Results:
Characteristics of specimens received
During January 23 through May 25, the NIC received 15,650 NP/OP specimens from 14,470 suspected cases from 28 cities and provinces in northern Vietnam. Samples were submitted from two types of suspected cases: those from 6,420 persons entering Vietnam from abroad (China during the first cluster and other countries during the second cluster of cases) and 8,050 from persons who were contacts of suspected or confirmed cases. During the first cluster from January 23 to February 25, 2020, 1,741 specimens (11% of all specimens) were collected from persons travelling from Wuhan, China, their families, and their close contacts. During the second cluster of cases from March 7 through May 25, 2020, we received an additional 13,909 (88.9%) samples with nearly two-thirds received from four locations (Hanoi, 5,366; Ha Giang, 1,603; Thai Binh, 1,118; Lai Chau, 1,011). (Table 1).
Detection of SARS-CoV-2 by Real-time RT-PCR
For the entire study period, 15,650 samples from 158 (1.14%) suspected and confirmed cases tested positive for SARS-CoV-2 (Table 2). Eighty-nine (56%) of these were detected among suspected cases imported from other countries and the remaining 69 (44%) were detected among community contacts of confirmed cases. Thirteen cases were confirmed during the first cluster among persons returning from China or their close contacts. Among the 158 confirmed cases, 143 (91%) were Vietnamese nationals and 96 (61%) were female, although we observed significant differences in the distribution of gender among imported cases (44/89, or 49% female) compared with cases detected among community contacts (52/69, or 75% female, P<0.0009 by chi-square). The median age was 41years (IQR: 3 months – 88 years old) for community contacts and 33 years (IQR :10 years -74 years old) for imported cases. Eleven (12%) of the 89 imported cases were only detected upon their second sampling while in quarantine.
Based on Ministry of Health guidelines, laboratory-confirmed cases required follow-up testing until at least two subsequent tests were negative. Most cases required three or four subsequent tests to meet this criterion, but we also observed some cases undergoing collection of 10-15 subsequent specimens (Table 3).
Correlation between Ct Values, Date of illness / Days since first positive sample, and Viral Culture results:
We analyzed the cycle threshold (Ct) values of 158 confirmed cases with SARS-CoV-2 infection with serial sampling during hospitalization until two consecutive negative results were obtained. The proportion of cases that tested positive declined with the number of times they were sampled. Among the 652 samples collected, 167 (26%) had Ct values less than 30 and 105 (63%) of these were identified at the first sampling. Among cases who were sampled a third and fourth time, only 12/124 (10%) and 6/60 (10%) cases, respectively, had Ct values less than 30 (Table 3).
We identified 99 positive specimens with Ct values greater than 30 including seven cases who tested positive again after having tested negative (“re-positives”). Cases with Ct values greater than 30 followed a pattern similar to those with Ct values less than 30: 84 (85%) cases were positive in the first three samples only and an additional 10 (11%) cases remained positive in one of the next three samples. One case was sampled 15 times with no positive results after the tenth sampling.
A total of 81/158 (51%) confirmed cases had appropriately stored samples with sufficient volume to be inoculated on Vero-E6 cells, from which we obtained 29 (36%) SARS-CoV-2 isolates. Of these, 20 samples had detectable cytophathic effects between 72 and 96 hours and an additional nine isolates were harvested after a second blind passage. We identified 28 samples with Ct values of less than 20 and, of these, 18 (64%) yielded culturable virus (Table 4). An additional 20 cases had Ct values of 20-25 and, from these, we were successful in culturing virus from 10 (50%). The additional nine isolates recovered during the second passage had Ct values of 25-30, suggesting a low load of viable virus. No viral isolates were recovered from samples with Ct values >30 (n=20).