) is currently spreading among men who have sex with men, outside of sub-Saharan Africa, and close contact during sex seems to be one of the key pathways of viral transmission in the current outbreak. Our aim was to describe the distribution of MPXV in the human body, as it might play a role in its dissemination through sexual contact.MethodsThe study population in this case series consisted of patients with confirmed MPXV infection attending the Pitié-Salpêtrière Hospital (Paris, France), who had been sampled from multiple anatomical sites, including skin, anus, throat, blood, urine, and semen, at diagnosis and 2 weeks later. We compared the proportion of positive samples and MPXV viral loads (given as PCR cycle thresholds [Ct]) between anatomical sites, and between day 0 (D0) and D14.FindingsOverall, 356 samples were collected between May 20 and June 13, 2022, from 50 men with a median age of 34 years (IQR 29–40). 22 (44%) of the 50 men were classified as HIV-negative on day (D)0, and 22 (44%) were living with HIV. At D0, MPXV detection was more frequent from skin (44 [88%] of 50), anus (30 [71%] of 42), and throat (36 [77%] of 47) than from blood (13 [29%] of 45), urine (nine [22%] of 41), or semen (13 [54%] of 24). Viral loads were significantly higher from skin lesions (Ct 19·8) and anal samples (Ct 20·9) than from throat (Ct 27·2), blood (Ct 32·8), urine (31·1), or semen samples (Ct 27·8). When analysing the 107 samples taken from 24 patients at D14, the proportion of positive samples strongly decreased between D0 and D14 at all sites: skin (four [22%] of 18), anus (two [9%] of 22), throat (none of 21), blood (one [5%] of 21), urine (none of 14), and semen (two [9%] of 11).InterpretationThese data contribute to a better understanding of how the virus might spread between sexual partners over a relatively short period of time. High MPXV viral loads from skin and mucosa, including genital and anal sites, suggest that transmission most likely occurs through direct body contact rather than through the respiratory route or contact with body fluids, which should help to refine the prevention messages delivered to individuals most exposed to the virus.FundingNone. Monkeypox virus (MPXV) is currently spreading among men who have sex with men, outside of sub-Saharan Africa, and close contact during sex seems to be one of the key pathways of viral transmission in the current outbreak. Our aim was to describe the distribution of MPXV in the human body, as it might play a role in its dissemination through sexual contact. The study population in this case series consisted of patients with confirmed MPXV infection attending the Pitié-Salpêtrière Hospital (Paris, France), who had been sampled from multiple anatomical sites, including skin, anus, throat, blood, urine, and semen, at diagnosis and 2 weeks later. We compared the proportion of positive samples and MPXV viral loads (given as PCR cycle thresholds [Ct]) between anatomical sites, and between day 0 (D0) and D14. Overall, 356 samples were collected between May 20 and June 13, 2022, from 50 men with a median age of 34 years (IQR 29–40). 22 (44%) of the 50 men were classified as HIV-negative on day (D)0, and 22 (44%) were living with HIV. At D0, MPXV detection was more frequent from skin (44 [88%] of 50), anus (30 [71%] of 42), and throat (36 [77%] of 47) than from blood (13 [29%] of 45), urine (nine [22%] of 41), or semen (13 [54%] of 24). Viral loads were significantly higher from skin lesions (Ct 19·8) and anal samples (Ct 20·9) than from throat (Ct 27·2), blood (Ct 32·8), urine (31·1), or semen samples (Ct 27·8). When analysing the 107 samples taken from 24 patients at D14, the proportion of positive samples strongly decreased between D0 and D14 at all sites: skin (four [22%] of 18), anus (two [9%] of 22), throat (none of 21), blood (one [5%] of 21), urine (none of 14), and semen (two [9%] of 11). These data contribute to a better understanding of how the virus might spread between sexual partners over a relatively short period of time. High MPXV viral loads from skin and mucosa, including genital and anal sites, suggest that transmission most likely occurs through direct body contact rather than through the respiratory route or contact with body fluids, which should help to refine the prevention messages delivered to individuals most exposed to the virus.

Coronavirus variant XBB.1.5 rises in the United States — is it a global threat?

Abstract: Prevalence of a new subvariant of Omicron is increasing, but whether it will cause a big surge in infections or hospitalizations isn’t clear. Prevalence of a new subvariant of Omicron is increasing, but whether it will cause a big surge in infections or hospitalizations isn’t clear.

Estimating the transmission dynamics of SARS-CoV-2 Omicron BF.7 in Beijing after adjustment of the zero-COVID policy in November–December 2022

Abstract: We tracked the effective reproduction number (Rt) of the predominant severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variant Omicron BF.7 in Beijing in November–December 2022 by fitting a transmission dynamic model parameterized with real-time mobility data to (i) the daily number of new symptomatic cases on 1–11 November (when China’s zero-COVID interventions were still strictly enforced) and (ii) the proportion of individuals who participated in online polls on 10–22 December and self-reported to have been test-positive since 1 November. After China’s announcement of 20 measures to transition from zero-COVID, we estimated that Rt increased to 3.44 (95% credible interval (CrI): 2.82–4.14) on 18 November and the infection incidence peaked on 11 December. We estimated that the cumulative infection attack rate (IAR; that is, proportion of the population infected since 1 November) in Beijing was 75.7% (95% CrI: 60.7–84.4) on 22 December 2022 and 92.3% (95% CrI: 91.4–93.1) on 31 January 2023. Surveillance programs should be rapidly set up to monitor the evolving epidemiology and evolution of SARS-CoV-2 across China. With the lifting of the zero-COVID policy and requirements governing reporting case numbers in China, it has become imperative to estimate the dynamics and cumulative infection rate of SARS-CoV-2 to help guide public health responses.

Early Treatment with Pegylated Interferon Lambda for Covid-19

Abstract: The efficacy of a single dose of pegylated interferon lambda in preventing clinical events among outpatients with acute symptomatic coronavirus disease 2019 (Covid-19) is unclear.

Convergent Evolution in SARS-CoV-2 Spike Creates a Variant Soup from Which New COVID-19 Waves Emerge

Abstract: The first 2 years of the COVID-19 pandemic were mainly characterized by recurrent mutations of SARS-CoV-2 Spike protein at residues K417, L452, E484, N501 and P681 emerging independently across different variants of concern (Alpha, Beta, Gamma, and Delta). Such homoplasy is a marker of convergent evolution. Since Spring 2022 and the third year of the pandemic, with the advent of Omicron and its sublineages, convergent evolution has led to the observation of different lineages acquiring an additional group of mutations at different amino acid residues, namely R346, K444, N450, N460, F486, F490, Q493, and S494. Mutations at these residues have become increasingly prevalent during Summer and Autumn 2022, with combinations showing increased fitness. The most likely reason for this convergence is the selective pressure exerted by previous infection- or vaccine-elicited immunity. Such accelerated evolution has caused failure of all anti-Spike monoclonal antibodies, including bebtelovimab and cilgavimab. While we are learning how fast coronaviruses can mutate and recombine, we should reconsider opportunities for economically sustainable escape-proof combination therapies, and refocus antibody-mediated therapeutic efforts on polyclonal preparations that are less likely to allow for viral immune escape.

VV116 versus Nirmatrelvir–Ritonavir for Oral Treatment of Covid-19

Abstract: Nirmatrelvir–ritonavir has been authorized for emergency use by many countries for the treatment of coronavirus disease 2019 (Covid-19). However, the supply falls short of the global demand, which creates a need for more options. VV116 is an oral antiviral agent with potent activity against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2).

Avian influenza overview September – December 2022

Abstract: Abstract Between October 2021 and September 2022 Europe has suffered the most devastating highly pathogenic avian influenza (HPAI) epidemic with a total of 2,520 outbreaks in poultry, 227 outbreaks in captive birds, and 3,867 HPAI virus detections in wild birds. The unprecedent geographical extent (37 European countries affected) resulted in 50 million birds culled in affected establishments. In the current reporting period, between 10 September and 2 December 2022, 1,163 HPAI virus detections were reported in 27 European countries in poultry (398), captive (151) and wild birds (613). A decrease in HPAI virus detections in colony‐breeding seabirds species and an increase in the number of detections in waterfowl has been observed. The continuous circulation of the virus in the wild reservoir has led to the frequent introduction of the virus into poultry populations. It is suspected that waterfowl might be more involved than seabirds in the incursion of HPAI virus into poultry establishments. In the coming months, the increasing infection pressure on poultry establishments might increase the risk of incursions in poultry, with potential further spread, primarily in areas with high poultry densities. The viruses detected since September 2022 (clade 2.3.4.4b) belong to eleven genotypes, three of which have circulated in Europe during the summer months, while eight represent new genotypes. HPAI viruses were also detected in wild and farmed mammal species in Europe and North America, showing genetic markers of adaptation to replication in mammals. Since the last report, two A(H5N1) detections in humans in Spain, one A(H5N1), one A(H5N6) and one A(H9N2) human infection in China as well as one A(H5) infection without NA‐type result in Vietnam were reported, respectively. The risk of infection is assessed as low for the general population in the EU/EEA, and low to medium for occupationally exposed people.

Virulence differences of mpox (monkeypox) virus clades I, IIa, and IIb.1 in a small animal model.

Abstract: Human mpox (monkeypox), a disease with similarities to smallpox, is endemic in Africa where it has persisted as a zoonosis with limited human-to-human spread. Unexpectedly, the disease expanded globally in 2022 driven by human-to-human transmission outside of Africa. It is not yet known whether the latter is due solely to behavioral and environmental factors or whether the mpox virus is adapting to a new host. Genome sequencing has revealed differences between the current outbreak strains, classified as clade IIb, and the prior clade IIa and clade I viruses, but whether these differences contribute to virulence or transmission has not been determined. We demonstrate that the wild-derived inbred castaneous mouse provides an exceptional animal model for investigating clade differences in mpox virus virulence and show that the order is clade I > clade IIa > clade IIb.1. The greatly reduced replication of the clade IIb.1 major outbreak strain in mice and absence of lethality at 100 times the lethal dose of a closely related clade IIa virus, despite similar multiplication in cell culture, suggest that clade IIb is evolving diminished virulence or adapting to other species.

Update of the Xylella spp. host plant database – systematic literature search up to 30 June 2022

Abstract: Abstract This scientific report provides an update of the Xylella spp. host plant database, aiming to provide information and scientific support to risk assessors, risk managers and researchers dealing with Xylella spp. Upon a mandate of the European Commission, EFSA created and regularly updates a database of host plant species of Xylella spp. The current mandate covers the period 2021–2026. This report is related to the seventh version of the database published in Zenodo in the EFSA Knowledge Junction community, covering literature published from 1 January 2022 up to 30 June 2022, and recent Europhyt outbreak notifications. Informative data have been extracted from 30 selected publications. Fifteen new host plants were identified and added to the database. Those plant species were reported from Brazil, France, Italy, Portugal and Spain, and infected by subsp. multiplex, pauca or unknown (i.e. not reported). No additional data were retrieved for X. taiwanensis. Two new STs (namely ST88 and ST89) belonging to subspecies multiplex were identified in host plants in natural conditions, and new information on the tolerant/resistant response of plant species to X. fastidiosa infection were added to the database. The overall number of Xylella spp. host plants determined with at least two different detection methods or positive with one method (between sequencing and pure culture isolation) reaches now 423 plant species, 194 genera and 68 families. Such numbers rise to 679 plant species, 304 genera and 88 families if considered regardless of the detection methods applied.

Covid-19: China stops counting cases as models predict a million or more deaths

Abstract: Anxious to avoid announcing high case numbers, from early in the pandemic China reported only symptomatic cases, contrary to World Health Organization recommendations and most countries’ practice. The government eventually relented to international criticism and began reporting asymptomatic cases. But last month, even before it stopped giving daily briefings, China adopted a new and unique definition of covid death that appears designed to keep mortality numbers low.

Multicenter Case–Control Study of COVID-19–Associated Mucormycosis Outbreak, India

Abstract: We found inappropriate glucocorticoid therapy and zinc supplementation were significantly associated with these illnesses.

Highly Pathogenic Avian Influenza A(H5N1) Virus Outbreak in New England Seals, United States

Abstract: We report the spillover of highly pathogenic avian influenza A(H5N1) into marine mammals in the northeastern United States, coincident with H5N1 in sympatric wild birds. Our data indicate monitoring both wild coastal birds and marine mammals will be critical to determine pandemic potential of influenza A viruses.

Effectiveness of one dose of MVA-BN smallpox vaccine against mpox in England using the case-coverage method: an observational study.

Abstract: The UK experienced a national outbreak of mpox (formerly known as monkeypox) disease that started in May, 2022, as did many other countries worldwide, with case numbers rising rapidly, mainly among gay, bisexual, and other men who have sex with men (GBMSM). To control the outbreak, Modified Vaccinia Ankara-Bavaria Nordic (MVA-BN), an attenuated smallpox vaccine, was offered to at-risk GBMSM. We aimed to assess the effectiveness of a single MVA-BN dose against symptomatic mpox disease in at-risk GBMSM.In this case-coverage study, mpox cases in England were sent questionnaires collecting information on demographics, vaccination history, symptoms, and sexual orientation. Returned questionnaires were linked to laboratory data and a public health case management system (HP Zone) to obtain additional information on symptom onset and specimen date. Cases with a rash onset date (or alternative proxy) between July 4 and Oct 9, 2022, were included. Females, heterosexual men, and those with missing vaccination information were excluded. Vaccine effectiveness was calculated using the case-coverage method in which vaccine coverage among cases is compared with coverage in the eligible population, estimated from doses given to GBMSM and the estimated size of at-risk GBMSM. Sensitivity analyses included an increase and decrease of 20% differences in the estimated high-risk GBMSM population size.By Nov 3, 2022, 1102 people had responded to questionnaires, of which 739 were excluded (52 females or self-declared male heterosexuals, 590 with an index date outside of the study period, and 97 missing a vaccination date). 363 cases were included in the analyses. Vaccine uptake among eligible GBMSM increased steadily from July, 2022, reaching 47% by Oct 9, 2022. Of the 363 confirmed cases, eight cases either did occur or were likely to have occurred at least 14 days after vaccination, 32 within 0-13 days after vaccination, and the rest were unvaccinated. The estimated vaccine effectiveness against symptomatic mpox at least 14 days after a single dose was 78% (95% CI 54 to 89) ranging from 71 to 85 in sensitivity analyses. Vaccine effectiveness within 0-13 days after vaccination was -4% (95% CI -50 to 29).A single MVA-BN dose was highly protective against symptomatic mpox disease among at-risk GBMSM, making it a useful tool for mpox outbreak control when rapid protection is needed. For cases in which numbers at highest risk of infection exceed vaccine supply, there might be benefit in prioritising delivery of first doses.UK Health Security Agency.

Correlates of Protection, Thresholds of Protection, and Immunobridging among Persons with SARS-CoV-2 Infection

Abstract: Several studies have shown that neutralizing antibody levels correlate with immune protection from COVID-19 and have estimated the relationship between neutralizing antibodies and protection. However, results of these studies vary in terms of estimates of the level of neutralizing antibodies required for protection. By normalizing antibody titers, we found that study results converge on a consistent relationship between antibody levels and protection from COVID-19. This finding can be useful for planning future vaccine use, determining population immunity, and reducing the global effects of the COVID-19 pandemic

Mpox Cases Among Cisgender Women and Pregnant Persons — United States, May 11–November 7, 2022

Abstract: Monkeypox (mpox) cases in the 2022 outbreak have primarily occurred among adult gay, bisexual, and other men who have sex with men (MSM); however, other populations have also been affected (1). To date, data on mpox in cisgender women and pregnant persons have been limited. Understanding transmission in these populations is critical for mpox prevention. In addition, among pregnant persons, Monkeypox virus can be transmitted to the fetus during pregnancy or to the neonate through close contact during or after birth (2-5). Adverse pregnancy outcomes, including spontaneous abortion and stillbirth, have been reported in previous mpox outbreaks (3). During May 11-November 7, 2022, CDC and U.S. jurisdictional health departments identified mpox in 769 cisgender women aged ≥15 years, representing 2.7% of all reported mpox cases.† Among cases with available data, 44% occurred in cisgender women who were non-Hispanic Black or African American (Black), 25% who were non-Hispanic White (White), and 23% who were Hispanic or Latino (Hispanic). Among cisgender women with available data, 73% reported sexual activity or close intimate contact as the likely route of exposure, with mpox lesions most frequently reported on the legs, arms, and genitals. Twenty-three mpox cases were reported in persons who were pregnant or recently pregnant§; all identified as cisgender women based on the mpox case report form.¶ Four pregnant persons required hospitalization for mpox. Eleven pregnant persons received tecovirimat, and no adverse reactions were reported. Continued studies on mpox transmission risks in populations less commonly affected during the outbreak, including cisgender women and pregnant persons, are important to assess and understand the impact of mpox on sexual, reproductive, and overall health.

Covid-19: What do we know about XBB.1.5 and should we be worried?

Abstract: The XBB.1.5 omicron variant of SARS-CoV-2 has been making headlines for weeks. Elisabeth Mahase reports what we know so far

Nirmatrelvir–ritonavir for the treatment of COVID‐19 patients: A systematic review and meta‐analysis

Abstract: Nirmatrelvir-ritonavir (Paxlovid™) is an oral antiviral that has been approved for the treatment of mild-to-moderate COVID-19. We aimed to conduct a meta-analysis to evaluate the efficacy and safety of nirmatrelvir-ritonavir in COVID-19 patients. Various databases including PubMed, the Cochrane Library, medRxiv and Embase were searched from inception till 10 October 2022 and results from 12 studies (two randomized controlled trials (RCTs) and 10 observational studies) were pooled using a random-effects model with risk ratio (RR) as the effect measure. Nirmatrelvir-ritonavir reduced the risk of mortality (RR 0.24; 95% CI:0.15-0.37, I2 =48%; moderate certainty) and hospitalization (RR 0.41; 95% CI:0.29-0.59, I2 =90%; low certainty) in both patients with or without previous immunity to SARS-CoV-2 without an increased risk of adverse events. Our study provides encouraging evidence for nirmatrelvir-ritonavir as a safe and efficacious agent for COVID-19 but large-scale RCTs are needed to confirm these findings. This article is protected by copyright. All rights reserved.