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1.
PLoS One ; 18(3): e0283664, 2023.
Article in English | MEDLINE | ID: covidwho-2273672

ABSTRACT

Understanding disease burden and transmission dynamics in resource-limited, low-income countries like Nepal are often challenging due to inadequate surveillance systems. These issues are exacerbated by limited access to diagnostic and research facilities throughout the country. Nepal has one of the highest COVID-19 case rates (915 cases per 100,000 people) in South Asia, with densely-populated Kathmandu experiencing the highest number of cases. Swiftly identifying case clusters (hotspots) and introducing effective intervention programs is crucial to mounting an effective containment strategy. The rapid identification of circulating SARS-CoV-2 variants can also provide important information on viral evolution and epidemiology. Genomic-based environmental surveillance can help in the early detection of outbreaks before clinical cases are recognized and identify viral micro-diversity that can be used for designing real-time risk-based interventions. This research aimed to develop a genomic-based environmental surveillance system by detecting and characterizing SARS-CoV-2 in sewage samples of Kathmandu using portable next-generation DNA sequencing devices. Out of 22 sites in the Kathmandu Valley from June to August 2020, sewage samples from 16 (80%) sites had detectable SARS-CoV-2. A heatmap was created to visualize the presence of SARS-CoV-2 infection in the community based on viral load intensity and corresponding geospatial data. Further, 47 mutations were observed in the SARS-CoV-2 genome. Some detected mutations (n = 9, 22%) were novel at the time of data analysis and yet to be reported in the global database, with one indicating a frameshift deletion in the spike gene. SNP analysis revealed possibility of assessing circulating major/minor variant diversity on environmental samples based on key mutations. Our study demonstrated the feasibility of rapidly obtaining vital information on community transmission and disease dynamics of SARS-CoV-2 using genomic-based environmental surveillance.


Subject(s)
COVID-19 , Sewage , Humans , SARS-CoV-2/genetics , COVID-19/diagnosis , COVID-19/epidemiology , Genomics
2.
Viruses ; 15(3)2023 03 20.
Article in English | MEDLINE | ID: covidwho-2268020

ABSTRACT

A One Health cross-sectoral surveillance approach was implemented to screen biological samples from bats, pigs, and humans at high-risk interfaces for zoonotic viral spillover for five viral families with zoonotic potential in Viet Nam. Over 1600 animal and human samples from bat guano harvesting sites, natural bat roosts, and pig farming operations were tested for coronaviruses (CoVs), paramyxoviruses, influenza viruses, filoviruses and flaviviruses using consensus PCR assays. Human samples were also tested using immunoassays to detect antibodies against eight virus groups. Significant viral diversity, including CoVs closely related to ancestors of pig pathogens, was detected in bats roosting at the human-animal interfaces, illustrating the high risk for CoV spillover from bats to pigs in Viet Nam, where pig density is very high. Season and reproductive period were significantly associated with the detection of bat CoVs, with site-specific effects. Phylogeographic analysis indicated localized viral transmission among pig farms. Our limited human sampling did not detect any known zoonotic bat viruses in human communities living close to the bat cave and harvesting bat guano, but our serological assays showed possible previous exposure to Marburg virus-like (Filoviridae), Crimean-Congo hemorrhagic fever virus-like (Bunyaviridae) viruses and flaviviruses. Targeted and coordinated One Health surveillance helped uncover this viral pathogen emergence hotspot.


Subject(s)
Chiroptera , Coronavirus Infections , Coronavirus , Filoviridae , One Health , Humans , Animals , Swine , Vietnam/epidemiology , Phylogeny , Zoonoses
3.
Front Public Health ; 10: 826116, 2022.
Article in English | MEDLINE | ID: covidwho-1771119

ABSTRACT

Despite the discovery of several closely related viruses in bats, the direct evolutionary progenitor of SARS-CoV-2 has not yet been identified. In this study, we investigated potential animal sources of SARS-related coronaviruses using archived specimens from Sunda pangolins (Manis javanica) and Chinese pangolins (Manis pentadactyla) confiscated from the illegal wildlife trade, and from common palm civets (Paradoxurus hermaphroditus) raised on wildlife farms in Viet Nam. A total of 696 pangolin and civet specimens were screened for the presence of viral RNA from five zoonotic viral families and from Sarbecoviruses using primers specifically designed for pangolin coronaviruses. We also performed a curated data collection of media reports of wildlife confiscation events involving pangolins in Viet Nam between January 2016 and December 2020, to illustrate the global pangolin supply chain in the context of Viet Nam where the trade confiscated pangolins were sampled for this study. All specimens from pangolins and civets sampled along the wildlife supply chains between February 2017 and July 2018, in Viet Nam and tested with conventional PCR assays designed to detect flavivirus, paramyxovirus, filovirus, coronavirus, and orthomyxovirus RNA were negative. Civet samples were also negative for Sarbecoviruses, but 12 specimens from seven live pangolins confiscated in Hung Yen province, northern Viet Nam, in 2018 were positive for Sarbecoviruses. Our phylogenetic trees based on two fragments of the RdRp gene revealed that the Sarbecoviruses identified in these pangolins were closely related to pangolin coronaviruses detected in pangolins confiscated from the illegal wildlife trade in Yunnan and Guangxi provinces, China. Our curated data collection of media reports of wildlife confiscation events involving pangolins in Viet Nam between January 2016 and December 2020, reflected what is known about pangolin trafficking globally. Pangolins confiscated in Viet Nam were largely in transit, moving toward downstream consumers in China. Confiscations included pangolin scales sourced originally from Africa (and African species of pangolins), or pangolin carcasses and live pangolins native to Southeast Asia (predominately the Sunda pangolin) sourced from neighboring range countries and moving through Viet Nam toward provinces bordering China.


Subject(s)
COVID-19 , Pangolins , Animals , Animals, Wild , China , Humans , Phylogeny , SARS-CoV-2 , Vietnam/epidemiology
4.
Zoonoses Public Health ; 69(6): 746-756, 2022 09.
Article in English | MEDLINE | ID: covidwho-1637270

ABSTRACT

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a viral pathogen that quickly became a global pandemic in the winter of 2020-2021. In response, governments issued social distancing orders to minimize transmission by reducing community contacts. We tested the efficacy of this social distancing at the state level during the first 2 months of the pandemic in the United States. We utilized data on daily SARS-CoV-2 case numbers and human community mobility (anonymized, aggregated cell phone location data stratified into six categories used as an index of social distancing), the date of government-issued social distancing orders, demographics, urbanization and public transportation. We implemented cross-correlation to identify lag times between declines in mobility and SARS-CoV-2 cases. Incorporating state-specific lag times, we tested for associations between case counts and mobility metrics using Bayesian multilevel models. Decreased mobility around grocery stores/pharmacies, retail/recreation locations, transit stations and workplaces was correlated with decreases in SARS-CoV-2 cases with significant lag times of ≥21 days. Social distancing orders were associated with fewer cumulative SARS-CoV-2 cases when they were put in place earlier. Community mobility had already started declining prior to most social distancing orders, especially the more restrictive orders implemented later in the pandemic. Social distancing is an important tool that has been implemented throughout the pandemic to decrease SARS-CoV-2 transmission, although with significant social and economic impacts. Our results suggest that declines in cases were observed several weeks subsequent to implementation of social distancing measures, and that implementing social distancing earlier could potentially minimize the duration of time these policies need to be in effect. Our findings can inform ongoing management of this pandemic and other emerging infectious disease outbreaks by identifying areas where reductions in mobility are associated with reduced disease transmission, and the expected time frame between behavioural changes and measurable population outcomes.


Subject(s)
COVID-19 , SARS-CoV-2 , Animals , Bayes Theorem , COVID-19/epidemiology , COVID-19/veterinary , Humans , Pandemics/prevention & control , Physical Distancing , United States/epidemiology
5.
Nat Commun ; 12(1): 6563, 2021 11 09.
Article in English | MEDLINE | ID: covidwho-1510593

ABSTRACT

Knowledge of the origin and reservoir of the coronavirus responsible for the ongoing COVID-19 pandemic is still fragmentary. To date, the closest relatives to SARS-CoV-2 have been detected in Rhinolophus bats sampled in the Yunnan province, China. Here we describe the identification of SARS-CoV-2 related coronaviruses in two Rhinolophus shameli bats sampled in Cambodia in 2010. Metagenomic sequencing identifies nearly identical viruses sharing 92.6% nucleotide identity with SARS-CoV-2. Most genomic regions are closely related to SARS-CoV-2, with the exception of a region of the spike, which is not compatible with human ACE2-mediated entry. The discovery of these viruses in a bat species not found in China indicates that SARS-CoV-2 related viruses have a much wider geographic distribution than previously reported, and suggests that Southeast Asia represents a key area to consider for future surveillance for coronaviruses.


Subject(s)
COVID-19/virology , Chiroptera/virology , SARS-CoV-2/genetics , Amino Acid Sequence , Animals , COVID-19/epidemiology , COVID-19/metabolism , Cambodia/epidemiology , Evolution, Molecular , Genome, Viral , Phylogeny , SARS-CoV-2/isolation & purification , SARS-CoV-2/metabolism , Sequence Alignment , Spike Glycoprotein, Coronavirus/genetics , Spike Glycoprotein, Coronavirus/metabolism
6.
Proc Natl Acad Sci U S A ; 118(15)2021 04 13.
Article in English | MEDLINE | ID: covidwho-1171893

ABSTRACT

The death toll and economic loss resulting from the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic are stark reminders that we are vulnerable to zoonotic viral threats. Strategies are needed to identify and characterize animal viruses that pose the greatest risk of spillover and spread in humans and inform public health interventions. Using expert opinion and scientific evidence, we identified host, viral, and environmental risk factors contributing to zoonotic virus spillover and spread in humans. We then developed a risk ranking framework and interactive web tool, SpillOver, that estimates a risk score for wildlife-origin viruses, creating a comparative risk assessment of viruses with uncharacterized zoonotic spillover potential alongside those already known to be zoonotic. Using data from testing 509,721 samples from 74,635 animals as part of a virus discovery project and public records of virus detections around the world, we ranked the spillover potential of 887 wildlife viruses. Validating the risk assessment, the top 12 were known zoonotic viruses, including SARS-CoV-2. Several newly detected wildlife viruses ranked higher than known zoonotic viruses. Using a scientifically informed process, we capitalized on the recent wealth of virus discovery data to systematically identify and prioritize targets for investigation. The publicly accessible SpillOver platform can be used by policy makers and health scientists to inform research and public health interventions for prevention and rapid control of disease outbreaks. SpillOver is a living, interactive database that can be refined over time to continue to improve the quality and public availability of information on viral threats to human health.


Subject(s)
COVID-19 , Communicable Diseases, Emerging , Pandemics , SARS-CoV-2 , Zoonoses , Animals , COVID-19/epidemiology , COVID-19/transmission , Communicable Diseases, Emerging/epidemiology , Communicable Diseases, Emerging/transmission , Humans , Zoonoses/epidemiology , Zoonoses/transmission
7.
Health Aff (Millwood) ; 40(2): 204-211, 2021 02.
Article in English | MEDLINE | ID: covidwho-1159333

ABSTRACT

The US has experienced a series of epidemics during the past five decades. None has tested the nation's resilience like the coronavirus disease 2019 (COVID-19) pandemic, which has laid bare critical weaknesses in US pandemic preparedness and domestic leadership and the nation's decline in global standing in public health. Pandemic response has been politicized, proven public health measures undermined, and public confidence in a science-based public health system reduced. This has been compounded by the large number of citizens without ready access to health care, who are overrepresented among infected, hospitalized, and fatal cases. Here, as part of the National Academy of Medicine's Vital Directions for Health and Health Care: Priorities for 2021 initiative, we review the US approach to pandemic preparedness and its impact on the response to COVID-19. We identify six steps that should be taken to strengthen US pandemic resilience, strengthen and modernize the US health care system, regain public confidence in government leadership in public health, and restore US engagement and leadership in global partnerships to address future pandemic threats domestically and around the world.


Subject(s)
COVID-19 , Civil Defense , Communicable Diseases, Emerging/prevention & control , Leadership , Public Health , Resilience, Psychological , Delivery of Health Care , Health Care Reform , Humans , Infection Control
8.
PLoS Pathog ; 16(9): e1008758, 2020 09.
Article in English | MEDLINE | ID: covidwho-742547

ABSTRACT

The COVID-19 pandemic highlights the substantial public health, economic, and societal consequences of virus spillover from a wildlife reservoir. Widespread human transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) also presents a new set of challenges when considering viral spillover from people to naïve wildlife and other animal populations. The establishment of new wildlife reservoirs for SARS-CoV-2 would further complicate public health control measures and could lead to wildlife health and conservation impacts. Given the likely bat origin of SARS-CoV-2 and related beta-coronaviruses (ß-CoVs), free-ranging bats are a key group of concern for spillover from humans back to wildlife. Here, we review the diversity and natural host range of ß-CoVs in bats and examine the risk of humans inadvertently infecting free-ranging bats with SARS-CoV-2. Our review of the global distribution and host range of ß-CoV evolutionary lineages suggests that 40+ species of temperate-zone North American bats could be immunologically naïve and susceptible to infection by SARS-CoV-2. We highlight an urgent need to proactively connect the wellbeing of human and wildlife health during the current pandemic and to implement new tools to continue wildlife research while avoiding potentially severe health and conservation impacts of SARS-CoV-2 "spilling back" into free-ranging bat populations.


Subject(s)
Animals, Wild/virology , Betacoronavirus/pathogenicity , Coronavirus Infections/virology , Pneumonia, Viral/virology , Animals , COVID-19 , Chiroptera/virology , Genome, Viral/genetics , Host Specificity/physiology , Humans , Pandemics , SARS-CoV-2
9.
PLoS One ; 15(4): e0230802, 2020.
Article in English | MEDLINE | ID: covidwho-46041

ABSTRACT

The recent emergence of bat-borne zoonotic viruses warrants vigilant surveillance in their natural hosts. Of particular concern is the family of coronaviruses, which includes the causative agents of severe acute respiratory syndrome (SARS), Middle East respiratory syndrome (MERS), and most recently, Coronavirus Disease 2019 (COVID-19), an epidemic of acute respiratory illness originating from Wuhan, China in December 2019. Viral detection, discovery, and surveillance activities were undertaken in Myanmar to identify viruses in animals at high risk contact interfaces with people. Free-ranging bats were captured, and rectal and oral swabs and guano samples collected for coronaviral screening using broadly reactive consensus conventional polymerase chain reaction. Sequences from positives were compared to known coronaviruses. Three novel alphacoronaviruses, three novel betacoronaviruses, and one known alphacoronavirus previously identified in other southeast Asian countries were detected for the first time in bats in Myanmar. Ongoing land use change remains a prominent driver of zoonotic disease emergence in Myanmar, bringing humans into ever closer contact with wildlife, and justifying continued surveillance and vigilance at broad scales.


Subject(s)
Chiroptera/virology , Coronavirus/classification , Coronavirus/isolation & purification , Anal Canal/virology , Animals , Coronavirus/genetics , Feces/virology , Mouth/virology , Myanmar , Population Surveillance
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