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1.
COVID ; 2(5):586-598, 2022.
Article in English | MDPI | ID: covidwho-1820194

ABSTRACT

Using classical and genomic epidemiology, we tracked the COVID-19 pandemic in Kenya over 23 months to determine the impact of SARS-CoV-2 variants on its progression. SARS-CoV-2 surveillance and testing data were obtained from the Kenya Ministry of Health, collected daily from 306 health facilities. COVID-19-associated fatality data were also obtained from these health facilities and communities. Whole SARS-CoV-2 genome sequencing were carried out on 1241 specimens. Over the pandemic duration (March 2020–January 2022), Kenya experienced five waves characterized by attack rates (AR) of between 65.4 and 137.6 per 100,000 persons, and intra-wave case fatality ratios (CFR) averaging 3.5%, two-fold higher than the national average COVID-19 associated CFR. The first two waves that occurred before emergence of global variants of concerns (VoC) had lower AR (65.4 and 118.2 per 100,000). Waves 3, 4, and 5 that occurred during the second year were each dominated by multiple introductions each, of Alpha (74.9% genomes), Delta (98.7%), and Omicron (87.8%) VoCs, respectively. During this phase, government-imposed restrictions failed to alleviate pandemic progression, resulting in higher attack rates spread across the country. In conclusion, the emergence of Alpha, Delta, and Omicron variants was a turning point that resulted in widespread and higher SARS-CoV-2 infections across the country.

2.
Microorganisms ; 10(2)2022 Feb 10.
Article in English | MEDLINE | ID: covidwho-1706054

ABSTRACT

As the COVID-19 pandemic moves into its third year, there remains a need for additional animal models better recapitulating severe COVID to study SARS-CoV-2 pathogenesis and develop countermeasures, especially treatment options. Pigs are known intermediate hosts for many viruses with zoonotic potential and are susceptible to infection with alpha, beta and delta genera of coronaviruses. Herein, we infected young (3 weeks of age) pigs with SARS-CoV-2 using a combination of respiratory and parenteral inoculation routes. Pigs did not develop clinical disease, nor macroscopic or microscopic pathologic lesions upon SARS-CoV-2 infection. Despite occasional low levels of SARS-CoV-2 genomic RNA in the respiratory tract, subgenomic RNA and infectious virus were never found, and SARS-CoV-2-specific adaptive immune responses were not detectable over the 13-day study period. We concluded that pigs are not susceptible to productive SARS-CoV-2 infection and do not serve as a SARS-CoV-2 reservoir for zoonotic transmission.

3.
Emerg Infect Dis ; 27(12): 3052-3062, 2021 12.
Article in English | MEDLINE | ID: covidwho-1528794

ABSTRACT

Middle East respiratory syndrome coronavirus (MERS-CoV) infects humans and dromedary camels and is responsible for an ongoing outbreak of severe respiratory illness in humans in the Middle East. Although some mutations found in camel-derived MERS-CoV strains have been characterized, most natural variation found across MERS-CoV isolates remains unstudied. We report on the environmental stability, replication kinetics, and pathogenicity of several diverse isolates of MERS-CoV, as well as isolates of severe acute respiratory syndrome coronavirus 2, to serve as a basis of comparison with other stability studies. Although most MERS-CoV isolates had similar stability and pathogenicity in our experiments, the camel-derived isolate C/KSA/13 had reduced surface stability, and another camel isolate, C/BF/15, had reduced pathogenicity in a small animal model. These results suggest that although betacoronaviruses might have similar environmental stability profiles, individual variation can influence this phenotype, underscoring the need for continual global viral surveillance.


Subject(s)
COVID-19 , Middle East Respiratory Syndrome Coronavirus , Aerosols , Animals , Camelus , Humans , Middle East Respiratory Syndrome Coronavirus/genetics , SARS-CoV-2 , Virulence , Zoonoses
4.
Philos Trans R Soc Lond B Biol Sci ; 376(1837): 20200358, 2021 11 08.
Article in English | MEDLINE | ID: covidwho-1429384

ABSTRACT

In the light of the urgency raised by the COVID-19 pandemic, global investment in wildlife virology is likely to increase, and new surveillance programmes will identify hundreds of novel viruses that might someday pose a threat to humans. To support the extensive task of laboratory characterization, scientists may increasingly rely on data-driven rubrics or machine learning models that learn from known zoonoses to identify which animal pathogens could someday pose a threat to global health. We synthesize the findings of an interdisciplinary workshop on zoonotic risk technologies to answer the following questions. What are the prerequisites, in terms of open data, equity and interdisciplinary collaboration, to the development and application of those tools? What effect could the technology have on global health? Who would control that technology, who would have access to it and who would benefit from it? Would it improve pandemic prevention? Could it create new challenges? This article is part of the theme issue 'Infectious disease macroecology: parasite diversity and dynamics across the globe'.


Subject(s)
Disease Reservoirs/virology , Global Health , Pandemics/prevention & control , Zoonoses/prevention & control , Zoonoses/virology , Animals , Animals, Wild , COVID-19/prevention & control , COVID-19/veterinary , Ecology , Humans , Laboratories , Machine Learning , Risk Factors , SARS-CoV-2 , Viruses , Zoonoses/epidemiology
6.
Cell ; 183(7): 1901-1912.e9, 2020 12 23.
Article in English | MEDLINE | ID: covidwho-950119

ABSTRACT

Long-term severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) shedding was observed from the upper respiratory tract of a female immunocompromised individual with chronic lymphocytic leukemia and acquired hypogammaglobulinemia. Shedding of infectious SARS-CoV-2 was observed up to 70 days, and of genomic and subgenomic RNA up to 105 days, after initial diagnosis. The infection was not cleared after the first treatment with convalescent plasma, suggesting a limited effect on SARS-CoV-2 in the upper respiratory tract of this individual. Several weeks after a second convalescent plasma transfusion, SARS-CoV-2 RNA was no longer detected. We observed marked within-host genomic evolution of SARS-CoV-2 with continuous turnover of dominant viral variants. However, replication kinetics in Vero E6 cells and primary human alveolar epithelial tissues were not affected. Our data indicate that certain immunocompromised individuals may shed infectious virus longer than previously recognized. Detection of subgenomic RNA is recommended in persistently SARS-CoV-2-positive individuals as a proxy for shedding of infectious virus.


Subject(s)
COVID-19/immunology , Common Variable Immunodeficiency/immunology , Leukemia, Lymphocytic, Chronic, B-Cell/immunology , SARS-CoV-2/isolation & purification , Aged , Antibodies, Viral/blood , Antibodies, Viral/immunology , COVID-19/complications , COVID-19/virology , Common Variable Immunodeficiency/blood , Common Variable Immunodeficiency/complications , Common Variable Immunodeficiency/virology , Female , Humans , Leukemia, Lymphocytic, Chronic, B-Cell/blood , Leukemia, Lymphocytic, Chronic, B-Cell/complications , Leukemia, Lymphocytic, Chronic, B-Cell/virology , Respiratory Tract Infections/blood , Respiratory Tract Infections/complications , Respiratory Tract Infections/immunology , Respiratory Tract Infections/virology , SARS-CoV-2/immunology , SARS-CoV-2/pathogenicity
7.
Trends Ecol Evol ; 35(12): 1062-1065, 2020 12.
Article in English | MEDLINE | ID: covidwho-752778

ABSTRACT

Most efforts to predict novel reservoirs of zoonotic pathogens use information about host exposure and infection rather than competence, defined as the ability to transmit pathogens. Better obtaining and integrating competence data into statistical models as covariates, as the response variable, and through postmodel validation should improve predictive research.


Subject(s)
Disease Reservoirs , Zoonoses , Animals
8.
Nat Rev Microbiol ; 18(8): 461-471, 2020 08.
Article in English | MEDLINE | ID: covidwho-596755

ABSTRACT

Most viral pathogens in humans have animal origins and arose through cross-species transmission. Over the past 50 years, several viruses, including Ebola virus, Marburg virus, Nipah virus, Hendra virus, severe acute respiratory syndrome coronavirus (SARS-CoV), Middle East respiratory coronavirus (MERS-CoV) and SARS-CoV-2, have been linked back to various bat species. Despite decades of research into bats and the pathogens they carry, the fields of bat virus ecology and molecular biology are still nascent, with many questions largely unexplored, thus hindering our ability to anticipate and prepare for the next viral outbreak. In this Review, we discuss the latest advancements and understanding of bat-borne viruses, reflecting on current knowledge gaps and outlining the potential routes for future research as well as for outbreak response and prevention efforts.


Subject(s)
Biodiversity , Chiroptera/virology , Communicable Diseases, Emerging/virology , Virus Diseases/virology , Virus Physiological Phenomena , Zoonoses/virology , Animals , Communicable Diseases, Emerging/prevention & control , Communicable Diseases, Emerging/transmission , Disease Outbreaks/prevention & control , Humans , Research/trends , Virus Diseases/prevention & control , Zoonoses/prevention & control , Zoonoses/transmission
9.
Emerg Infect Dis ; 26(9)2020 09.
Article in English | MEDLINE | ID: covidwho-574540

ABSTRACT

We found that environmental conditions affect the stability of severe acute respiratory syndrome coronavirus 2 in nasal mucus and sputum. The virus is more stable at low-temperature and low-humidity conditions, whereas warmer temperature and higher humidity shortened half-life. Although infectious virus was undetectable after 48 hours, viral RNA remained detectable for 7 days.


Subject(s)
Betacoronavirus/genetics , Coronavirus Infections/virology , Mucus/virology , Pneumonia, Viral/virology , RNA, Viral/analysis , Sputum/virology , COVID-19 , Hot Temperature , Humans , Humidity , Nasal Cavity/virology , Pandemics , RNA Stability , SARS-CoV-2
10.
Emerg Infect Dis ; 26(9)2020 09.
Article in English | MEDLINE | ID: covidwho-505770

ABSTRACT

The coronavirus pandemic has created worldwide shortages of N95 respirators. We analyzed 4 decontamination methods for effectiveness in deactivating severe acute respiratory syndrome coronavirus 2 virus and effect on respirator function. Our results indicate that N95 respirators can be decontaminated and reused, but the integrity of respirator fit and seal must be maintained.


Subject(s)
Betacoronavirus , Coronavirus Infections/prevention & control , Decontamination/methods , Equipment Reuse , Pandemics/prevention & control , Pneumonia, Viral/prevention & control , Ventilators, Mechanical/virology , COVID-19 , Coronavirus Infections/virology , Humans , Pneumonia, Viral/virology , SARS-CoV-2
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