The outbreak of SARS‐CoV‐2 Omicron lineages, immune escape, and vaccine effectivity

Journal of Medical Virology, Journal Year: 2022, Volume and Issue: 95(1)

Published: Sept. 13, 2022

As of November 2021, several SARS-CoV-2 variants appeared and became dominant epidemic strains in many countries, including five concern (VOCs) Alpha, Beta, Gamma, Delta, Omicron defined by the World Health Organization during COVID-19 pandemic. August 2022, is classified into main lineages, BA.1, BA.2, BA.3, BA.4, BA.5 some sublineages (BA.1.1, BA.2.12.1, BA.2.11, BA.2.75, BA.4.6) (https://www.gisaid.org/). Compared to previous VOCs (Alpha, Delta), all lineages have most highly mutations spike protein, with 50 accumulated throughout genome. Early data indicated that BA.2 sublineage had higher infectivity more immune escape than early wild-type (WT) strain, VOCs, BA.1. Recently, global surveillance suggest a transmissibility BA.4/BA.5 BA.1.1 becoming strain countries globally.

Language: Английский

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Risk of reinfection, vaccine protection, and severity of infection with the BA.5 omicron subvariant: a nation-wide population-based study in Denmark

The Lancet Infectious Diseases, Journal Year: 2022, Volume and Issue: 23(2), P. 167 - 176

Published: Oct. 18, 2022

Language: Английский

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Risk Factors of Severe COVID-19: A Review of Host, Viral and Environmental Factors

Viruses, Journal Year: 2023, Volume and Issue: 15(1), P. 175 - 175

Published: Jan. 7, 2023

The clinical course and outcome of COVID-19 are highly variable, ranging from asymptomatic infections to severe disease death. Understanding the risk factors is relevant both in setting at epidemiological level. Here, we provide an overview host, viral environmental that have been shown or (in some cases) hypothesized be associated with outcomes. considered detail include age frailty, genetic polymorphisms, biological sex (and pregnancy), co- superinfections, non-communicable comorbidities, immunological history, microbiota, lifestyle patient; variation infecting dose; socioeconomic factors; air pollution. For each category, compile (sometimes conflicting) evidence for association factor outcomes (including strength effect) outline possible action mechanisms. We also discuss complex interactions between various factors.

Language: Английский

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SARS‐CoV‐2 in animals: susceptibility of animal species, risk for animal and public health, monitoring, prevention and control

EFSA Journal, Journal Year: 2023, Volume and Issue: 21(2)

Published: Feb. 1, 2023

Abstract The epidemiological situation of SARS-CoV-2 in humans and animals is continually evolving. To date, animal species known to transmit are American mink, raccoon dog, cat, ferret, hamster, house mouse, Egyptian fruit bat, deer mouse white-tailed deer. Among farmed animals, mink have the highest likelihood become infected from or further SARS-CoV-2. In EU, 44 outbreaks were reported 2021 farms seven MSs, while only six 2022 two thus representing a decreasing trend. introduction into usually via humans; this can be controlled by systematically testing people entering adequate biosecurity. current most appropriate monitoring approach for outbreak confirmation based on suspicion, dead clinically sick case increased mortality positive farm personnel genomic surveillance virus variants. analysis showed mink-specific clusters with potential spill back human population. companion cats, ferrets hamsters those at risk infection, which likely originates an human, has no very low impact circulation wild (including zoo animals), mostly carnivores, great apes been naturally cases wildlife so far. Proper disposal waste advised reduce risks spill-over wildlife. Furthermore, contact wildlife, especially if dead, should minimised. No specific recommended apart hunter-harvested clinical signs found-dead. Bats monitored as natural host many coronaviruses.

Language: Английский

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Association of SARS-CoV-2 BA.4/BA.5 Omicron lineages with immune escape and clinical outcome

Nature Communications, Journal Year: 2023, Volume and Issue: 14(1)

Published: March 14, 2023

Abstract Expansion of the SARS-CoV-2 BA.4 and BA.5 Omicron subvariants in populations with prevalent immunity from prior infection vaccination, associated burden severe COVID-19, has raised concerns about epidemiologic characteristics these lineages including their association immune escape or clinical outcomes. Here we show that BA.4/BA.5 cases a large US healthcare system had at least 55% (95% confidence interval: 43–69%) higher adjusted odds documented than time-matched BA.2 cases, as well 15% (9–21%) 38% (27–49%) having received 3 ≥4 COVID-19 vaccine doses, respectively. However, after adjusting for differences among each lineage, was not differential risk emergency department presentation, hospital admission, intensive care unit admission following an initial outpatient diagnosis. This finding held sensitivity analyses correcting potential exposure misclassification resulting unascertained infections. Our results demonstrate reduced severity (BA.1 BA.2) lineages, relative to Delta variant, persisted BA.4/BA.5, despite increased breakthrough previously vaccinated infected individuals.

Language: Английский

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Omicron subvariant BA.5 efficiently infects lung cells

Nature Communications, Journal Year: 2023, Volume and Issue: 14(1)

Published: June 13, 2023

The SARS-CoV-2 Omicron subvariants BA.1 and BA.2 exhibit reduced lung cell infection relative to previously circulating variants, which may account for their pathogenicity. However, it is unclear whether by BA.5, displaced these remains attenuated. Here, we show that the spike (S) protein of BA.5 exhibits increased cleavage at S1/S2 site drives cell-cell fusion entry with higher efficiency than its counterparts from BA.2. Increased depends on mutation H69Δ/V70Δ associated efficient replication in cultured cells. Further, replicates lungs female Balb/c mice nasal cavity ferrets much BA.1. These results suggest has acquired ability efficiently infect cells, a prerequisite causing severe disease, suggesting evolution can result partial loss attenuation.

Language: Английский

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COVID-19 infection, reinfection, and the transition to endemicity

The Lancet, Journal Year: 2023, Volume and Issue: 401(10379), P. 798 - 800

Published: Feb. 16, 2023

Language: Английский

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SARS-CoV-2 omicron BA.5 and XBB variants have increased neurotropic potential over BA.1 in K18-hACE2 mice and human brain organoids

Frontiers in Microbiology, Journal Year: 2023, Volume and Issue: 14

Published: Nov. 23, 2023

The reduced pathogenicity of the omicron BA.1 sub-lineage compared to earlier variants is well described, although whether such attenuation retained for later like BA.5 and XBB remains controversial. We show that isolates were significantly more pathogenic in K18-hACE2 mice than a isolate, showing increased neurotropic potential, resulting fulminant brain infection mortality, similar seen original ancestral isolates. also infected human cortical organoids greater extent In brains mice, neurons main target infection, neuronal progenitor cells immature infected. results herein suggest evolving may have increasing potential.

Language: Английский

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SARS-CoV-2 Viral Replication Persists in the Human Lung for Several Weeks after Symptom Onset

American Journal of Respiratory and Critical Care Medicine, Journal Year: 2024, Volume and Issue: 209(7), P. 840 - 851

Published: Jan. 16, 2024

Rationale: In the upper respiratory tract replicating (culturable) SARS-CoV-2 is recoverable for ~ 4 to 8 days after symptom onset, however, there paucity of data about frequency or duration virus in lower (i.e. human lung). Objectives: We undertook lung tissue sampling (needle biopsy), shortly death, 42 mechanically ventilated decedents during Beta and Delta waves. An independent group 18 ambulatory patents served as a control group. Methods: Lung biopsy cores from underwent viral culture, histopathological analysis, electron microscopy, transcriptomic profiling immunohistochemistry. Results: 38% (16/42) had culturable median 15 (persisting up weeks) onset. culture positivity was not associated with comorbidities steroid use. but variant accelerated death secondary bacterial infection (p<0.05). Nasopharyngeal negative 23.1% (6/26) despite positivity. This, hitherto, undescribed bio-phenotype lung-specific persisting replication an enhanced pulmonary pro-inflammatory response concurrent Conclusions: Concurrent, rather than sequential active continues drive heightened beyond second week illness variant-specific increased mortality morbidity. These findings have potential implications design interventional strategies clinical management patients severe COVID-19 disease. This article open access distributed under terms Creative Commons Attribution 4.0 International License (https://creativecommons.org/licenses/by/4.0/).

Language: Английский

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The latest Omicron BA.4 and BA.5 lineages are frowning toward COVID‐19 preventive measures: A threat to global public health

Health Science Reports, Journal Year: 2022, Volume and Issue: 5(6)

Published: Oct. 13, 2022

A cluster of pneumonia cases was reported by the Wuhan Municipal Health Commission, China, Hubei Province, resulting in identification a novel coronavirus (SARS-CoV-2).1 As September 19, 2022, more than 609 million and 6.5 deaths have been recorded worldwide. The highest number COVID-19 Europe, followed Americas, Western Pacific, South-East Asia, Eastern Mediterranean, Africa regions.2 country, US contributed deaths.2 SARS-CoV-2 is constantly mutating dodging antibodies to infect people. Epidemiologists South detected fifth latest "variant concern" (VOC) SARS-CoV-2. They this new variant World Organization (WHO) on November 24, 2021. This VOC contains 30 mutations its viral spike proteins allow it transmissibility infection rates.1 WHO named as Omicron (B.1.1.529) 26, 2021.2 became leading after inception. At present, only circulating VOC. Initially, had three subvariants (e.g., BA.1, BA.2, BA.3). BA.1 predominant during fourth wave pandemic Africa. However, global pattern inconsistent some other countries. BA.2 responsible for hospitalizations most Africa.3 Currently, includes five lineages descendant subvariants.4 that rapidly spread across globe.5, 6 were subvariant BA.4 BA.5 variants are now Europe United States.7 classified BA.4, BA.5, BA.2.12.1, BA.2.75 VOC-subvariants under monitoring.4 European Centre Disease Prevention Control categorized from VOI May 12, 2022.8 Therefore, we recommend prioritized monitoring epidemiology due subvariants. article aims present an update their potential impact public health. Scientists sample collected early 2022.9 similarities with parent based genotype phenotype both Omicron. These all had. identical similar BA.1.10 fueled surge spring despite having widespread pre-existing immunity virus. not high earlier waves, did rise sharply Africa.10 analogous BA.2. further at positions 69-70del, L452R, F486V, there wild-type AA position Q493 like BA.2.10 Moreover, has extra triple amino acid deletion N: P151S, ORF7b: L11F, NSP1:141-143del, respectively, outside protein. M: D3N mutation region. Similar additional reversions ORF6:D61 nucleotide 26,858 27,259.10 alterations antigenic characteristics proxy marker S-gene fails identify these 69–70 two differ each area.10 achieved power biological changes them people quickly. There noticeable L452R increasing transmissibility. Delta mutation. can become contagious because helps attachment human cell. Another vital F486V.10 occurs protein region close attaching site idea virus deceive our immune system. could be capable escaping assumed capacity fully immunized forms Omicron.11 Many countries implementing inadequate measures control 2.5 years since introduction pandemic.12-16 population risk getting infected lineages. quickly substituted half sequenced April 2022. Within couple months, they world.17 ages. also double benefit contagiousness unique mutations. replaced started 50% cases.17 induced any previous variants.18, 19 According COVID Data Tracker Centers Prevention, account about 52% States.20 appeared overtaking subvariants, States.11 In Switzerland, prevalence much higher, comparatively lower.17 will effect time. symptoms severity still known. subtypes so distinct scientists able conclude severity.10 We do know whether cause severe diseases types or not. Though originated Africa, saw went away again. damage may several reasons behind this. One reason might mass vaccination natural big country. Several studies demonstrated avoiding triggered infections.21-23 vaccinated populations multiple infections. claimed F486V powering escape rapidly.10 Waasila Jassat, epidemiologist said "despite case numbers, experienced small wave." rate increase disease burden. study observed BA.4/BA.5 waves risks hospitalization death. Also, showed reduced death waves. case, prior infections protective against developing symptoms.24 Outside very Portugal. rates associated first wave.17 demographic Portugal, where older variants. meta-analysis aged 70 above higher individuals 70.25 face burden Epidemiologic suggest consecutive converting milder.24 viruses automatically change less lethal.26-29 healthcare authorities globe need careful 12 billion vaccine doses administered worldwide.2 5.3 got least one dose, 4.9 vaccinated.2 role vaccines curb mortality.30, 31 corona last 6–9 months body. definite evidence reduces complications.30 Studies shown rate, complications, mortality lower among population. occurred subvariants.10 Because acquired wave. reduce help fight well.10 Some companies trying bring customized tough say come before many Mass immunization provides mild rate. January included nine different emergency use listing prevention COVID-19.32 oral antiviral drugs moderate stopping multiplication paxlovid tablets (nirmatrelvir ritonavir co-packaged Pfizer) lagevrio (molnupiravir Merck).33 nasal delivery antibody (58G6) protection variants.34 Nitric oxide spray (NONS) symptoms, severity, patients.35 recommended monoclonal (mAbs) high-risk ambulatory patients better outcomes.36, 37 It difficult eradicate world.38, 39 Newer would create emerging threat dominating strain India spreading countries.40, 41 should implement health safety vaccinate maximum possible. think omicron options well protected. wear mask. what type inhale, mask stop all. long masks strictly. awareness tests. without proper sequencing specimen, impossible monitor understand nature Md. Rabiul Islam: Conceptualization; writing–review editing. Mohammad Shahriar: Writing–original draft. Mohiuddin Ahmed Bhuiyan: authors declare no conflict interest. lead author Islam affirms manuscript honest, accurate, transparent being reported; important aspects omitted; discrepancies planned (and, if relevant, registered) explained. sharing applicable data created analyzed study.

Language: Английский

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