Detection and Genetic Characterization of Community-Based SARS-CoV-2 Infections — New York City, March 2020
In order to limit the introduction of sars-cov-2 (Coronavirus disease causing virus 2019 (covid-19)), the United States restricted travel from China on February 2, 2020 and Europe on March 13, 2020. To determine whether sars-cov-2 is locally transmitted - cov-2 can be detected, the Department of health and mental health (DOHMH) of New York City (NYC) conducted unidentified sentinel surveillance on the emergency departments (ED) of six New York City hospitals from March 1 to 20. On March 8, DOHMH announced the continued spread of sars-cov-2 (1) in the community, although the test availability of sars-cov-2 was still limited. At this time, 26 New York city residents confirmed covid-19, and the number of influenza like diseases * at emergency visits increased, despite the decrease in the spread of influenza virus The following week, March 15, when 7 (13%) of 56 patients with known contact history contacted outside New York City, the spread of sars-cov-2 in the community increased from continuous community transmission to extensive community transmission (2). Through sentinel surveillance from March 1 to 20, the Ministry of Health (MOH) began to report influenza like symptoms (ILS) § 544 specimens were collected from the patients, which were negative for influenza and some other respiratory pathogens. ¶ All 544 samples were tested for sars-cov-2 in CDC; 36 (6.6%) were positive. Through gene sequencing, CDC confirmed that most of the sars-cov-2 positive samples were similar to those circulating in Europe, which indicated that sars-cov-2 might be introduced from Europe, other parts of the United States, and from New York. These findings suggest that collaboration with health care institutions and the development of systems for rapid sentinel surveillance, coupled with the ability to sequence genes prior to an outbreak, can help develop containment and mitigation strategies in a timely manner.
DOHMH collected uncertain residual nasopharyngeal swabs from ILS patients in six sentinel emergency departments from March 1 to 20, 2020. As there is no known virological diagnosis, it is worried that travelers returning from China may introduce sars-cov-2. Due to the high utilization rate of patients who live in the postcode and have more than 20% self recognition ability in Chinese, five kinds of emergency rooms were selected** There are two emergency rooms in Manhattan, two in Queens, one in Brooklyn and one in the Bronx. Frozen specimens were released to DOHMH 48 hours after collection, and frozen specimens were released 1 week after collection. Specimens were collected from patients of all ages from March 1 to 9. Since little is known about sars-cov-2 infection in children, DOHMH only collected sars-cov-2 from March 10 to 20<
Real time reverse transcription polymerase chain reaction (RT-PCR) analysis of 2019 ncov was used, and the samples were sent to CDC on March 23, 2020 for sars-cov-2 detection. [. In order to save resources, the sample pool with up to five samples is tested together, and the single sample in positive sample pool or non conclusion sample pool is retested. Then the nucleic acids were extracted from RT-PCR positive samples and sequenced by Oxford nanopore minion, and the complete genome sequence was generated using the method described previously (3). The nextstrain pipeline was used to infer phylogenetic relationships (4), including 36 sars-cov-2 positive sentinel samples and selected complete genome sequences (5) available from gisaid since April 1, 2020. The project was identified as non research public health monitoring by DOHMH and CDC. Therefore, approval from the agency's institutional review board is not required.
Considering the limited availability of tests and in order to better understand the prevalence of SARS cov-2 infection without NYC population prevalence data, DOHMH calculated the estimated number of people who did not find SARS cov-2 infection per week in the target population. DOHMH estimation §§ The weekly target population, defined as any NYC ed and ILS who has negative laboratory evidence for influenza assessment of these people (and in some cases, for other respiratory pathogens). ED visits to ILs were obtained using ed symptom monitoring data, and weekly summary was conducted through sentinel ed in the whole city. Each sentinel ed provided DOHMH with weekly influenza tests and results. The estimated prevalence of SARS cov-2 in the target population was calculated using the estimated real prevalence tool ¶¶ The sensitivity of RT-PCR analysis of SARS cov-2 was 85% (range 75% - 95%) and 99% specificity; Use R statistical software (version 3.6.3; R Foundation) analyzed the results.
544 specimens were collected from six designated ed from March 1 to 20 (table). Thirty six (6.6%) samples were positive for SARS cov-2, including 22 of 425 patients of all ages (5.2%) and 14 (11.8%) of 119 patients under 18 years old. Of the 36 SARS cov-2 positive specimens, 32 (89%) were obtained in three days, August 10 and March 17-19, which lasted for three days.
In the target population, the estimated prevalence of SARS cov-2 in all age groups was 0.3% in the week on March 1, 11.3% in the week on March 8, of which about 15 and 1170 patients with undetected SARS cov-2 infection were in all age groups in each corresponding week (table). Among the target population, the estimated prevalence of SARS cov-2 in patients younger than 18 years old was 2.0% in the week on March 8, 17.7% on March 15, and 103 and 227 undetected SARS cov-2 infections were investigated in the target population (table). In the week of March 1 and March 8, 26 and 1917 cases of covid-19 were diagnosed in all ages in New York City, respectively. Within the weeks of March 8 and March 15
The complete genome sequence was produced from all 36 positive SARS cov-2 samples. All sequences are divided into three groups (a, B and C) defined at any one time (supplementary figure, https://stacks.cdc.gov/view/cdc/90347). Two NYC sequences gathered in group A are mainly from cases diagnosed in the United States, most of them from Washington state and other sequences from New York. Seven sequences in group B, including early and other global sequences detected in China, and other sequences from New York. The remaining 27 sequences are most closely associated with the New York sequence in group C, which is largely controlled by the sequences found in Europe and North America.
During the period from March 5 to 14, while collecting samples of the ILS crowd sentinel monitoring in New York City, public health officials in Santa Clara County, California found that the prevalence of SARS cov-2 in the tested samples was 11 per cent negative (6) from patients of all ages in four outpost emergency care sites; In addition, SARS was positive coronavirus 2 (7) in 5.3 percent of patients who had not known travel experience or had contact with travelers in a medical center in Los Angeles from March 12 to 13 and March 15-16 for a mild influenza like disease assessment. Both Santa Clara County and Los Angeles use established surveillance methods, including collecting patient information about age, gender and travel history, while New York City uses ambiguous methods. Therefore, the differences of sampling methods and populations limit direct comparison; However, it is recognized that various methods of sentinel surveillance can find value.
In the weeks of March 8 and 15 March, the number of confirmed covid-19 cases in New York City under 18 years old increased. During the same period, DOHMH estimated an increase in the prevalence of covid-19 and no cases found in people under 18 years old who had ILS and negative influenza test results. The increase in these reports and estimates suggests the need to further investigate the role of children in community communication and the possible impact of closing schools as mitigation strategies.
The March 2 2020 sequence (the first sentinel sample collected) is clustered with the early sequences of Europe and the United States (group B), while the European and American sequences are also associated with those of China. No sentinel sequence was directly related to the sequence in Wuhan, China. This is unexpected because most zip ED is used by patients with high zip codes and Chinese speaking. Instead, sequence analysis shows that SARS cov-2 may be introduced from Europe and elsewhere in the United States, and from within New York. On February 2, the provisions on the inspection of domestic airports and the prohibition of foreign citizens from traveling from China were implemented*** However, similar travel restrictions in Schengen, Europe, began only on March 13. Although travel restrictions are an important mitigation strategy, the import and community spread of SARS cov-2 have occurred in New York City by the time of European restrictions.
According to the target population, many sars-cov-2 infections may not be found during the surveillance period in New York City. Expanding the testing criteria to include any travel exposure and ILS patients without alternative diagnosis at the beginning of the outbreak will increase the number of cases detected through passive monitoring. Limited testing capacity and strict test standards have prevented many covid-19 cases from being found, slowing down DOHMH's ability to use surveillance to make timely public health decisions, and ultimately leading to continuous community spread (1).
The findings in this report are subject to at least six limitations. First, uncertain surveillance methods exclude the collection of epidemiological information, including any personal identification number, demographic information, travel and contact history, and specific sentinel ed, in order to support the interpretation of genetic association between specimens or further research clustering. Second, changes in age eligibility criteria during surveillance limited comparisons throughout the week. Third, the combination method used for laboratory testing may dilute low viral load samples, resulting in false negative results. Fourth, the small number of patients tested leads to the uncertainty of the estimated prevalence of sars-cov-2 and the number of covid-19 cases not found in the target population. Fifth, a population survey was not completed until the late stage of the pandemic to estimate the number of ILs infected people who did not seek medical assistance, so these data cannot be used to estimate the infection rate in the general population of New York City. Finally, the potential bias introduced by the selected outposts and the population served affected the universality of these findings.
If sentinel surveillance and gene sequencing are carried out in advance after the emergence or reappearance of new diseases, it can guide public health coping strategies. DOHMH urged jurisdictions to use existing or new infrastructure to set up sentinel surveillance and sample sequencing to prepare for subsequent waves and future outbreaks in the cowid-19 pandemic.