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).