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Timing the SARS-CoV-2 Index Case in Hubei Province.

ABSTRACT: Understanding when SARS-CoV-2 emerged is critical to evaluating our current approach to monitoring novel zoonotic pathogens and understanding the failure of early containment and mitigation efforts for COVID-19. We employed a coalescent framework to combine retrospective molecular clock inference with forward epidemiological simulations to determine how long SARS-CoV-2 could have circulated prior to the time of the most recent common ancestor. Our results define the period between mid-October and mid-November 2019 as the plausible interval when the first case of SARS-CoV-2 emerged in Hubei province. By characterizing the likely dynamics of the virus before it was discovered, we show that over two-thirds of SARS-CoV-2-like zoonotic events would be self-limited, dying out without igniting a pandemic. Our findings highlight the shortcomings of zoonosis surveillance approaches for detecting highly contagious pathogens with moderate mortality rates.

SUBMITTER: Pekar J

PROVIDER: S-EPMC7709179 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:BackgroundThe role of subclinical severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections in perpetuating the COVID-19 pandemic is unknown because population seroprevalence data are absent. We aimed to establish the sensitivity and specificity of our enzyme immunoassay and microneutralisation assay, and the seroprevalence of SARS-CoV-2 in Hong Kong before and after the pandemic, as well as in Hong Kong residents evacuated from Hubei province, China.MethodsWe did a multicohort study in a hospital and university in Hong Kong. We evaluated the sensitivity of our enzyme immunoassay and microneutralisation assay with RT-PCR data from patients positive for SARS-CoV-2 and the specificity of our enzyme immunoassay and microneutralisation assay with archived serum samples collected before 2019. We compared the seropositivity of the general population of Hong Kong before and after the pandemic had begun, and determined the seropositivity of Hong Kong residents evacuated from Hubei province, China, in March, 2020.FindingsBetween Feb 26 and March 18, 2020, we assessed RT-PCR samples from 45 patients who had recovered from COVID-19 to establish the sensitivity of our enzyme immunoassay and microneutralisation assay. To establish the specificity of these assays, we retrieved archived serum. The sensitivity was 91·1% (41 of 45 [95% CI 78·8-97·5]) for the microneutralisation assay, 57·8% (26 of 45 [42·2-72·3]) for anti-nucleoprotein IgG, 66·7% (30 of 45 [51·1-80·0]) for anti-spike protein receptor binding domain (RBD) IgG, and 73·3% (33 of 45 [58·1-85·4]) for enzyme immunoassay (either positive for anti-nucleoprotein or anti-RBD IgG). The specificity was 100% (152 of 152 [95% CI 97·6-100·0]) for both the enzyme immunoassay and microneutralisation assay. Among the Hong Kong general population, 53 (2·7%) of 1938 were enzyme immunoassay positive, but of those who were positive, all 53 were microneutralisation negative, and no significant increase was seen in the seroprevalence between April 12, 2018, and Feb 13, 2020. Among asymptomatic Hubei returnees, 17 (4%) of 452 were seropositive with the enzyme immunoassay or the microneutralisation assay, with 15 (88%) of 17 seropositive with the microneutralisation assay, and two familial clusters were identified.InterpretationOur serological data suggest that SARS-CoV-2 is a new emerging virus. The seropositivity rate in Hubei returnees indicates that RT-PCR-confirmed patients only represent a small proportion of the total number of cases. The low seroprevalence suggests that most of the Hong Kong and Hubei population remain susceptible to COVID-19. Future waves of the outbreak are inevitable without a vaccine or antiviral prophylaxis. The role of age-related cross reactive non-neutralising antibodies in the pathogenesis of COVID-19 warrants further investigation.FundingRichard and Carol Yu, May Tam Mak Mei Yin, Shaw Foundation (Hong Kong), Michael Tong, Marina Lee, and the Government Consultancy Service (see acknowledgments for full list).

Project description:High-intensity urban development and economic exploitation have led to the fragmentation and isolation of regional habitat patches, and biodiversity is under serious threat. Scientific identification and effective optimization of ecological networks are essential for maintaining and restoring regional ecosystem connectivity and guiding sustainable socio-economic development. Taking the mountainous areas of southwest Hubei Province (MASHP) in central China as an example, this study first developed a new integrated approach to identify ecological sources based on a quantitative assessment of ecosystem services and the morphological spatial pattern analysis (MSPA) method; it then used the Linkage Mapper tool to extract ecological corridors, applied the principle of hydrological analysis to identify ecological nodes, evaluated each ecological element to quantify its importance, and finally constructed the ecological network and further proposed some optimization countermeasures. The results show that the ecological network in the MASHP is dominated by ecological resources composed of forestland. Connectivity in the central region is significantly better than in other regions, including 49 ecological sources with an area of 3837.92 km2, 125 ecological corridors with a total length of 2014.61 km, and 46 ecological nodes. According to the spatial distribution of crucial ecological landscape elements, a complete and systematic ecological framework of "two verticals, three belts, three groups, and multiple nodes" was proposed. The internal optimization of the ecological network in mountainous areas should focus on improving ecological flow, and strategies such as enhancing the internal connectivity of ecosystems, unblocking ecological corridors, and dividing ecological functional zones can be adopted. Based on the above analyses, this study also made recommendations for ecological protection and development and construction planning in mountainous areas. This study can provide realistic paths and scientific guidelines for ecological security and high-quality development in the MASHP, and it can also have implications for the construction of ecological networks and comprehensive ecological management in other mountainous areas.

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Timing the SARS-CoV-2 Index Case in Hubei Province.

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