Introductions and early spread of SARS-CoV-2 in the New York City area

Gonzalez‐Reiche, Ana S.; Hernandez, Matthew M.; Sullivan, Mitchell J.; Ciferri, Brianne; Alshammary, Hala; Obla, Ajay; Fabre, Shelcie; Kleiner, Giulio; Polanco, Jose; Khan, Zenab; Alburquerque, Bremy; Guchte, Adriana van de; Dutta, Jayeeta; Francoeur, Nancy; Melo, Betsaida Salom; Oussenko, Irina; Deikus, Gintaras; Soto, Juan; Sridhar, Shwetha Hara; Wang, Ying Chih; Twyman, Kathryn; Kasarskis, Andrew; Altman, Deena R.; Smith, Melissa; Sebra, Robert; Aberg, Judith A.; Krammer, Florian; Garcı́a-Sastre, Adolfo; Łuksza, Marta; Patel, Gopi; Paniz‐Mondolfi, Alberto; Gitman, Melissa R.; Sordillo, Emilia Mia; Simon, Viviana; Bakel, Harm van

doi:10.1126/science.abc1917

Cited by 404 publications

(467 citation statements)

References 20 publications

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“…Particularly worth noting is that our inverse procedure gives two results that are mutually consistent: the virus was already in Europe as early as the end of December 2019 and the earliest possible date for New York city to have the virus is around January 10. This consistence gives credence at a quantitative level to the widely believed proposition that the virus in New York city was from Europe through air travel [1].…”

Section: Discussionsupporting

confidence: 53%

“…More specifically, knowing this time in combination with knowledge about the symptomatic individuals in the early stage of the disease spreading enables: (1) an effective reduction in the range of contact tracing, which increases the chance of accurately locating the source of infection with limited resources, (2) an assessment of the infectability of the virus and the way by which it spreads, providing guidance for early control measures, (3) determination of the interstate and international propagation paths of the virus, and (4) providing unequivocal early warnings for the governments. In this regard, a recent work based on gene sequencing analysis found clusters of related viruses in patients living in different neighborhoods of New York city, suggesting that multiple, independent but isolated introductions of the virus had mainly come from Europe and other parts of the US [1]. In another study [2], the frequencies of the key words such as coughing and fevers on Twitter were used for model analysis, with the finding that the actual outbreak time can be 5-19 days earlier than officially reported.…”

Section: Introductionmentioning

confidence: 99%

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When did COVID-19 start? - Optimal inference of time ZERO

Zhai

Long

Tang

et al. 2020

Preprint

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According to the official report, the first case of COVID-19 and the first death in the United States occurred on January 20 and February 29, 2020, respectively. On April 21, California reported that the first death in the state occurred on February 6, implying that community spreading of COVID-19 might have started earlier than previously thought. Exactly what is time ZERO, i.e., when did COVID-19 emerge and begin to spread in the US and other countries? We develop a comprehensive predictive modeling framework to address this question. Using available data of confirmed infections to obtain the optimal values of the key parameters, we validate the model and demonstrate its predictive power. We then carry out an inverse inference analysis to determine time ZERO for ten representative States in the US, plus New York city, UK, Italy, and Spain. The main finding is that, in both the US and Europe, COVID-19 started around the new year day.

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Section: Discussionsupporting

confidence: 53%

Section: Introductionmentioning

confidence: 99%

When did COVID-19 start? - Optimal inference of time ZERO

Zhai

Long

Tang

et al. 2020

Preprint

View full text Add to dashboard Cite

show abstract

“…2a). Using the first sequenced SARS-CoV-2 isolate from New York City (USA/NY1-PV08001/2020) as a reference 20 , we evaluated how many individual SARS-CoV-2 genomes each reference gRNA can target (Fig. 2b).…”

Section: Introductionmentioning

confidence: 99%

Transcriptome-wide Cas13 guide RNA design for model organisms and viral RNA pathogens

Guo

Wessels

Méndez-Mancilla

et al. 2020

Preprint

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CRISPR-Cas13 mediates robust transcript knockdown in human cells through direct RNA targeting. Compared to DNA-targeting CRISPR enzymes like Cas9, RNA targeting by Cas13 is transcript- and strand-specific: It can distinguish and specifically knock-down processed transcripts, alternatively spliced isoforms and overlapping genes, all of which frequently serve different functions. Previously, we identified optimal design rules for RfxCas13d guide RNAs (gRNAs), and developed a computational model to predict gRNA efficacy for all human protein-coding genes. However, there is a growing interest to target other types of transcripts, such as noncoding RNAs (ncRNAs) or viral RNAs, and to target transcripts in other commonly-used organisms. Here, we predicted relative Cas13-driven knock-down for gRNAs targeting messenger RNAs and ncRNAs in six model organisms (human, mouse, zebrafish, fly, nematode and flowering plants) and four abundant RNA virus families (SARS-CoV-2, HIV-1, H1N1 influenza and MERS). To allow for more flexible gRNA efficacy prediction, we also developed a web-based application to predict optimal gRNAs for any RNA target entered by the user. Given the lack of Cas13 guide design tools, we anticipate this resource will facilitate CRISPR-Cas13 RNA targeting in common model organisms, emerging viral threats to human health, and novel RNA targets.

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“…The case number keepsincreasing. As of June 9, 2020, the global con rmed COVID-19 cases and deaths increased to 7039918 and 404396, respectively [2].Family clustering and hospital-based transmission were the two major epidemiological features of this outbreak at the early stage, and continued to be an important cause of community-based SARS-CoV-2 transmission in a low prevalence region [3][4][5][6][7][8].However, data concerning SARS-CoV-2 transmissibility in the incubation period and the diversity in disease progression among affected family members are very limited.…”

Section: Introductionmentioning

confidence: 99%

Presymptomatic Transmission and Diverse Progression of Familial Clustering Covid-19 Cases in Zhoushan, China

Liu

Liu²,

et al. 2020

Preprint

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Background Novel coronavirus disease 2019 (COVID-19), severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-caused emerging infectious disease, firstly identified in Wuhan (Hubei, China), is pandemic. However, data concerning presymptomatic SARS-CoV-2 transmission and disease diversity among family members are limited. Herein, We investigated the epidemiological and clinical characteristics of presymptomatic transmission-caused familial clustering cases of SARS-CoV-2 infection in Zhoushan island, China. Methods All family members were tested for SARS-CoV-2 genomic RNA by quantitative reverse transcription PCR in 3 different samples and serum antibody immunoglobin M (IgM) and IgG against SARS-CoV-2. Exposure identification, laboratory test, and imaging were performed according to the national guideline of COVID-19 (7th edition, China). Results Of the 6 cases, index case who ever met his relative with COVID-19 from Xianning, Hubei on January 26–31, 2020, transmitted SARS-CoV-2 to his family members in Zhoushan via visiting family during January 31 and February 3, 2020. The index was identified as common-type COVID-19 on February 6, 2020. All 5 family members were infected with SARS-CoV-2. Of those, a 7-year-old girl was an asymptomatic carrier whereas her grandparents, especially her grandfather, were very sick. Case 6 (grandfather) remained positive for SARS-CoV-2 RNA in his sputum specimen in subsequent 2 months. Case 2 (mother) tested negative for SARS-CoV-2 RNA in all samples but positive for IgM and IgG to SARS-CoV-2 since February 9, 2020. Conclusions Presymptomatic transmission of SARS-CoV-2 causes familial cluster of COVID-19. Exposed to the same source of infection, family members present their differences in disease severity and viral clearance.

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Introductions and early spread of SARS-CoV-2 in the New York City area

Cited by 404 publications

References 20 publications

When did COVID-19 start? - Optimal inference of time ZERO

When did COVID-19 start? - Optimal inference of time ZERO

Transcriptome-wide Cas13 guide RNA design for model organisms and viral RNA pathogens

Presymptomatic Transmission and Diverse Progression of Familial Clustering Covid-19 Cases in Zhoushan, China

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